2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8f1bfcb9fed1/ Changeset: 8f1bfcb9fed1 User: dannon Date: 2015-01-21 15:46:06+00:00 Summary: Update Routes egg to 2.1. This is an attempt to fix the intermittent url_for issues seen on main. Affected #: 1 file diff -r df1ebf696eaac7f2885117e0f4f2007b645cf17f -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -61,7 +61,7 @@ python_daemon = 1.5.5 pytz = 2013.9 requests = 2.2.1 -Routes = 1.12.3 +Routes = 2.1 simplejson = 2.1.1 six = 1.9.0 sqlalchemy_migrate = 0.7.2 https://bitbucket.org/galaxy/galaxy-central/commits/00b83babd1eb/ Changeset: 00b83babd1eb User: dannon Date: 2015-01-21 15:46:39+00:00 Summary: merge. Affected #: 22 files diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 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 @@ -79,6 +79,10 @@ /** Highlights errors */ _errors: function(options) { + // hide previous error statements + this.trigger('reset'); + + // highlight all errors if (options && options.errors) { var error_messages = this.tree.matchResponse(options.errors); for (var input_id in this.element_list) { @@ -124,9 +128,6 @@ // rebuild the underlying data structure this.tree.finalize(); - // show 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 diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 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 @@ -272,7 +272,7 @@ var process_id = this.deferred.register(); // build model url for request - var model_url = galaxy_config.root + 'workflow/editor_form_post?tool_id=' + this.options.id; + var model_url = galaxy_config.root + 'workflow/editor_form_post?tool_id=' + this.options.id + '&__is_dynamic__=False'; // post job Utils.request({ @@ -282,7 +282,7 @@ success : function(data) { // update node in workflow module self.node.update_field_data(data); - + // highlight errors self._errors(data && data.tool_model); diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 client/galaxy/scripts/mvc/tools/tools-input.js --- a/client/galaxy/scripts/mvc/tools/tools-input.js +++ b/client/galaxy/scripts/mvc/tools/tools-input.js @@ -53,7 +53,7 @@ error: function(text) { if (!this.field.skip) { this.$error_text.html(text); - this.$error.fadeIn(); + this.$error.fadeIn('fast'); this.$el.addClass('ui-error'); } }, diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -449,8 +449,8 @@ */ _fieldData : function(input_def) { if (this.app.workflow) { - var extensions = Utils.textify(input_def.extensions.toString()); - input_def.info = 'Data input \'' + input_def.name + '\' (' + extensions + ')'; + input_def.info = 'Data input \'' + input_def.name + '\' (' + Utils.textify(input_def.extensions.toString()) + ')'; + input_def.value = null; return this._fieldHidden(input_def); } var self = this; @@ -471,9 +471,6 @@ _fieldSelect : function (input_def) { // show text field in workflow if (this.app.workflow && input_def.is_dynamic) { - if (!Utils.validate(input_def.value)) { - input_def.value = ''; - } return this._fieldText(input_def); } @@ -515,6 +512,12 @@ /** Drill down options field */ _fieldDrilldown : function (input_def) { + // show text field in workflow + if (this.app.workflow && input_def.is_dynamic) { + return this._fieldText(input_def); + } + + // create drill down field var self = this; return new Ui.Drilldown.View({ id : 'field-' + input_def.id, @@ -529,6 +532,24 @@ /** Text input field */ _fieldText : function(input_def) { + // format field for multiple entries + if (input_def.multiple) { + // show text area field + input_def.area = true; + + // format value to text + if (!Utils.validate(input_def.value)) { + input_def.value = ''; + } else { + if (input_def.value instanceof Array) { + input_def.value = value.toString(); + } else { + input_def.value = String(input_def.value).replace(/[\[\]'"\s]/g, '').replace(/,/g, '\n'); + } + } + } + + // create input element var self = this; return new Ui.Input({ id : 'field-' + input_def.id, diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -123,7 +123,7 @@ } // handle simple value - if (!field.skip ) { + if (!field.skip || self.app.workflow) { if (field.validate && !field.validate()) { value = null; } diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 client/galaxy/scripts/utils/utils.js --- a/client/galaxy/scripts/utils/utils.js +++ b/client/galaxy/scripts/utils/utils.js @@ -96,6 +96,9 @@ * @param{Function} error - Callback on error */ function request (options) { + // this avoids adding brackets to array parameter names + $.ajaxSetup({ traditional: true }); + // prepare ajax var ajaxConfig = { contentType : 'application/json', diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -75,7 +75,7 @@ wsgiref = 0.1.2 Babel = 1.3 wchartype = 0.1 -Whoosh = 0.3.18 +Whoosh = 2.5.7 ; fluent_logger = 0.3.3 raven = 3.1.8 diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2251,7 +2251,8 @@ """ 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 job = None if job_id: @@ -2345,10 +2346,16 @@ def check_state(trans, input, default_value, context): value = default_value error = 'State validation failed.' + + # skip dynamic fields if deactivated + if not is_dynamic and input.is_dynamic: + return [value, None] + + # validate value content try: # resolves the inconsistent definition of boolean parameters (see base.py) without modifying shared code if input.type == 'boolean' and isinstance(default_value, basestring): - value, error = [util.string_as_bool(default_value), None] + value, error = [string_as_bool(default_value), None] else: value, error = check_param(trans, input, default_value, context) except Exception, err: @@ -2463,7 +2470,7 @@ sanitize_state(state[k]) else: state[k] = jsonify(state[k]) - + # do param translation here, used by datasource tools if self.input_translator: self.input_translator.translate( params ) diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -47,6 +47,7 @@ self.name = input_source.get("name") self.type = input_source.get("type") self.hidden = input_source.get("hidden", False) + self.is_dynamic = False self.label = input_source.parse_label() self.help = input_source.parse_help() sanitizer_elem = input_source.parse_sanitizer_elem() @@ -215,6 +216,7 @@ tool_dict[ 'model_class' ] = self.__class__.__name__ tool_dict[ 'optional' ] = self.optional tool_dict[ 'hidden' ] = self.hidden + tool_dict[ 'is_dynamic' ] = self.is_dynamic if hasattr( self, 'value' ): tool_dict[ 'value' ] = self.value return tool_dict @@ -1042,7 +1044,6 @@ d['display'] = self.display d['multiple'] = self.multiple - d['is_dynamic'] = self.is_dynamic return d @@ -1451,7 +1452,6 @@ if not os.path.isabs( from_file ): from_file = os.path.join( tool.app.config.tool_data_path, from_file ) elem = XML( "<root>%s</root>" % open( from_file ).read() ) - self.is_dynamic = False self.dynamic_options = elem.get( 'dynamic_options', None ) if self.dynamic_options: self.is_dynamic = True @@ -1541,6 +1541,8 @@ else: value = value.split( "\n" ) return UnvalidatedValue( value ) + if not value and not self.optional: + raise ValueError( "An invalid option was selected for %s, 'None', please verify" % (self.name) ) if not value: return None if not isinstance( value, list ): @@ -1663,9 +1665,8 @@ # will sometimes error if self.is_dynamic and self.filtered # bc we dont/cant fill out other_values above ({}) pass - d[ 'options' ] = options - d[ 'display' ] = self.display - d[ 'is_dynamic' ] = self.is_dynamic + d['options'] = options + d['display'] = self.display return d @@ -1768,6 +1769,7 @@ self.validators.append( validation.MetadataValidator() ) self._parse_formats( trans, tool, input_source ) self.multiple = input_source.get_bool('multiple', False) + self.is_dynamic = True self._parse_options( input_source ) # Load conversions required for the dataset input self.conversions = [] @@ -2114,7 +2116,6 @@ d = super( DataToolParameter, self ).to_dict( trans ) d['extensions'] = self.extensions d['multiple'] = self.multiple - d['is_dynamic'] = True d['options'] = {'hda': [], 'hdca': []} # return default content if context is not available @@ -2169,6 +2170,7 @@ self._parse_formats( trans, tool, input_source ) self._collection_type = input_source.get("collection_type", None) self.multiple = False # Accessed on DataToolParameter a lot, may want in future + self.is_dynamic = True self._parse_options( input_source ) # TODO: Review and test. @property @@ -2355,7 +2357,6 @@ d = super( DataCollectionToolParameter, self ).to_dict( trans ) d['extensions'] = self.extensions d['multiple'] = self.multiple - d['is_dynamic'] = False d['options'] = {'hda': [], 'hdca': []} # return default content if context is not available diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 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 @@ -79,6 +79,10 @@ /** Highlights errors */ _errors: function(options) { + // hide previous error statements + this.trigger('reset'); + + // highlight all errors if (options && options.errors) { var error_messages = this.tree.matchResponse(options.errors); for (var input_id in this.element_list) { @@ -124,9 +128,6 @@ // rebuild the underlying data structure this.tree.finalize(); - // show 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 diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 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 @@ -272,7 +272,7 @@ var process_id = this.deferred.register(); // build model url for request - var model_url = galaxy_config.root + 'workflow/editor_form_post?tool_id=' + this.options.id; + var model_url = galaxy_config.root + 'workflow/editor_form_post?tool_id=' + this.options.id + '&__is_dynamic__=False'; // post job Utils.request({ @@ -282,7 +282,7 @@ success : function(data) { // update node in workflow module self.node.update_field_data(data); - + // highlight errors self._errors(data && data.tool_model); diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 static/scripts/mvc/tools/tools-input.js --- a/static/scripts/mvc/tools/tools-input.js +++ b/static/scripts/mvc/tools/tools-input.js @@ -53,7 +53,7 @@ error: function(text) { if (!this.field.skip) { this.$error_text.html(text); - this.$error.fadeIn(); + this.$error.fadeIn('fast'); this.$el.addClass('ui-error'); } }, diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -449,8 +449,8 @@ */ _fieldData : function(input_def) { if (this.app.workflow) { - var extensions = Utils.textify(input_def.extensions.toString()); - input_def.info = 'Data input \'' + input_def.name + '\' (' + extensions + ')'; + input_def.info = 'Data input \'' + input_def.name + '\' (' + Utils.textify(input_def.extensions.toString()) + ')'; + input_def.value = null; return this._fieldHidden(input_def); } var self = this; @@ -471,9 +471,6 @@ _fieldSelect : function (input_def) { // show text field in workflow if (this.app.workflow && input_def.is_dynamic) { - if (!Utils.validate(input_def.value)) { - input_def.value = ''; - } return this._fieldText(input_def); } @@ -515,6 +512,12 @@ /** Drill down options field */ _fieldDrilldown : function (input_def) { + // show text field in workflow + if (this.app.workflow && input_def.is_dynamic) { + return this._fieldText(input_def); + } + + // create drill down field var self = this; return new Ui.Drilldown.View({ id : 'field-' + input_def.id, @@ -529,6 +532,24 @@ /** Text input field */ _fieldText : function(input_def) { + // format field for multiple entries + if (input_def.multiple) { + // show text area field + input_def.area = true; + + // format value to text + if (!Utils.validate(input_def.value)) { + input_def.value = ''; + } else { + if (input_def.value instanceof Array) { + input_def.value = value.toString(); + } else { + input_def.value = String(input_def.value).replace(/[\[\]'"\s]/g, '').replace(/,/g, '\n'); + } + } + } + + // create input element var self = this; return new Ui.Input({ id : 'field-' + input_def.id, diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -123,7 +123,7 @@ } // handle simple value - if (!field.skip ) { + if (!field.skip || self.app.workflow) { if (field.validate && !field.validate()) { value = null; } diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 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){console.debug(l);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.options=l;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){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();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:(!this.workflow&&"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.$el.hide()}var m=new k.ButtonMenu({icon:"fa-cubes",title:(!this.workflow&&"Versions")||null,tooltip:"Select another tool version"});if(u.versions&&u.versions.length>1){for(var o in u.versions){var r=u.versions[o];if(r!=u.version){m.addMenu({title:"Switch to "+r,version:r,icon:"fa-cube",onclick:function(){u.id=u.id.replace(u.version,this.version);u.version=this.version;t.deferred.reset();t.deferred.execute(function(){t._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!this.workflow&&"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,cls:"ui-table-plain"});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(this.options.workflow){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.$el.append(s)}if(u.message){this.message.update({persistent:true,status:"warning",message:u.message})}}})}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){console.debug(l);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.options=l;this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(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.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_buildForm:function(){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);var m=this.options;this._renderForm(m);this.tree.finalize();this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},_renderForm:function(u){var t=this;this.message=new k.Message();var q=new k.ButtonIcon({icon:"fa-info-circle",title:(!this.workflow&&"Requirements")||null,tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;t.message.update({persistent:true,message:c.requirements(u),status:"info"})}else{this.visible=false;t.message.update({message:""})}}});if(!u.requirements||u.requirements.length==0){q.$el.hide()}var m=new k.ButtonMenu({icon:"fa-cubes",title:(!this.workflow&&"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.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!this.workflow&&"Options")||null,tooltip:"View available options"});if(u.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(u.biostar_url+"/t/"+u.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+u.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+u.id+"/download"}})}this.section=new j.View(t,{inputs:u.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+u.name+"</b> "+u.description+" (Galaxy Tool Version "+u.version+")",cls:"ui-portlet-slim",operations:{requirements:q,menu:p,versions:m},buttons:this.buttons});if(this.options.workflow){this.portlet.$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 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 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.workflow=true;this.options=e;b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down"]).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:"Edit Step Attributes",type:"section",expand:this.node.annotation,inputs:[{label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or notes to this step; annotations are available when a workflow is viewed.",value:this.node.annotation}]};this.post_job_actions=this.node.post_job_actions;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:"None"});var f={label:"Edit Step Action: '"+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:"None",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:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"text",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."},{action:"EmailAction",label:"Email notification",type:"boolean",value:"false",ignore:"false",help:"This action will send an email notifying you when the job is done.",payload:{host:window.location.host}},{action:"DeleteIntermediatesAction",label:"Delete non-outputs",type:"boolean",value:"false",ignore:"false",help:"All non-output steps of this workflow will have datasets deleted if they are no longer being used as job inputs when the job this action is attached to is finished. You *must* be using workflow outputs (the snowflake) in your workflow for this to have any effect."}]};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;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.workflow=true;this.options=e;b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down"]).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:"Edit Step Attributes",type:"section",expand:this.node.annotation,inputs:[{label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or notes to this step; annotations are available when a workflow is viewed.",value:this.node.annotation}]};this.post_job_actions=this.node.post_job_actions;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:"None"});var f={label:"Edit Step Action: '"+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:"None",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:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"text",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."},{action:"EmailAction",label:"Email notification",type:"boolean",value:"false",ignore:"false",help:"This action will send an email notifying you when the job is done.",payload:{host:window.location.host}},{action:"DeleteIntermediatesAction",label:"Delete non-outputs",type:"boolean",value:"false",ignore:"false",help:"All non-output steps of this workflow will have datasets deleted if they are no longer being used as job inputs when the job this action is attached to is finished. You *must* be using workflow outputs (the snowflake) in your workflow for this to have any effect."}]};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 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 static/scripts/packed/mvc/tools/tools-input.js --- a/static/scripts/packed/mvc/tools/tools-input.js +++ b/static/scripts/packed/mvc/tools/tools-input.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.field=c.field;this.defaultvalue=c.defaultvalue;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&((this.field.validate&&!this.field.validate())||!b||(b==this.defaultvalue)||(Number(b)==Number(this.defaultvalue))||(JSON.stringify(b)==JSON.stringify(this.defaultvalue))));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){if(!this.field.skip){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")}},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable")}else{this.reset();this.$field.hide();this.$title_optional.html("Enable");this.field.value&&this.field.value(this.defaultvalue)}this.app.trigger("refresh")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span> [<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file +define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.field=c.field;this.defaultvalue=c.defaultvalue;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&((this.field.validate&&!this.field.validate())||!b||(b==this.defaultvalue)||(Number(b)==Number(this.defaultvalue))||(JSON.stringify(b)==JSON.stringify(this.defaultvalue))));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){if(!this.field.skip){this.$error_text.html(a);this.$error.fadeIn("fast");this.$el.addClass("ui-error")}},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable")}else{this.reset();this.$field.hide();this.$title_optional.html("Enable");this.field.value&&this.field.value(this.defaultvalue)}this.app.trigger("refresh")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span> [<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs,cls:"ui-table-plain"});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;function n(i,u){var t=p.id+"-section-"+(q++);var v=null;if(u){v=function(){l.del(t);l.retitle(p.title);s.app.trigger("refresh")}}var w=new g(s.app,{inputs:i,cls:"ui-table-plain"});l.add({id:t,title:p.title,$el:w.$el,ondel:v});l.retitle(p.title)}var l=new c.View({title_new:p.title,max:p.max,onnew:function(){n(p.inputs,true);s.app.trigger("refresh")}});var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o,m>=j)}var k=new f(this.app,{label:p.title,help:p.help,field:l});k.$el.addClass("ui-table-form-section");this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs,cls:"ui-table-plain"});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});if(i.expand){l.$header.trigger("click")}this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;var j=this._createField(i);this.app.field_list[l]=j;var k=new f(this.app,{label:i.label,defaultvalue:i.defaultvalue,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(this.app.workflow){var k=e.textify(i.extensions.toString());i.info="Data input '"+i.name+"' ("+k+")";return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(this.app.workflow&&j.is_dynamic){if(!e.validate(j.value)){j.value=""}return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs,cls:"ui-table-plain"});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;function n(i,u){var t=p.id+"-section-"+(q++);var v=null;if(u){v=function(){l.del(t);l.retitle(p.title);s.app.trigger("refresh")}}var w=new g(s.app,{inputs:i,cls:"ui-table-plain"});l.add({id:t,title:p.title,$el:w.$el,ondel:v});l.retitle(p.title)}var l=new c.View({title_new:p.title,max:p.max,onnew:function(){n(p.inputs,true);s.app.trigger("refresh")}});var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o,m>=j)}var k=new f(this.app,{label:p.title,help:p.help,field:l});k.$el.addClass("ui-table-form-section");this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs,cls:"ui-table-plain"});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});if(i.expand){l.$header.trigger("click")}this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;var j=this._createField(i);this.app.field_list[l]=j;var k=new f(this.app,{label:i.label,defaultvalue:i.defaultvalue,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(this.app.workflow){i.info="Data input '"+i.name+"' ("+e.textify(i.extensions.toString())+")";i.value=null;return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(this.app.workflow&&j.is_dynamic){return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){if(this.app.workflow&&i.is_dynamic){return this._fieldText(i)}var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){if(i.multiple){i.area=true;if(!e.validate(i.value)){i.value=""}else{if(i.value instanceof Array){i.value=value.toString()}else{i.value=String(i.value).replace(/[\[\]'"\s]/g,"").replace(/,/g,"\n")}}}var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(g[u.type]){v=g[u.type](v)}if(!t.skip){if(t.validate&&!t.validate()){v=null}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(g[u.type]){v=g[u.type](v)}if(!t.skip||b.app.workflow){if(t.validate&&!t.validate()){v=null}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 static/scripts/packed/utils/utils.js --- a/static/scripts/packed/utils/utils.js +++ b/static/scripts/packed/utils/utils.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(m){function n(r,q){for(var o in r){var p=r[o];if(p&&typeof(p)=="object"){q(p);n(p,q)}}}function d(o){return $("<div/>").text(o).html()}function l(p){if(!(p instanceof Array)){p=[p]}for(var o in p){if(["None",null,"null",undefined,"undefined"].indexOf(p[o])>-1){return false}}return true}function h(o){var o=o.toString();if(o){o=o.replace(/,/g,", ");var p=o.lastIndexOf(", ");if(p!=-1){o=o.substr(0,p)+" or "+o.substr(p+1)}return o}return""}function e(o){top.__utils__get__=top.__utils__get__||{};if(o.cache&&top.__utils__get__[o.url]){o.success&&o.success(top.__utils__get__[o.url]);console.debug("utils.js::get() - Fetching from cache ["+o.url+"].")}else{i({url:o.url,data:o.data,success:function(p){top.__utils__get__[o.url]=p;o.success&&o.success(p)},error:function(p){o.error&&o.error(p)}})}}function i(p){var o={contentType:"application/json",type:p.type||"GET",data:p.data||{},url:p.url};if(o.type=="GET"||o.type=="DELETE"){if(o.url.indexOf("?")==-1){o.url+="?"}else{o.url+="&"}o.url=o.url+$.param(o.data);o.data=null}else{o.dataType="json";o.url=o.url;o.data=JSON.stringify(o.data)}$.ajax(o).done(function(q){if(typeof q==="string"){try{q=q.replace("Infinity,",'"Infinity",');q=jQuery.parseJSON(q)}catch(r){console.debug(r)}}p.success&&p.success(q)}).fail(function(r){var q=null;try{q=jQuery.parseJSON(r.responseText)}catch(s){q=r.responseText}p.error&&p.error(q,r)})}function j(r,o){var p=$('<div class="'+r+'"></div>');p.appendTo(":eq(0)");var q=p.css(o);p.remove();return q}function g(o){if(!$('link[href^="'+o+'"]').length){$('<link href="'+galaxy_config.root+o+'" rel="stylesheet">').appendTo("head")}}function k(o,p){if(o){return m.defaults(o,p)}else{return p}}function b(p,r){var q="";if(p>=100000000000){p=p/100000000000;q="TB"}else{if(p>=100000000){p=p/100000000;q="GB"}else{if(p>=100000){p=p/100000;q="MB"}else{if(p>=100){p=p/100;q="KB"}else{if(p>0){p=p*10;q="b"}else{return"<strong>-</strong>"}}}}}var o=(Math.round(p)/10);if(r){return o+" "+q}else{return"<strong>"+o+"</strong> "+q}}function a(){return"x"+Math.random().toString(36).substring(2,9)}function c(o){var p=$("<p></p>");p.append(o);return p}function f(){var q=new Date();var o=(q.getHours()<10?"0":"")+q.getHours();var p=(q.getMinutes()<10?"0":"")+q.getMinutes();var r=q.getDate()+"/"+(q.getMonth()+1)+"/"+q.getFullYear()+", "+o+":"+p;return r}return{cssLoadFile:g,cssGetAttribute:j,get:e,merge:k,bytesToString:b,uuid:a,time:f,wrap:c,request:i,sanitize:d,textify:h,validate:l,deepeach:n}}); \ No newline at end of file +define(["libs/underscore"],function(m){function n(r,q){for(var o in r){var p=r[o];if(p&&typeof(p)=="object"){q(p);n(p,q)}}}function d(o){return $("<div/>").text(o).html()}function l(p){if(!(p instanceof Array)){p=[p]}for(var o in p){if(["None",null,"null",undefined,"undefined"].indexOf(p[o])>-1){return false}}return true}function h(o){var o=o.toString();if(o){o=o.replace(/,/g,", ");var p=o.lastIndexOf(", ");if(p!=-1){o=o.substr(0,p)+" or "+o.substr(p+1)}return o}return""}function e(o){top.__utils__get__=top.__utils__get__||{};if(o.cache&&top.__utils__get__[o.url]){o.success&&o.success(top.__utils__get__[o.url]);console.debug("utils.js::get() - Fetching from cache ["+o.url+"].")}else{i({url:o.url,data:o.data,success:function(p){top.__utils__get__[o.url]=p;o.success&&o.success(p)},error:function(p){o.error&&o.error(p)}})}}function i(p){$.ajaxSetup({traditional:true});var o={contentType:"application/json",type:p.type||"GET",data:p.data||{},url:p.url};if(o.type=="GET"||o.type=="DELETE"){if(o.url.indexOf("?")==-1){o.url+="?"}else{o.url+="&"}o.url=o.url+$.param(o.data);o.data=null}else{o.dataType="json";o.url=o.url;o.data=JSON.stringify(o.data)}$.ajax(o).done(function(q){if(typeof q==="string"){try{q=q.replace("Infinity,",'"Infinity",');q=jQuery.parseJSON(q)}catch(r){console.debug(r)}}p.success&&p.success(q)}).fail(function(r){var q=null;try{q=jQuery.parseJSON(r.responseText)}catch(s){q=r.responseText}p.error&&p.error(q,r)})}function j(r,o){var p=$('<div class="'+r+'"></div>');p.appendTo(":eq(0)");var q=p.css(o);p.remove();return q}function g(o){if(!$('link[href^="'+o+'"]').length){$('<link href="'+galaxy_config.root+o+'" rel="stylesheet">').appendTo("head")}}function k(o,p){if(o){return m.defaults(o,p)}else{return p}}function b(p,r){var q="";if(p>=100000000000){p=p/100000000000;q="TB"}else{if(p>=100000000){p=p/100000000;q="GB"}else{if(p>=100000){p=p/100000;q="MB"}else{if(p>=100){p=p/100;q="KB"}else{if(p>0){p=p*10;q="b"}else{return"<strong>-</strong>"}}}}}var o=(Math.round(p)/10);if(r){return o+" "+q}else{return"<strong>"+o+"</strong> "+q}}function a(){return"x"+Math.random().toString(36).substring(2,9)}function c(o){var p=$("<p></p>");p.append(o);return p}function f(){var q=new Date();var o=(q.getHours()<10?"0":"")+q.getHours();var p=(q.getMinutes()<10?"0":"")+q.getMinutes();var r=q.getDate()+"/"+(q.getMonth()+1)+"/"+q.getFullYear()+", "+o+":"+p;return r}return{cssLoadFile:g,cssGetAttribute:j,get:e,merge:k,bytesToString:b,uuid:a,time:f,wrap:c,request:i,sanitize:d,textify:h,validate:l,deepeach:n}}); \ No newline at end of file diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 static/scripts/utils/utils.js --- a/static/scripts/utils/utils.js +++ b/static/scripts/utils/utils.js @@ -96,6 +96,9 @@ * @param{Function} error - Callback on error */ function request (options) { + // this avoids adding brackets to array parameter names + $.ajaxSetup({ traditional: true }); + // prepare ajax var ajaxConfig = { contentType : 'application/json', diff -r 8f1bfcb9fed157f6188a6248c7c536d99b009f3a -r 00b83babd1eb6bbce63c28f418d877fa76e87796 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 @@ -6,7 +6,9 @@ ## TEMPORARY: create tool dictionary in mako while both tool forms are in use. ## This avoids making two separate requests since the classic form requires the mako anyway. from galaxy.tools.parameters import params_to_incoming - incoming = {} + incoming = { + '__is_dynamic__' : False + } params_to_incoming( incoming, tool.inputs, module.state.inputs, trans.app ) self.form_config = tool.to_json(trans, **incoming) self.form_config.update({ 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