From da63f0bef9f8ac1d350a4c613e5d896e4906d279 Mon Sep 17 00:00:00 2001 From: guerler Date: Tue, 19 May 2015 00:27:59 -0400 Subject: [PATCH 1/9] Add RuntimeValue handling for new workflow editor form --- client/galaxy/scripts/mvc/form/form-data.js | 5 +++++ client/galaxy/scripts/mvc/form/form-input.js | 18 +++++++----------- .../galaxy/scripts/mvc/form/form-section.js | 1 + client/galaxy/scripts/mvc/form/form-view.js | 4 ++-- .../scripts/mvc/tools/tools-form-workflow.js | 16 +++++++++++----- lib/galaxy/tools/__init__.py | 19 +++++++++++-------- lib/galaxy/tools/parameters/basic.py | 4 +++- static/maps/mvc/form/form-data.js.map | 2 +- static/maps/mvc/form/form-input.js.map | 2 +- static/maps/mvc/form/form-section.js.map | 2 +- static/maps/mvc/form/form-view.js.map | 2 +- .../maps/mvc/tools/tools-form-workflow.js.map | 2 +- static/scripts/mvc/form/form-data.js | 2 +- static/scripts/mvc/form/form-input.js | 2 +- static/scripts/mvc/form/form-section.js | 2 +- static/scripts/mvc/form/form-view.js | 2 +- .../scripts/mvc/tools/tools-form-workflow.js | 2 +- 17 files changed, 50 insertions(+), 37 deletions(-) diff --git a/client/galaxy/scripts/mvc/form/form-data.js b/client/galaxy/scripts/mvc/form/form-data.js index cc7f7dceabe..8aa4d95cc89 100644 --- a/client/galaxy/scripts/mvc/form/form-data.js +++ b/client/galaxy/scripts/mvc/form/form-data.js @@ -109,6 +109,11 @@ return Backbone.Model.extend({ // ignore certain values if (input.ignore === undefined || input.ignore != value) { + // replace value by collapsible value + if (field.collapsed && input.collapsible_value) { + value = input.collapsible_value; + } + // add value to submission add (job_input_id, input.id, value); diff --git a/client/galaxy/scripts/mvc/form/form-input.js b/client/galaxy/scripts/mvc/form/form-input.js index ac9aa076e94..3d1b50a29b5 100644 --- a/client/galaxy/scripts/mvc/form/form-input.js +++ b/client/galaxy/scripts/mvc/form/form-input.js @@ -16,6 +16,7 @@ define([], function() { // link field this.field = options.field; this.default_value = options.default_value; + this.value = options.value; // set element this.setElement(this._template(options)); @@ -31,13 +32,7 @@ define([], function() { this.$field.prepend(this.field.$el); // decide wether to expand or collapse optional fields - this.field.skip = false; - var v = this.field.value && this.field.value(); - this.field.skip = Boolean(options.collapsible && - (v === this.default_value || - String(v) === String(this.default_value) || - Number(v) === Number(this.default_value) || - JSON.stringify(v) === JSON.stringify(this.default_value))); + this.field.collapsed = options.collapsible && this.value && this.value['__class__']; // refresh view this._refresh(); @@ -46,7 +41,7 @@ define([], function() { var self = this; this.$optional.on('click', function() { // flip flag - self.field.skip = !self.field.skip; + self.field.collapsed = !self.field.collapsed; // refresh view self._refresh(); @@ -78,18 +73,19 @@ define([], function() { this.$optional_icon.removeClass().addClass('icon'); // identify state - if (!this.field.skip) { + if (!this.field.collapsed) { // enable input field this.$field.fadeIn('fast'); this._tooltip(this.text_disable, this.cls_disable); - } else { // disable input field this.$field.hide(); this._tooltip(this.text_enable, this.cls_enable); - // reset field value this.field.value && this.field.value(this.default_value); } + + // refresh form data + this.app.trigger('change', true); }, /** Set tooltip text diff --git a/client/galaxy/scripts/mvc/form/form-section.js b/client/galaxy/scripts/mvc/form/form-section.js index d84271c2fcc..58a9f6950a1 100644 --- a/client/galaxy/scripts/mvc/form/form-section.js +++ b/client/galaxy/scripts/mvc/form/form-section.js @@ -317,6 +317,7 @@ define(['utils/utils', // create input field wrapper var input_element = new InputElement(this.app, { label : input_def.label || input_def.name, + value : input_def.value, default_value : input_def.default_value, collapsible : input_def.collapsible, help : input_def.help, diff --git a/client/galaxy/scripts/mvc/form/form-view.js b/client/galaxy/scripts/mvc/form/form-view.js index d74bff73e4f..6283504cd5e 100644 --- a/client/galaxy/scripts/mvc/form/form-view.js +++ b/client/galaxy/scripts/mvc/form/form-view.js @@ -176,9 +176,9 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', // add listener which triggers on checksum change var current_check = this.data.checksum(); - this.on('change', function() { + this.on('change', function(changed) { var new_check = self.data.checksum(); - if (new_check != current_check) { + if (new_check != current_check || changed) { current_check = new_check; self.options.onchange && self.options.onchange(); } diff --git a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js index 672cf8f784c..f876bea277b 100644 --- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js @@ -37,15 +37,21 @@ define(['utils/utils', 'mvc/tools/tools-form-base'], } }); - // declare conditional fields as not optional + // mark values which can be determined at runtime + Utils.deepeach(options.inputs, function(item) { + if (item.type) { + if ((['data', 'data_collection']).indexOf(item.type) == -1) { + item.collapsible = true; + item.collapsible_value = {'__class__': 'RuntimeValue'}; + } + } + }); + + // declare conditional and data input fields as not collapsible Utils.deepeach(options.inputs, function(item) { if (item.type) { if (item.type == 'conditional') { item.test_param.collapsible = false; - } else { - if ((['data', 'data_collection']).indexOf(item.type) == -1) { - item.collapsible = true; - } } } }); diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 22ea22c0b92..a85ea018a46 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2337,6 +2337,8 @@ class Tool( object, Dictifiable ): return 'false' elif isinstance(v, basestring) or isnumber: return v + elif isinstance(v, dict) and hasattr(v, '__class__'): + return v else: return None @@ -2364,21 +2366,22 @@ class Tool( object, Dictifiable ): dict[key] = value # check the current state of a value and update it if necessary - def check_state(trans, input, default_value, context): - value = default_value + def check_state(trans, input, value, context): error = 'State validation failed.' - # skip dynamic fields if deactivated - if is_workflow and input.is_dynamic: - return [value, None] + # do not check unvalidated values + if isinstance(value, galaxy.tools.parameters.basic.RuntimeValue): + return [ { '__class__' : 'RuntimeValue' }, None ] + if isinstance( value, dict ) and hasattr( value, '__class__' ): + 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 = [string_as_bool(default_value), None] + if input.type == 'boolean' and isinstance(value, basestring): + value, error = [string_as_bool(value), None] else: - value, error = check_param(trans, input, default_value, context) + value, error = check_param(trans, input, value, context) except Exception, err: log.error('Checking parameter %s failed. %s', input.name, str(err)) pass diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 63bd9194a65..30175035c3b 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -159,6 +159,8 @@ class ToolParameter( object, Dictifiable ): def value_to_basic( self, value, app ): if isinstance( value, RuntimeValue ): return { "__class__": "RuntimeValue" } + elif isinstance( value, dict ) and hasattr( value, '__class__'): + return value return self.to_string( value, app ) def value_from_basic( self, value, app, ignore_errors=False ): @@ -631,7 +633,7 @@ class FTPFileToolParameter( ToolParameter ): value = [ value ] lst = [] for val in value: - if val is None: + if val in [ None, '' ]: lst = [] break if isinstance( val, dict ): diff --git a/static/maps/mvc/form/form-data.js.map b/static/maps/mvc/form/form-data.js.map index ea0f95980ee..9efdfdce35e 100644 --- a/static/maps/mvc/form/form-data.js.map +++ b/static/maps/mvc/form/form-data.js.map @@ -1 +1 @@ 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q=c.matchCase(h,p);-1!=q&&b(i,e[h.id+"-section-"+q]);break;case"section":b(!h.flat&&i||"",g);break;default:var r=c.app.field_list[h.id];if(r&&r.value){var p=r.value();if((void 0===h.ignore||h.ignore!=p)&&(a(i,h.id,p),h.payload))for(var s in h.payload)a(s,h.id,h.payload[s])}}}}}var c=this,d={};this._iterate(this.app.section.$el,d);var e={};return this.map_dict={},b("",d),e},match:function(a){return this.map_dict&&this.map_dict[a]},matchCase:function(a,b){"boolean"==a.test_param.type&&(b="true"==b?a.test_param.truevalue||"true":a.test_param.falsevalue||"false");for(var c in a.cases)if(a.cases[c].value==b)return c;return-1},matchModel:function(a,b){function c(a,d){for(var f in d){var g=d[f],h=g.name;switch(""!=a&&(h=a+"|"+h),g.type){case"repeat":for(var i in g.cache)c(h+"_"+i,g.cache[i]);break;case"conditional":var j=g.test_param&&g.test_param.value,k=e.matchCase(g,j);-1!=k&&c(h,g.cases[k].inputs);break;case"section":c(h,g.inputs);break;default:var l=e.map_dict[h];l&&b(l,g)}}}var 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n=m.indexOf(j);-1!=n&&(n+=j.length,k.push(parseInt(m.substr(n))),l||(l=m.substr(0,n)))}k.sort(function(a,b){return a-b});var f=0;for(var o in k)b(i+"_"+f++,g[l+k[o]]);break;case"conditional":var p=c.app.field_list[h.id].value();a(i+"|"+h.test_param.name,h.id,p);var q=c.matchCase(h,p);-1!=q&&b(i,e[h.id+"-section-"+q]);break;case"section":b(!h.flat&&i||"",g);break;default:var r=c.app.field_list[h.id];if(r&&r.value){var p=r.value();if((void 0===h.ignore||h.ignore!=p)&&(r.collapsed&&h.collapsible_value&&(p=h.collapsible_value),a(i,h.id,p),h.payload))for(var s in h.payload)a(s,h.id,h.payload[s])}}}}}var c=this,d={};this._iterate(this.app.section.$el,d);var e={};return this.map_dict={},b("",d),e},match:function(a){return this.map_dict&&this.map_dict[a]},matchCase:function(a,b){"boolean"==a.test_param.type&&(b="true"==b?a.test_param.truevalue||"true":a.test_param.falsevalue||"false");for(var c in a.cases)if(a.cases[c].value==b)return c;return-1},matchModel:function(a,b){function 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b/static/scripts/mvc/form/form-input.js index 1579c2f54c2..d5c8ac12dbf 100644 --- a/static/scripts/mvc/form/form-input.js +++ b/static/scripts/mvc/form/form-input.js @@ -1,2 +1,2 @@ -define([],function(){return Backbone.View.extend({initialize:function(a,b){this.app=a,this.text_enable=a.options.text_enable||"Enable",this.text_disable=a.options.text_disable||"Disable",this.cls_enable=a.options.cls_enable||"fa fa-plus-square",this.cls_disable=a.options.cls_disable||"fa fa-minus-square",this.field=b.field,this.default_value=b.default_value,this.setElement(this._template(b)),this.$field=this.$el.find(".ui-table-form-field"),this.$optional=this.$el.find(".ui-table-form-optional"),this.$optional_icon=this.$el.find(".ui-table-form-optional").find(".icon"),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=!1;var 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',a.help&&(b+=a.help),b+="
",b+="
"}})}); +define([],function(){return Backbone.View.extend({initialize:function(a,b){this.app=a,this.text_enable=a.options.text_enable||"Enable",this.text_disable=a.options.text_disable||"Disable",this.cls_enable=a.options.cls_enable||"fa fa-plus-square",this.cls_disable=a.options.cls_disable||"fa fa-minus-square",this.field=b.field,this.default_value=b.default_value,this.value=b.value,this.setElement(this._template(b)),this.$field=this.$el.find(".ui-table-form-field"),this.$optional=this.$el.find(".ui-table-form-optional"),this.$optional_icon=this.$el.find(".ui-table-form-optional").find(".icon"),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.collapsed=b.collapsible&&this.value&&this.value.__class__,this._refresh();var c=this;this.$optional.on("click",function(){c.field.collapsed=!c.field.collapsed,c._refresh(),c.app.trigger("change")})},error:function(a){this.$error_text.html(a),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$optional_icon.removeClass().addClass("icon"),this.field.collapsed?(this.$field.hide(),this._tooltip(this.text_enable,this.cls_enable),this.field.value&&this.field.value(this.default_value)):(this.$field.fadeIn("fast"),this._tooltip(this.text_disable,this.cls_disable)),this.app.trigger("change",!0)},_tooltip:function(a,b){this.$optional.length&&this.$optional_icon.addClass(b).tooltip({placement:"bottom"}).attr("data-original-title",a).tooltip("fixTitle").tooltip("hide")},_template:function(a){var b='
';return b+=a.collapsible?'
'+a.label+"
":a.label,b+='
',b+='
',a.help&&(b+=a.help),b+="
",b+="
"}})}); //# sourceMappingURL=../../../maps/mvc/form/form-input.js.map \ No newline at end of file diff --git a/static/scripts/mvc/form/form-section.js b/static/scripts/mvc/form/form-section.js index d707dd0ad17..042a170ae1d 100644 --- a/static/scripts/mvc/form/form-section.js +++ b/static/scripts/mvc/form/form-section.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(a,c){this.app=a,this.inputs=c.inputs,c.cls="ui-table-plain",c.cls_tr="section-row",this.table=new b.View(c),this.parameters=new g(a,c),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var a in this.inputs)this.add(this.inputs[a])},add:function(b){var c=jQuery.extend(!0,{},b);c.id=b.id=a.uid(),this.app.input_list[c.id]=c;var d=c.type;switch(d){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id;var c=this._addRow(a.test_param);c.options.onchange=function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=a.id+"-section-"+e,h=b.table.get(g),i=!1;for(var j in f.inputs)if(!f.inputs[j].hidden){i=!0;break}e==d&&i?h.fadeIn("fast"):h.hide()}b.app.trigger("change")};for(var d in a.cases){var e=a.id+"-section-"+d,f=new h(this.app,{inputs:a.cases[d].inputs});f.$el.addClass("ui-table-section"),this.table.add(f.$el),this.table.append(e)}c.trigger("change")},_addRepeat:function(a){function b(b){var e=a.id+"-section-"+d++,f=new h(c.app,{inputs:b});g.add({id:e,$el:f.$el,ondel:function(){g.del(e),c.app.trigger("change")}})}for(var c=this,d=0,g=new e.View({title:a.title,title_new:a.title,min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=a.min,j=_.size(a.cache),k=0;kk?a.cache[k]:a.inputs,b(l)}var m=new f(this.app,{label:a.title,help:a.help,field:g});this.table.add(m.$el),this.table.append(a.id)},_addSection:function(a){var b=this,e=new h(b.app,{inputs:a.inputs}),f=new c.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),g=new d.View({title:a.title,cls:"ui-portlet-section",operations:{button_visible:f}});g.append(e.$el),g.append($("
").addClass("ui-table-form-info").html(a.help));var i=!1;g.$content.hide(),g.$header.css("cursor","pointer"),g.$header.on("click",function(){i?(i=!1,g.$content.hide(),f.setIcon("fa-eye-slash")):(i=!0,g.$content.fadeIn("fast"),f.setIcon("fa-eye"))}),this.app.on("expand",function(a){g.$el.find("#"+a).length>0&&!i&&g.$header.trigger("click")}),a.expanded&&g.$header.trigger("click"),this.table.add(g.$el),this.table.append(a.id)},_addRow:function(a){var b=a.id,c=this.parameters.create(a);this.app.field_list[b]=c;var d=new f(this.app,{label:a.label||a.name,default_value:a.default_value,collapsible:a.collapsible,help:a.help,field:c});return this.app.element_list[b]=d,this.table.add(d.$el),this.table.append(b),a.hidden&&this.table.get(b).hide(),c}});return{View:h}}); +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(a,c){this.app=a,this.inputs=c.inputs,c.cls="ui-table-plain",c.cls_tr="section-row",this.table=new b.View(c),this.parameters=new g(a,c),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var a in this.inputs)this.add(this.inputs[a])},add:function(b){var c=jQuery.extend(!0,{},b);c.id=b.id=a.uid(),this.app.input_list[c.id]=c;var d=c.type;switch(d){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id;var c=this._addRow(a.test_param);c.options.onchange=function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=a.id+"-section-"+e,h=b.table.get(g),i=!1;for(var j in f.inputs)if(!f.inputs[j].hidden){i=!0;break}e==d&&i?h.fadeIn("fast"):h.hide()}b.app.trigger("change")};for(var d in a.cases){var e=a.id+"-section-"+d,f=new h(this.app,{inputs:a.cases[d].inputs});f.$el.addClass("ui-table-section"),this.table.add(f.$el),this.table.append(e)}c.trigger("change")},_addRepeat:function(a){function b(b){var e=a.id+"-section-"+d++,f=new h(c.app,{inputs:b});g.add({id:e,$el:f.$el,ondel:function(){g.del(e),c.app.trigger("change")}})}for(var c=this,d=0,g=new e.View({title:a.title,title_new:a.title,min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=a.min,j=_.size(a.cache),k=0;kk?a.cache[k]:a.inputs,b(l)}var m=new f(this.app,{label:a.title,help:a.help,field:g});this.table.add(m.$el),this.table.append(a.id)},_addSection:function(a){var b=this,e=new h(b.app,{inputs:a.inputs}),f=new c.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),g=new d.View({title:a.title,cls:"ui-portlet-section",operations:{button_visible:f}});g.append(e.$el),g.append($("
").addClass("ui-table-form-info").html(a.help));var i=!1;g.$content.hide(),g.$header.css("cursor","pointer"),g.$header.on("click",function(){i?(i=!1,g.$content.hide(),f.setIcon("fa-eye-slash")):(i=!0,g.$content.fadeIn("fast"),f.setIcon("fa-eye"))}),this.app.on("expand",function(a){g.$el.find("#"+a).length>0&&!i&&g.$header.trigger("click")}),a.expanded&&g.$header.trigger("click"),this.table.add(g.$el),this.table.append(a.id)},_addRow:function(a){var b=a.id,c=this.parameters.create(a);this.app.field_list[b]=c;var d=new f(this.app,{label:a.label||a.name,value:a.value,default_value:a.default_value,collapsible:a.collapsible,help:a.help,field:c});return this.app.element_list[b]=d,this.table.add(d.$el),this.table.append(b),a.hidden&&this.table.get(b).hide(),c}});return{View:h}}); //# sourceMappingURL=../../../maps/mvc/form/form-section.js.map \ No newline at end of file diff --git a/static/scripts/mvc/form/form-view.js b/static/scripts/mvc/form/form-view.js index f9194281381..0d170e005af 100644 --- a/static/scripts/mvc/form/form-view.js +++ b/static/scripts/mvc/form/form-view.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.optionsDefault={is_workflow:!1,narrow:!1,initial_errors:!1,cls:"ui-portlet-limited"},this.options=a.merge(b,this.optionsDefault),console.debug(this.options);var d=parent.Galaxy;this.modal=d&&d.modal?d.modal:new c.Modal.View,this.setElement("
"),this._build()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[a];if(d&&d.options&&!_.isEqual(d.options,c.options)){d.options=c.options;var e=b.field_list[a];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in c.options){var h=c.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),console.debug("Updating options for "+a)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&(a?c.wait():c.unwait())}},reciept:function(a){this.$el.empty(),this.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];d&&(d.error(b||"Please verify this parameter."),this.trigger("expand",a),c||$("html, body").animate({scrollTop:d.$el.offset().top-20},500))},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(){var c=a.data.checksum();c!=b&&(b=c,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){return this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.incompatible?(this.$el.hide(),void $("#tool-form-classic").show()):(this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$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}),void 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("
"),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."),this.trigger("expand",a),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(c){var d=a.data.checksum();(d!=b||c)&&(b=d,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){return this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.incompatible?(this.$el.hide(),void $("#tool-form-classic").show()):(this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$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}),void console.debug("tools-form-base::initialize() - Completed."))}})}); //# sourceMappingURL=../../../maps/mvc/form/form-view.js.map \ No newline at end of file diff --git a/static/scripts/mvc/tools/tools-form-workflow.js b/static/scripts/mvc/tools/tools-form-workflow.js index 44a7ad2ce78..9d8dd1070f0 100644 --- a/static/scripts/mvc/tools/tools-form-workflow.js +++ b/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_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.collapsible=!1:-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0))});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].expanded=!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.labelhere 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",flat:!0,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&&-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0,a.collapsible_value={__class__:"RuntimeValue"})}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.collapsible=!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].expanded=!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.labelhere 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",flat:!0,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 \ No newline at end of file From 4fcd23c0f39f5e62b79c244e4d699963c6ef4cab Mon Sep 17 00:00:00 2001 From: guerler Date: Tue, 19 May 2015 18:41:51 -0400 Subject: [PATCH 2/9] Extend checksum to account for collapsed input tool parameters --- client/galaxy/scripts/mvc/form/form-data.js | 2 +- client/galaxy/scripts/mvc/form/form-input.js | 4 +--- client/galaxy/scripts/mvc/form/form-view.js | 4 ++-- static/maps/mvc/form/form-data.js.map | 2 +- static/maps/mvc/form/form-input.js.map | 2 +- static/maps/mvc/form/form-view.js.map | 2 +- static/scripts/mvc/form/form-data.js | 2 +- static/scripts/mvc/form/form-input.js | 2 +- static/scripts/mvc/form/form-view.js | 2 +- 9 files changed, 10 insertions(+), 12 deletions(-) diff --git a/client/galaxy/scripts/mvc/form/form-data.js b/client/galaxy/scripts/mvc/form/form-data.js index e81f080cd3e..1e9d541ed4b 100644 --- a/client/galaxy/scripts/mvc/form/form-data.js +++ b/client/galaxy/scripts/mvc/form/form-data.js @@ -17,7 +17,7 @@ return Backbone.Model.extend({ var id = $(this).attr('id'); var field = self.app.field_list[id]; if (field) { - sum += id + ':' + JSON.stringify(field.value && field.value()) + ';'; + sum += id + ':' + JSON.stringify(field.value && field.value()) + ':' + field.collapsed + ';'; } }); return sum; diff --git a/client/galaxy/scripts/mvc/form/form-input.js b/client/galaxy/scripts/mvc/form/form-input.js index 3d1b50a29b5..629e897c989 100644 --- a/client/galaxy/scripts/mvc/form/form-input.js +++ b/client/galaxy/scripts/mvc/form/form-input.js @@ -77,15 +77,13 @@ define([], function() { // enable input field this.$field.fadeIn('fast'); this._tooltip(this.text_disable, this.cls_disable); + this.app.trigger('change'); } else { // disable input field this.$field.hide(); this._tooltip(this.text_enable, this.cls_enable); this.field.value && this.field.value(this.default_value); } - - // refresh form data - this.app.trigger('change', true); }, /** Set tooltip text diff --git a/client/galaxy/scripts/mvc/form/form-view.js b/client/galaxy/scripts/mvc/form/form-view.js index 6283504cd5e..d74bff73e4f 100644 --- a/client/galaxy/scripts/mvc/form/form-view.js +++ b/client/galaxy/scripts/mvc/form/form-view.js @@ -176,9 +176,9 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', // add listener which triggers on checksum change var current_check = this.data.checksum(); - this.on('change', function(changed) { + this.on('change', function() { var new_check = self.data.checksum(); - if (new_check != current_check || changed) { + if (new_check != current_check) { current_check = new_check; self.options.onchange && self.options.onchange(); } diff --git a/static/maps/mvc/form/form-data.js.map b/static/maps/mvc/form/form-data.js.map index 9856a5e0782..a41a3d5549a 100644 --- a/static/maps/mvc/form/form-data.js.map +++ 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"}})}); //# sourceMappingURL=../../../maps/mvc/form/form-input.js.map \ No newline at end of file diff --git a/static/scripts/mvc/form/form-view.js b/static/scripts/mvc/form/form-view.js index 0d170e005af..f9194281381 100644 --- a/static/scripts/mvc/form/form-view.js +++ b/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_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("
"),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.$el.append(a)},highlight:function(a,b,c){var d=this.element_list[a];d&&(d.error(b||"Please verify this parameter."),this.trigger("expand",a),c||$("html, body").animate({scrollTop:d.$el.offset().top-20},500))},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},_build:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();this.on("change",function(c){var d=a.data.checksum();(d!=b||c)&&(b=d,a.options.onchange&&a.options.onchange())}),this.on("reset",function(){for(var a in this.element_list)this.element_list[a].reset()})},_renderForm:function(){return this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.incompatible?(this.$el.hide(),void $("#tool-form-classic").show()):(this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$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}),void 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("
"),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."),this.trigger("expand",a),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(){return this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.incompatible?(this.$el.hide(),void $("#tool-form-classic").show()):(this.portlet=new b.View({icon:"fa-wrench",title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons}),this.portlet.append(this.message.$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}),void console.debug("tools-form-base::initialize() - Completed."))}})}); //# sourceMappingURL=../../../maps/mvc/form/form-view.js.map \ No newline at end of file From ea1b1e778a2ab62d75d6f3245e27f0163a01cb81 Mon Sep 17 00:00:00 2001 From: guerler Date: Tue, 19 May 2015 23:02:48 -0400 Subject: [PATCH 3/9] Explicitly specify runtime value in check state --- lib/galaxy/tools/__init__.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index cc4954c063a..a229517e203 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2389,8 +2389,9 @@ class Tool( object, Dictifiable ): # do not check unvalidated values if isinstance(value, galaxy.tools.parameters.basic.RuntimeValue): return [ { '__class__' : 'RuntimeValue' }, None ] - if isinstance( value, dict ) and hasattr( value, '__class__' ): - return[ value, None ] + if isinstance( value, dict ): + if value.get('__class__') == 'RuntimeValue': + return[ value, None ] # validate value content try: From 45b7a625ae0f6d311ec8e4b3b83e6ca1bcf97806 Mon Sep 17 00:00:00 2001 From: guerler Date: Tue, 19 May 2015 23:21:32 -0400 Subject: [PATCH 4/9] Explicitly identify runtime value in handling process --- client/galaxy/scripts/mvc/form/form-input.js | 4 ++-- client/galaxy/scripts/mvc/form/form-section.js | 13 +++++++------ lib/galaxy/tools/__init__.py | 4 ++-- lib/galaxy/tools/parameters/basic.py | 7 ++++--- static/maps/mvc/form/form-input.js.map | 2 +- static/maps/mvc/form/form-section.js.map | 2 +- static/scripts/mvc/form/form-input.js | 2 +- static/scripts/mvc/form/form-section.js | 2 +- 8 files changed, 19 insertions(+), 17 deletions(-) diff --git a/client/galaxy/scripts/mvc/form/form-input.js b/client/galaxy/scripts/mvc/form/form-input.js index 629e897c989..f81f50cc94c 100644 --- a/client/galaxy/scripts/mvc/form/form-input.js +++ b/client/galaxy/scripts/mvc/form/form-input.js @@ -16,7 +16,6 @@ define([], function() { // link field this.field = options.field; this.default_value = options.default_value; - this.value = options.value; // set element this.setElement(this._template(options)); @@ -32,7 +31,8 @@ define([], function() { this.$field.prepend(this.field.$el); // decide wether to expand or collapse optional fields - this.field.collapsed = options.collapsible && this.value && this.value['__class__']; + this.field.collapsed = options.collapsible && options.value && + JSON.stringify(options.value) == JSON.stringify(options.collapsible_value); // refresh view this._refresh(); diff --git a/client/galaxy/scripts/mvc/form/form-section.js b/client/galaxy/scripts/mvc/form/form-section.js index 58a9f6950a1..51eed523457 100644 --- a/client/galaxy/scripts/mvc/form/form-section.js +++ b/client/galaxy/scripts/mvc/form/form-section.js @@ -316,12 +316,13 @@ define(['utils/utils', // create input field wrapper var input_element = new InputElement(this.app, { - label : input_def.label || input_def.name, - value : input_def.value, - default_value : input_def.default_value, - collapsible : input_def.collapsible, - help : input_def.help, - field : field + label : input_def.label || input_def.name, + value : input_def.value, + default_value : input_def.default_value, + collapsible : input_def.collapsible, + collapsible_value : input_def.collapsible_value, + help : input_def.help, + field : field }); // add to element list diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index a229517e203..9432baa0c82 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2389,9 +2389,9 @@ class Tool( object, Dictifiable ): # do not check unvalidated values if isinstance(value, galaxy.tools.parameters.basic.RuntimeValue): return [ { '__class__' : 'RuntimeValue' }, None ] - if isinstance( value, dict ): + elif isinstance( value, dict ): if value.get('__class__') == 'RuntimeValue': - return[ value, None ] + return [ value, None ] # validate value content try: diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 9bfc4a9bcbc..6aaf7d0fffa 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -158,9 +158,10 @@ class ToolParameter( object, Dictifiable ): def value_to_basic( self, value, app ): if isinstance( value, RuntimeValue ): - return { "__class__": "RuntimeValue" } - elif isinstance( value, dict ) and hasattr( value, '__class__'): - return value + return { '__class__': 'RuntimeValue' } + elif isinstance( value, dict ): + if value.get('__class__') == 'RuntimeValue': + return value return self.to_string( value, app ) def value_from_basic( self, value, app, ignore_errors=False ): diff --git a/static/maps/mvc/form/form-input.js.map b/static/maps/mvc/form/form-input.js.map index 6558e37ff21..b012dea247b 100644 --- a/static/maps/mvc/form/form-input.js.map +++ b/static/maps/mvc/form/form-input.js.map @@ -1 +1 @@ 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"}})}); +define([],function(){return Backbone.View.extend({initialize:function(a,b){this.app=a,this.text_enable=a.options.text_enable||"Enable",this.text_disable=a.options.text_disable||"Disable",this.cls_enable=a.options.cls_enable||"fa fa-plus-square",this.cls_disable=a.options.cls_disable||"fa fa-minus-square",this.field=b.field,this.default_value=b.default_value,this.setElement(this._template(b)),this.$field=this.$el.find(".ui-table-form-field"),this.$optional=this.$el.find(".ui-table-form-optional"),this.$optional_icon=this.$el.find(".ui-table-form-optional").find(".icon"),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.collapsed=b.collapsible&&b.value&&JSON.stringify(b.value)==JSON.stringify(b.collapsible_value),this._refresh();var c=this;this.$optional.on("click",function(){c.field.collapsed=!c.field.collapsed,c._refresh(),c.app.trigger("change")})},error:function(a){this.$error_text.html(a),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$optional_icon.removeClass().addClass("icon"),this.field.collapsed?(this.$field.hide(),this._tooltip(this.text_enable,this.cls_enable),this.field.value&&this.field.value(this.default_value)):(this.$field.fadeIn("fast"),this._tooltip(this.text_disable,this.cls_disable),this.app.trigger("change"))},_tooltip:function(a,b){this.$optional.length&&this.$optional_icon.addClass(b).tooltip({placement:"bottom"}).attr("data-original-title",a).tooltip("fixTitle").tooltip("hide")},_template:function(a){var b='
';return b+=a.collapsible?'
'+a.label+"
":a.label,b+='
',b+='
',a.help&&(b+=a.help),b+="
",b+="
"}})}); //# sourceMappingURL=../../../maps/mvc/form/form-input.js.map \ No newline at end of file diff --git a/static/scripts/mvc/form/form-section.js b/static/scripts/mvc/form/form-section.js index 042a170ae1d..0eb007029ec 100644 --- a/static/scripts/mvc/form/form-section.js +++ b/static/scripts/mvc/form/form-section.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(a,c){this.app=a,this.inputs=c.inputs,c.cls="ui-table-plain",c.cls_tr="section-row",this.table=new b.View(c),this.parameters=new g(a,c),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var a in this.inputs)this.add(this.inputs[a])},add:function(b){var c=jQuery.extend(!0,{},b);c.id=b.id=a.uid(),this.app.input_list[c.id]=c;var d=c.type;switch(d){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id;var c=this._addRow(a.test_param);c.options.onchange=function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=a.id+"-section-"+e,h=b.table.get(g),i=!1;for(var j in f.inputs)if(!f.inputs[j].hidden){i=!0;break}e==d&&i?h.fadeIn("fast"):h.hide()}b.app.trigger("change")};for(var d in a.cases){var e=a.id+"-section-"+d,f=new h(this.app,{inputs:a.cases[d].inputs});f.$el.addClass("ui-table-section"),this.table.add(f.$el),this.table.append(e)}c.trigger("change")},_addRepeat:function(a){function b(b){var e=a.id+"-section-"+d++,f=new h(c.app,{inputs:b});g.add({id:e,$el:f.$el,ondel:function(){g.del(e),c.app.trigger("change")}})}for(var c=this,d=0,g=new e.View({title:a.title,title_new:a.title,min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=a.min,j=_.size(a.cache),k=0;kk?a.cache[k]:a.inputs,b(l)}var m=new f(this.app,{label:a.title,help:a.help,field:g});this.table.add(m.$el),this.table.append(a.id)},_addSection:function(a){var b=this,e=new h(b.app,{inputs:a.inputs}),f=new c.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),g=new d.View({title:a.title,cls:"ui-portlet-section",operations:{button_visible:f}});g.append(e.$el),g.append($("
").addClass("ui-table-form-info").html(a.help));var i=!1;g.$content.hide(),g.$header.css("cursor","pointer"),g.$header.on("click",function(){i?(i=!1,g.$content.hide(),f.setIcon("fa-eye-slash")):(i=!0,g.$content.fadeIn("fast"),f.setIcon("fa-eye"))}),this.app.on("expand",function(a){g.$el.find("#"+a).length>0&&!i&&g.$header.trigger("click")}),a.expanded&&g.$header.trigger("click"),this.table.add(g.$el),this.table.append(a.id)},_addRow:function(a){var b=a.id,c=this.parameters.create(a);this.app.field_list[b]=c;var d=new f(this.app,{label:a.label||a.name,value:a.value,default_value:a.default_value,collapsible:a.collapsible,help:a.help,field:c});return this.app.element_list[b]=d,this.table.add(d.$el),this.table.append(b),a.hidden&&this.table.get(b).hide(),c}});return{View:h}}); +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({initialize:function(a,c){this.app=a,this.inputs=c.inputs,c.cls="ui-table-plain",c.cls_tr="section-row",this.table=new b.View(c),this.parameters=new g(a,c),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var a in this.inputs)this.add(this.inputs[a])},add:function(b){var c=jQuery.extend(!0,{},b);c.id=b.id=a.uid(),this.app.input_list[c.id]=c;var d=c.type;switch(d){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id;var c=this._addRow(a.test_param);c.options.onchange=function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=a.id+"-section-"+e,h=b.table.get(g),i=!1;for(var j in f.inputs)if(!f.inputs[j].hidden){i=!0;break}e==d&&i?h.fadeIn("fast"):h.hide()}b.app.trigger("change")};for(var d in a.cases){var e=a.id+"-section-"+d,f=new h(this.app,{inputs:a.cases[d].inputs});f.$el.addClass("ui-table-section"),this.table.add(f.$el),this.table.append(e)}c.trigger("change")},_addRepeat:function(a){function b(b){var e=a.id+"-section-"+d++,f=new h(c.app,{inputs:b});g.add({id:e,$el:f.$el,ondel:function(){g.del(e),c.app.trigger("change")}})}for(var c=this,d=0,g=new e.View({title:a.title,title_new:a.title,min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=a.min,j=_.size(a.cache),k=0;kk?a.cache[k]:a.inputs,b(l)}var m=new f(this.app,{label:a.title,help:a.help,field:g});this.table.add(m.$el),this.table.append(a.id)},_addSection:function(a){var b=this,e=new h(b.app,{inputs:a.inputs}),f=new c.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),g=new d.View({title:a.title,cls:"ui-portlet-section",operations:{button_visible:f}});g.append(e.$el),g.append($("
").addClass("ui-table-form-info").html(a.help));var i=!1;g.$content.hide(),g.$header.css("cursor","pointer"),g.$header.on("click",function(){i?(i=!1,g.$content.hide(),f.setIcon("fa-eye-slash")):(i=!0,g.$content.fadeIn("fast"),f.setIcon("fa-eye"))}),this.app.on("expand",function(a){g.$el.find("#"+a).length>0&&!i&&g.$header.trigger("click")}),a.expanded&&g.$header.trigger("click"),this.table.add(g.$el),this.table.append(a.id)},_addRow:function(a){var b=a.id,c=this.parameters.create(a);this.app.field_list[b]=c;var d=new f(this.app,{label:a.label||a.name,value:a.value,default_value:a.default_value,collapsible:a.collapsible,collapsible_value:a.collapsible_value,help:a.help,field:c});return this.app.element_list[b]=d,this.table.add(d.$el),this.table.append(b),a.hidden&&this.table.get(b).hide(),c}});return{View:h}}); //# sourceMappingURL=../../../maps/mvc/form/form-section.js.map \ No newline at end of file From 77966eb5f13a57c0619cdeab3ae7480f71f78061 Mon Sep 17 00:00:00 2001 From: guerler Date: Tue, 19 May 2015 23:33:27 -0400 Subject: [PATCH 5/9] Fix parsing of unvalidated values --- lib/galaxy/tools/__init__.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 9432baa0c82..5060a1a32c9 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2393,6 +2393,10 @@ class Tool( object, Dictifiable ): if value.get('__class__') == 'RuntimeValue': return [ value, None ] + # skip dynamic fields if deactivated + if is_workflow 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 From 0742b43cc7a03940285771aad2ab3719df803d02 Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 20 May 2015 01:09:20 -0400 Subject: [PATCH 6/9] Change set at runtime icons --- client/galaxy/scripts/mvc/form/form-input.js | 4 ++-- static/maps/mvc/form/form-input.js.map | 2 +- static/scripts/mvc/form/form-input.js | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/client/galaxy/scripts/mvc/form/form-input.js b/client/galaxy/scripts/mvc/form/form-input.js index f81f50cc94c..0195db7be68 100644 --- a/client/galaxy/scripts/mvc/form/form-input.js +++ b/client/galaxy/scripts/mvc/form/form-input.js @@ -10,8 +10,8 @@ define([], function() { // set text labels and icons for optional button this.text_enable = app.options.text_enable || 'Enable'; this.text_disable = app.options.text_disable || 'Disable'; - this.cls_enable = app.options.cls_enable || 'fa fa-plus-square'; - this.cls_disable = app.options.cls_disable || 'fa fa-minus-square'; + this.cls_enable = app.options.cls_enable || 'fa fa-caret-square-o-down'; + this.cls_disable = app.options.cls_disable || 'fa fa-caret-square-o-up'; // link field this.field = options.field; diff --git a/static/maps/mvc/form/form-input.js.map b/static/maps/mvc/form/form-input.js.map index b012dea247b..e5eee681d89 100644 --- a/static/maps/mvc/form/form-input.js.map +++ b/static/maps/mvc/form/form-input.js.map @@ -1 +1 @@ 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\ No newline at end of file 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\ No newline at end of file diff --git a/static/scripts/mvc/form/form-input.js b/static/scripts/mvc/form/form-input.js index c20bc9d45b8..db95c53940b 100644 --- a/static/scripts/mvc/form/form-input.js +++ b/static/scripts/mvc/form/form-input.js @@ -1,2 +1,2 @@ -define([],function(){return Backbone.View.extend({initialize:function(a,b){this.app=a,this.text_enable=a.options.text_enable||"Enable",this.text_disable=a.options.text_disable||"Disable",this.cls_enable=a.options.cls_enable||"fa fa-plus-square",this.cls_disable=a.options.cls_disable||"fa fa-minus-square",this.field=b.field,this.default_value=b.default_value,this.setElement(this._template(b)),this.$field=this.$el.find(".ui-table-form-field"),this.$optional=this.$el.find(".ui-table-form-optional"),this.$optional_icon=this.$el.find(".ui-table-form-optional").find(".icon"),this.$error_text=this.$el.find(".ui-table-form-error-text"),this.$error=this.$el.find(".ui-table-form-error"),this.$field.prepend(this.field.$el),this.field.collapsed=b.collapsible&&b.value&&JSON.stringify(b.value)==JSON.stringify(b.collapsible_value),this._refresh();var c=this;this.$optional.on("click",function(){c.field.collapsed=!c.field.collapsed,c._refresh(),c.app.trigger("change")})},error:function(a){this.$error_text.html(a),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$optional_icon.removeClass().addClass("icon"),this.field.collapsed?(this.$field.hide(),this._tooltip(this.text_enable,this.cls_enable),this.field.value&&this.field.value(this.default_value)):(this.$field.fadeIn("fast"),this._tooltip(this.text_disable,this.cls_disable),this.app.trigger("change"))},_tooltip:function(a,b){this.$optional.length&&this.$optional_icon.addClass(b).tooltip({placement:"bottom"}).attr("data-original-title",a).tooltip("fixTitle").tooltip("hide")},_template:function(a){var b='
';return b+=a.collapsible?'
'+a.label+"
":a.label,b+='
',b+='
',a.help&&(b+=a.help),b+="
",b+="
"}})}); +define([],function(){return Backbone.View.extend({initialize:function(a,b){this.app=a,this.text_enable=a.options.text_enable||"Enable",this.text_disable=a.options.text_disable||"Disable",this.cls_enable=a.options.cls_enable||"fa fa-caret-square-o-down",this.cls_disable=a.options.cls_disable||"fa fa-caret-square-o-up",this.field=b.field,this.default_value=b.default_value,this.setElement(this._template(b)),this.$field=this.$el.find(".ui-table-form-field"),this.$optional=this.$el.find(".ui-table-form-optional"),this.$optional_icon=this.$el.find(".ui-table-form-optional").find(".icon"),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.collapsed=b.collapsible&&b.value&&JSON.stringify(b.value)==JSON.stringify(b.collapsible_value),this._refresh();var c=this;this.$optional.on("click",function(){c.field.collapsed=!c.field.collapsed,c._refresh(),c.app.trigger("change")})},error:function(a){this.$error_text.html(a),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$optional_icon.removeClass().addClass("icon"),this.field.collapsed?(this.$field.hide(),this._tooltip(this.text_enable,this.cls_enable),this.field.value&&this.field.value(this.default_value)):(this.$field.fadeIn("fast"),this._tooltip(this.text_disable,this.cls_disable),this.app.trigger("change"))},_tooltip:function(a,b){this.$optional.length&&this.$optional_icon.addClass(b).tooltip({placement:"bottom"}).attr("data-original-title",a).tooltip("fixTitle").tooltip("hide")},_template:function(a){var b='
';return b+=a.collapsible?'
'+a.label+"
":a.label,b+='
',b+='
',a.help&&(b+=a.help),b+="
",b+="
"}})}); //# sourceMappingURL=../../../maps/mvc/form/form-input.js.map \ No newline at end of file From 70fab5c31910e557e6151ff28f7c5d117d25e792 Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 20 May 2015 01:19:27 -0400 Subject: [PATCH 7/9] Enable new workflow editor form by default --- config/galaxy.ini.sample | 2 +- templates/webapps/galaxy/workflow/editor.mako | 2 +- templates/webapps/galaxy/workflow/editor_tool_form.mako | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 10c3f633a7e..c9be8ab844a 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -836,7 +836,7 @@ use_interactive = True #toolform_upgrade = True # Use new tool form in workflow editor -#workflow_toolform_upgrade = False +#workflow_toolform_upgrade = True # Enable Galaxy to communicate directly with a sequencer #enable_sequencer_communication = False diff --git a/templates/webapps/galaxy/workflow/editor.mako b/templates/webapps/galaxy/workflow/editor.mako index 136bd7d6c94..9575c99b74f 100644 --- a/templates/webapps/galaxy/workflow/editor.mako +++ b/templates/webapps/galaxy/workflow/editor.mako @@ -33,7 +33,7 @@ diff --git a/templates/webapps/galaxy/workflow/editor.mako b/templates/webapps/galaxy/workflow/editor.mako index 9575c99b74f..46aee1150ef 100644 --- a/templates/webapps/galaxy/workflow/editor.mako +++ b/templates/webapps/galaxy/workflow/editor.mako @@ -14,16 +14,17 @@ - ${h.js( "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.drop", "libs/jquery/jquery.event.hover", "libs/jquery/jquery.form", "libs/jquery/jstorage", + "libs/jquery/jquery-ui", "galaxy.workflow_editor.canvas", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", - "galaxy.workflows" )} + "galaxy.workflows", + "libs/bibtex" )}