WorkflowForm: Use is_workflow instead of is_dynamic for workflow editor

static/scripts/mvc/form/form-parameters.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-color-picker"],function(a,b,c,d,e){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary"},initialize:function(a){this.app=a},create:function(a){void 0===a.value&&(a.value=null),void 0===a.default_value&&(a.default_value=a.value);var b=null,c=this.types[a.type];return c&&"function"==typeof this[c]&&(b=this[c].call(this,a)),b||(this.app.incompatible=!0,b=a.options?this._fieldSelect(a):this._fieldText(a),console.debug("tools-form::_addRow() : Auto matched field type ("+a.type+").")),void 0!==a.value&&b.value(a.value),b},_fieldData:function(b){if(!this.app.options.is_dynamic)return b.info="Data input '"+b.name+"' ("+a.textify(b.extensions.toString())+")",b.value=null,this._fieldHidden(b);var d=this;return new c.View(this.app,{id:"field-"+b.id,extensions:b.extensions,optional:b.optional,multiple:b.multiple,type:b.type,data:b.options,onchange:function(){d.app.trigger("change")}})},_fieldSelect:function(a){if(!this.app.options.is_dynamic&&a.is_dynamic)return this._fieldText(a);"data_column"==a.type&&(a.error_text="Missing columns in referenced dataset.");var c=[];for(var d in a.options){var e=a.options[d];c.push({label:e[0],value:e[1]})}var f=b.Select;switch(a.display){case"checkboxes":f=b.Checkbox;break;case"radio":f=b.Radio}var g=this;return new f.View({id:"field-"+a.id,data:c,error_text:a.error_text||"No options available",optional:a.optional&&null===a.default_value,multiple:a.multiple,optional:a.optional,searchable:a.searchable,onchange:function(){g.app.trigger("change")}})},_fieldDrilldown:function(a){if(!this.app.options.is_dynamic&&a.is_dynamic)return this._fieldText(a);var c=this;return new b.Drilldown.View({id:"field-"+a.id,data:a.options,display:a.display,onchange:function(){c.app.trigger("change")}})},_fieldText:function(c){if(c.options)if(c.area=c.multiple,a.validate(c.value)){if($.isArray(c.value)){var d="";for(var e in c.value){if(d+=String(c.value[e]),!c.multiple)break;d+="\n"}c.value=d}}else c.value="";var f=this;return new b.Input({id:"field-"+c.id,area:c.area,onchange:function(){f.app.trigger("change")}})},_fieldSlider:function(a){var c=this;return new b.Slider.View({id:"field-"+a.id,precise:"float"==a.type,min:a.min,max:a.max,onchange:function(){c.app.trigger("change")}})},_fieldHidden:function(a){return new b.Hidden({id:"field-"+a.id,info:a.info})},_fieldBoolean:function(a){var c=this;return new b.RadioButton.View({id:"field-"+a.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){c.app.trigger("change")}})},_fieldColor:function(a){var b=this;return new e({id:"field-"+a.id,onchange:function(){b.app.trigger("change")}})},_fieldLibrary:function(a){var b=this;return new d.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})}})});
+define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-select-content","mvc/ui/ui-select-library","mvc/ui/ui-color-picker"],function(a,b,c,d,e){return Backbone.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary"},initialize:function(a){this.app=a},create:function(a){void 0===a.value&&(a.value=null),void 0===a.default_value&&(a.default_value=a.value);var b=null,c=this.types[a.type];return c&&"function"==typeof this[c]&&(b=this[c].call(this,a)),b||(this.app.incompatible=!0,b=a.options?this._fieldSelect(a):this._fieldText(a),console.debug("tools-form::_addRow() : Auto matched field type ("+a.type+").")),void 0!==a.value&&b.value(a.value),b},_fieldData:function(b){if(this.app.options.is_workflow)return b.info="Data input '"+b.name+"' ("+a.textify(b.extensions.toString())+")",b.value=null,this._fieldHidden(b);var d=this;return new c.View(this.app,{id:"field-"+b.id,extensions:b.extensions,optional:b.optional,multiple:b.multiple,type:b.type,data:b.options,onchange:function(){d.app.trigger("change")}})},_fieldSelect:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);"data_column"==a.type&&(a.error_text="Missing columns in referenced dataset.");var c=[];for(var d in a.options){var e=a.options[d];c.push({label:e[0],value:e[1]})}var f=b.Select;switch(a.display){case"checkboxes":f=b.Checkbox;break;case"radio":f=b.Radio}var g=this;return new f.View({id:"field-"+a.id,data:c,error_text:a.error_text||"No options available",optional:a.optional&&null===a.default_value,multiple:a.multiple,optional:a.optional,searchable:a.searchable,onchange:function(){g.app.trigger("change")}})},_fieldDrilldown:function(a){if(0==a.options.length&&this.app.options.is_workflow)return this._fieldText(a);var c=this;return new b.Drilldown.View({id:"field-"+a.id,data:a.options,display:a.display,onchange:function(){c.app.trigger("change")}})},_fieldText:function(c){if(c.options)if(c.area=c.multiple,a.validate(c.value)){if($.isArray(c.value)){var d="";for(var e in c.value){if(d+=String(c.value[e]),!c.multiple)break;d+="\n"}c.value=d}}else c.value="";var f=this;return new b.Input({id:"field-"+c.id,area:c.area,onchange:function(){f.app.trigger("change")}})},_fieldSlider:function(a){var c=this;return new b.Slider.View({id:"field-"+a.id,precise:"float"==a.type,min:a.min,max:a.max,onchange:function(){c.app.trigger("change")}})},_fieldHidden:function(a){return new b.Hidden({id:"field-"+a.id,info:a.info})},_fieldBoolean:function(a){var c=this;return new b.RadioButton.View({id:"field-"+a.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){c.app.trigger("change")}})},_fieldColor:function(a){var b=this;return new e({id:"field-"+a.id,onchange:function(){b.app.trigger("change")}})},_fieldLibrary:function(a){var b=this;return new d.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:function(){b.app.trigger("change")}})}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-parameters.js.map

static/scripts/mvc/form/form-view.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_dynamic:!0,narrow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault),console.debug(this.options);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("<div/>"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),console.debug("Updating options for "+a)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];d&&(d.error(b||"Please verify this parameter."),c||$("html, body").animate({scrollTop:d.$el.offset().top-20},500))},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),console.debug("tools-form-base::initialize() - Completed.")}})});
+define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_workflow:!1,narrow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault),console.debug(this.options);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("<div/>"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),console.debug("Updating options for "+a)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];d&&(d.error(b||"Please verify this parameter."),c||$("html, body").animate({scrollTop:d.$el.offset().top-20},500))},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),console.debug("tools-form-base::initialize() - Completed.")}})});
 //# sourceMappingURL=../../../maps/mvc/form/form-view.js.map

static/scripts/mvc/tools/tools-form-workflow.js

@@ -1,2 +1,2 @@
-define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){if(this.node=workflow.active_node,!this.node)return void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_dynamic:!1,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&(a.optional=-1==["data","data_hidden","hidden","repeat","conditional"].indexOf(a.type))}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.optional=!1)});var d=this;a.get({url:galaxy_config.root+"api/datatypes",cache:!0,success:function(a){d.datatypes=a,d._makeSections(c.inputs),b.prototype.initialize.call(d,c)}})},_makeSections:function(b){b[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var c=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(c){b[a.uid()]={name:"pja__"+c+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+c])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},b[a.uid()]={name:"pja__"+c+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+c])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var d in this.node.output_terminals)b[a.uid()]=this._makeSection(d)}},_makeSection:function(a){function b(c,d){d=d||[],d.push(c);for(var f in c.inputs){var g=c.inputs[f];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=e.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expand=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&b(g,d.slice(0))}}var c=[];for(key in this.datatypes)c.push({0:this.datatypes[key],1:this.datatypes[key]});c.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),c.unshift({0:"Sequences",1:"Sequences"}),c.unshift({0:"Roadmaps",1:"Roadmaps"}),c.unshift({0:"Leave unchanged",1:"__empty__"});var d={title:"Add Actions: '"+a+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:c,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."},{title:"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."}]},e=this;return b(d),d}});return{View:c}});
+define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){if(this.node=workflow.active_node,!this.node)return void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.optional=!1)});var d=this;a.get({url:galaxy_config.root+"api/datatypes",cache:!0,success:function(a){d.datatypes=a,d._makeSections(c.inputs),b.prototype.initialize.call(d,c)}})},_makeSections:function(b){b[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var c=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(c){b[a.uid()]={name:"pja__"+c+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+c])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},b[a.uid()]={name:"pja__"+c+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+c])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var d in this.node.output_terminals)b[a.uid()]=this._makeSection(d)}},_makeSection:function(a){function b(c,d){d=d||[],d.push(c);for(var f in c.inputs){var g=c.inputs[f];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=e.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expand=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&b(g,d.slice(0))}}var c=[];for(key in this.datatypes)c.push({0:this.datatypes[key],1:this.datatypes[key]});c.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),c.unshift({0:"Sequences",1:"Sequences"}),c.unshift({0:"Roadmaps",1:"Roadmaps"}),c.unshift({0:"Leave unchanged",1:"__empty__"});var d={title:"Add Actions: '"+a+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:c,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."},{title:"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."}]},e=this;return b(d),d}});return{View:c}});
 //# sourceMappingURL=../../../maps/mvc/tools/tools-form-workflow.js.map