From aa90e346dd4e10850482e38c7331864bef50f007 Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 2 Dec 2015 02:12:27 -0500 Subject: [PATCH] Revise form base Fix style --- client/galaxy/scripts/mvc/form/form-view.js | 23 +++----------- .../galaxy/scripts/mvc/tool/tool-form-base.js | 30 ++++++++----------- .../scripts/mvc/tool/tool-form-composite.js | 8 +++-- .../scripts/mvc/tool/tool-form-workflow.js | 2 +- client/galaxy/scripts/mvc/tool/tool-form.js | 30 +++++++++---------- lib/galaxy/tools/parameters/basic.py | 8 ++--- static/maps/mvc/form/form-view.js.map | 2 +- static/maps/mvc/tool/tool-form-base.js.map | 2 +- .../maps/mvc/tool/tool-form-composite.js.map | 2 +- .../maps/mvc/tool/tool-form-workflow.js.map | 2 +- static/maps/mvc/tool/tool-form.js.map | 2 +- static/scripts/mvc/form/form-view.js | 2 +- static/scripts/mvc/tool/tool-form-base.js | 2 +- .../scripts/mvc/tool/tool-form-composite.js | 2 +- static/scripts/mvc/tool/tool-form-workflow.js | 2 +- static/scripts/mvc/tool/tool-form.js | 2 +- 16 files changed, 52 insertions(+), 69 deletions(-) diff --git a/client/galaxy/scripts/mvc/form/form-view.js b/client/galaxy/scripts/mvc/form/form-view.js index 6602ab0d979..8fd494e2c39 100644 --- a/client/galaxy/scripts/mvc/form/form-view.js +++ b/client/galaxy/scripts/mvc/form/form-view.js @@ -6,28 +6,12 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'mvc/form/form-sec return Backbone.View.extend({ initialize: function(options) { this.options = Utils.merge(options, { - // shows errors on start initial_errors : false, cls : 'ui-portlet-limited', icon : '' }); - - // log options - Galaxy.emit.debug('form-view::initialize()', 'Ready to build form.', this.options); - - // link galaxy modal or create one - var galaxy = parent.Galaxy; - if (galaxy && galaxy.modal) { - this.modal = galaxy.modal; - } else { - this.modal = new Ui.Modal.View(); - } - - // set element + this.modal = ( parent.Galaxy && parent.Galaxy.modal ) || new Ui.Modal.View(); this.setElement('
'); - - // build this form - this._build(); }, /** Update available options */ @@ -127,9 +111,9 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'mvc/form/form-sec } }, - /** Main tool form build function. This function is called once a new model is available. + /** Render tool form */ - _build: function() { + render: function() { // link this var self = this; @@ -176,6 +160,7 @@ define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'mvc/form/form-sec this.element_list[i].reset(); } }); + return this; }, /** Renders the UI elements required for the form diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js index 20f5048e195..bc1632e640f 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form-base.js +++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js @@ -3,11 +3,10 @@ */ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/tool/tool-template', 'mvc/citation/citation-model', 'mvc/citation/citation-view'], - function(Utils, Deferred, Ui, Form, ToolTemplate, CitationModel, CitationView) { - return Backbone.View.extend({ + function(Utils, Deferred, Ui, FormBase, ToolTemplate, CitationModel, CitationView) { + return FormBase.extend({ initialize: function(options) { - this.options = Utils.merge(options, {}); - this.setElement('
'); + FormBase.prototype.initialize.call(this, options); this.deferred = new Deferred(); if (options.inputs) { this._buildForm(options); @@ -24,7 +23,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', var self = this; this.$el.hide(); this.deferred.execute(function(){ - Backbone.View.prototype.remove.call(self); + FormBase.prototype.remove.call(self); Galaxy.emit.debug('tool-form-base::remove()', 'Destroy view.'); }); }, @@ -45,12 +44,10 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', } }, this.options); this.options.customize && this.options.customize( this.options ); - this.form = new Form(this.options); + this.render(); if ( !this.options.collapsible ) { - this.form.$el.append( $( '
' ).addClass( 'ui-margin-top-large' ).append( this._footer() ) ); + this.$el.append( $( '
' ).addClass( 'ui-margin-top-large' ).append( this._footer() ) ); } - this.$el.empty(); - this.$el.append(this.form.$el); }, /** Builds a new model through api call and recreates the entire form @@ -80,7 +77,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', data : build_data, success : function(new_model) { self._buildForm(new_model['tool_model'] || new_model); - !hide_message && self.form.message.update({ + !hide_message && self.message.update({ status : 'success', message : 'Now you are using \'' + self.options.name + '\' version ' + self.options.version + '.', persistent : false @@ -121,13 +118,12 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', // link this var self = this; var model_url = this.options.update_url || Galaxy.root + 'api/tools/' + this.options.id + '/build'; - var form = this.form; var current_state = { tool_id : this.options.id, tool_version : this.options.version, - inputs : $.extend(true, {}, self.form.data.create()) + inputs : $.extend(true, {}, self.data.create()) } - form.wait(true); + this.wait(true); // log tool state Galaxy.emit.debug('tool-form-base::_updateModel()', 'Sending current state.', current_state); @@ -138,9 +134,9 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', url : model_url, data : current_state, success : function(new_model) { - self.form.update(new_model['tool_model'] || new_model); + self.update(new_model['tool_model'] || new_model); self.options.update && self.options.update(new_model); - form.wait(false); + self.wait(false); Galaxy.emit.debug('tool-form-base::_updateModel()', 'Received new model.', new_model); process.resolve(); }, @@ -242,14 +238,14 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view', onclick : function() { if (!this.visible) { this.visible = true; - self.form.message.update({ + self.message.update({ persistent : true, message : ToolTemplate.requirements(options), status : 'info' }); } else { this.visible = false; - self.form.message.update({ + self.message.update({ message : '' }); } diff --git a/client/galaxy/scripts/mvc/tool/tool-form-composite.js b/client/galaxy/scripts/mvc/tool/tool-form-composite.js index 6667f0a0067..5bf340d28d1 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form-composite.js +++ b/client/galaxy/scripts/mvc/tool/tool-form-composite.js @@ -46,7 +46,7 @@ define([ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/form/form-d text_enable : 'Edit', text_disable : 'Undo', cls_enable : 'fa fa-edit', - cls_disable : 'fa fa-undo', + cls_disable : 'fa fa-undo' }, step ); // build forms @@ -55,6 +55,7 @@ define([ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/form/form-d form = new Form( Utils.merge({ title : '' + step.name + '' }, step )); + form.render(); } else if ( step.step_type == 'tool' ) { // configure input elements Utils.deepeach( step.inputs, function( input ) { @@ -84,7 +85,7 @@ define([ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/form/form-d FormData.matchContext( step.inputs, 'data_ref', function( input, reference ) { input.is_workflow = !reference.options || self._isWorkflowParameter( input.value ); }); - form = new ToolFormBase( step ).form; + form = new ToolFormBase( step ); } // backup objects @@ -130,6 +131,7 @@ define([ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/form/form-d }); }); }}); + wp_form.render(); _.each( wp_form.field_list, function( wp_field, i ) { wp_style( wp_field, wp_form.input_list[ i ].color, 'ui-form-wp-source' ); }); @@ -177,7 +179,7 @@ define([ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/form/form-d }] }); this.$el.append( '

' ).addClass( 'ui-margin-top' ); - this.$el.append( this.history_form.$el ); + this.$el.append( this.history_form.render().$el ); } // add execute button diff --git a/client/galaxy/scripts/mvc/tool/tool-form-workflow.js b/client/galaxy/scripts/mvc/tool/tool-form-workflow.js index c096da807e0..d66d53138f4 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form-workflow.js +++ b/client/galaxy/scripts/mvc/tool/tool-form-workflow.js @@ -36,7 +36,7 @@ define(['utils/utils', 'mvc/tool/tool-form-base'], update_url : galaxy_config.root + 'api/workflows/build_module', update : function(data) { self.node.update_field_data(data); - self.form.errors(data && data.tool_model) + self.errors(data && data.tool_model) } }); diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js index a404e77f4e5..98acf38cb5b 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form.js +++ b/client/galaxy/scripts/mvc/tool/tool-form.js @@ -18,10 +18,10 @@ define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/tool/tool-form-base', 'mvc/tool/to floating : 'clear', onclick : function() { execute_btn.wait(); - self.form.portlet.disable(); + self.portlet.disable(); self.submit( options, function() { execute_btn.unwait(); - self.form.portlet.enable(); + self.portlet.enable(); } ); } }) @@ -52,9 +52,9 @@ define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/tool/tool-form-base', 'mvc/tool/to var job_def = { tool_id : options.id, tool_version : options.version, - inputs : this.form.data.create() + inputs : this.data.create() } - this.form.trigger( 'reset' ); + this.trigger( 'reset' ); if ( !self.validate( job_def ) ) { Galaxy.emit.debug( 'tool-form::submit()', 'Submission canceled. Validation failed.' ); callback && callback(); @@ -67,25 +67,25 @@ define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/tool/tool-form-base', 'mvc/tool/to data : job_def, success : function( response ) { callback && callback(); - self.form.$el.replaceWith( ToolTemplate.success( response ) ); + self.$el.empty().append( ToolTemplate.success( response ) ); parent.Galaxy && parent.Galaxy.currHistoryPanel && parent.Galaxy.currHistoryPanel.refreshContents(); }, error : function( response ) { callback && callback(); Galaxy.emit.debug( 'tool-form::submit', 'Submission failed.', response ); if ( response && response.err_data ) { - var error_messages = self.form.data.matchResponse( response.err_data ); + var error_messages = self.data.matchResponse( response.err_data ); for (var input_id in error_messages) { - self.form.highlight( input_id, error_messages[ input_id ]); + self.highlight( input_id, error_messages[ input_id ]); break; } } else { - self.form.modal.show({ + self.modal.show({ title : 'Job submission failed', body : ( response && response.err_msg ) || ToolTemplate.error( job_def ), buttons : { 'Close' : function() { - self.form.modal.hide(); + self.modal.hide(); } } }); @@ -103,15 +103,15 @@ define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/tool/tool-form-base', 'mvc/tool/to var batch_src = null; for ( var job_input_id in job_inputs ) { var input_value = job_inputs[ job_input_id ]; - var input_id = this.form.data.match( job_input_id ); - var input_field = this.form.field_list[ input_id ]; - var input_def = this.form.input_list[ input_id ]; + var input_id = this.data.match( job_input_id ); + var input_field = this.field_list[ input_id ]; + var input_def = this.input_list[ input_id ]; if ( !input_id || !input_def || !input_field ) { Galaxy.emit.debug('tool-form::validate()', 'Retrieving input objects failed.'); continue; } if ( !input_def.optional && input_value == null ) { - this.form.highlight( input_id ); + this.highlight( input_id ); return false; } if ( input_value && input_value.batch ) { @@ -121,14 +121,14 @@ define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/tool/tool-form-base', 'mvc/tool/to if ( batch_src === null ) { batch_src = src; } else if ( batch_src !== src ) { - this.form.highlight( input_id, 'Please select either dataset or dataset list fields for all batch mode fields.' ); + this.highlight( input_id, 'Please select either dataset or dataset list fields for all batch mode fields.' ); return false; } } if ( batch_n === -1 ) { batch_n = n; } else if ( batch_n !== n ) { - this.form.highlight( input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains ' + n + ' selection(s) while a previous field contains ' + batch_n + '.' ); + this.highlight( input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains ' + n + ' selection(s) while a previous field contains ' + batch_n + '.' ); return false; } } diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 17654dbd9d1..46ff71f2903 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -342,7 +342,7 @@ class IntegerToolParameter( TextToolParameter ): return int( value ) except: if isinstance( value, basestring ): - if value.startswith( "$" ) and (trans is None or trans.workflow_building_mode): + if value.startswith( "$" ) and ( trans is None or trans.workflow_building_mode ): return value elif not value and self.optional: return "" @@ -353,7 +353,7 @@ class IntegerToolParameter( TextToolParameter ): return int( value ) except Exception, err: if isinstance( value, basestring ): - if value.startswith( "$" ) and (trans is None or trans.workflow_building_mode): + if value.startswith( "$" ) and ( trans is None or trans.workflow_building_mode ): return value elif not value and self.optional: return None @@ -420,7 +420,7 @@ class FloatToolParameter( TextToolParameter ): return float( value ) except: if isinstance( value, basestring ): - if value.startswith( "$" ) and (trans is None or trans.workflow_building_mode): + if value.startswith( "$" ) and ( trans is None or trans.workflow_building_mode ): return value elif not value and self.optional: return "" @@ -431,7 +431,7 @@ class FloatToolParameter( TextToolParameter ): return float( value ) except Exception, err: if isinstance( value, basestring ): - if value.startswith( "$" ) and (trans is None or trans.workflow_building_mode): + if value.startswith( "$" ) and ( trans is None or trans.workflow_building_mode ): return value elif not value and self.optional: return None diff --git a/static/maps/mvc/form/form-view.js.map b/static/maps/mvc/form/form-view.js.map index 40053109313..76bffb61110 100644 --- a/static/maps/mvc/form/form-view.js.map +++ 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\ 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 2ff5e533f34..b1e790e38a6 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.options=a.merge(b,{initial_errors:!1,cls:"ui-portlet-limited",icon:""}),Galaxy.emit.debug("form-view::initialize()","Ready to build form.",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"),Galaxy.emit.debug("form-view::update()","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())}},highlight:function(a,b,c){var d=this.element_list[a];if(d&&(d.error(b||"Please verify this parameter."),this.trigger("expand",a),!c))if(self==top){var e=this.$el.parents().filter(function(){return"auto"==$(this).css("overflow")}).first();e.animate({scrollTop:e.scrollTop()+d.$el.offset().top-50},500)}else $("html, body").animate({scrollTop:d.$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.Manager(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}),$(".tooltip").remove(),this.portlet=new b.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$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}),Galaxy.emit.debug("form-view::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.options=a.merge(b,{initial_errors:!1,cls:"ui-portlet-limited",icon:""}),this.modal=parent.Galaxy&&parent.Galaxy.modal||new c.Modal.View,this.setElement("
")},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"),Galaxy.emit.debug("form-view::update()","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())}},highlight:function(a,b,c){var d=this.element_list[a];if(d&&(d.error(b||"Please verify this parameter."),this.trigger("expand",a),!c))if(self==top){var e=this.$el.parents().filter(function(){return"auto"==$(this).css("overflow")}).first();e.animate({scrollTop:e.scrollTop()+d.$el.offset().top-50},500)}else $("html, body").animate({scrollTop:d.$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)}}},render:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e.Manager(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();return 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()}),this},_renderForm:function(){this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),$(".tooltip").remove(),this.portlet=new b.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$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}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}); //# sourceMappingURL=../../../maps/mvc/form/form-view.js.map \ No newline at end of file diff --git a/static/scripts/mvc/tool/tool-form-base.js b/static/scripts/mvc/tool/tool-form-base.js index 1b569da354a..68c85045282 100644 --- a/static/scripts/mvc/tool/tool-form-base.js +++ b/static/scripts/mvc/tool/tool-form-base.js @@ -1,2 +1,2 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tool/tool-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return Backbone.View.extend({initialize:function(c){if(this.options=a.merge(c,{}),this.setElement("
"),this.deferred=new b,c.inputs)this._buildForm(c);else{var d=this;this.deferred.execute(function(a){d._buildModel(a,c,!0)})}},remove:function(){var a=this;this.$el.hide(),this.deferred.execute(function(){Backbone.View.prototype.remove.call(a),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:void 0===b.icon&&"fa-wrench"||"",title:""+b.name+" "+b.description+" (Galaxy Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(a){c._updateModel(a)})}},this.options),this.options.customize&&this.options.customize(this.options),this.form=new d(this.options),this.options.collapsible||this.form.$el.append($("
").addClass("ui-margin-top-large").append(this._footer())),this.$el.empty(),this.$el.append(this.form.$el)},_buildModel:function(b,d,e){var f=this;this.options.id=d.id,this.options.version=d.version;var g="",h={};d.job_id?g=Galaxy.root+"api/jobs/"+d.job_id+"/build_for_rerun":(g=Galaxy.root+"api/tools/"+d.id+"/build",Galaxy.params&&Galaxy.params.tool_id==d.id&&(h=$.extend({},Galaxy.params),d.version&&(h.tool_version=d.version))),a.request({type:"GET",url:g,data:h,success:function(a){f._buildForm(a.tool_model||a),!e&&f.form.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:!1}),Galaxy.emit.debug("tool-form-base::initialize()","Initial tool model ready.",a),b.resolve()},error:function(a){var d=a&&a.err_msg||"Uncaught error.";f.$el.is(":empty")?f.$el.prepend(new c.Message({message:d,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:d,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form::initialize()","Initial tool model request failed.",a),b.reject()}})},_updateModel:function(b){var c=this,d=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",e=this.form,f={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.form.data.create())};e.wait(!0),Galaxy.emit.debug("tool-form-base::_updateModel()","Sending current state.",f),a.request({type:"POST",url:d,data:f,success:function(a){c.form.update(a.tool_model||a),c.options.update&&c.options.update(a),e.wait(!1),Galaxy.emit.debug("tool-form-base::_updateModel()","Received new model.",a),b.resolve()},error:function(a){Galaxy.emit.debug("tool-form-base::_updateModel()","Refresh request failed.",a),b.reject()}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.sustain_version&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(b){a._buildModel(b,{id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.form.message.update({message:""})):(this.visible=!0,a.form.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options,b=$("
").append(e.help(a));if(a.citations){var c=$("
"),d=new f.ToolCitationCollection;d.tool_id=a.id;var h=new g.CitationListView({el:c,collection:d});h.render(),d.fetch(),b.append(c)}return b}})}); +define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/tool/tool-template","mvc/citation/citation-model","mvc/citation/citation-view"],function(a,b,c,d,e,f,g){return d.extend({initialize:function(a){if(d.prototype.initialize.call(this,a),this.deferred=new b,a.inputs)this._buildForm(a);else{var c=this;this.deferred.execute(function(b){c._buildModel(b,a,!0)})}},remove:function(){var a=this;this.$el.hide(),this.deferred.execute(function(){d.prototype.remove.call(a),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(b){var c=this;this.options=a.merge(b,this.options),this.options=a.merge({icon:void 0===b.icon&&"fa-wrench"||"",title:""+b.name+" "+b.description+" (Galaxy Version "+b.version+")",operations:this._operations(),onchange:function(){c.deferred.reset(),c.deferred.execute(function(a){c._updateModel(a)})}},this.options),this.options.customize&&this.options.customize(this.options),this.render(),this.options.collapsible||this.$el.append($("
").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(b,d,e){var f=this;this.options.id=d.id,this.options.version=d.version;var g="",h={};d.job_id?g=Galaxy.root+"api/jobs/"+d.job_id+"/build_for_rerun":(g=Galaxy.root+"api/tools/"+d.id+"/build",Galaxy.params&&Galaxy.params.tool_id==d.id&&(h=$.extend({},Galaxy.params),d.version&&(h.tool_version=d.version))),a.request({type:"GET",url:g,data:h,success:function(a){f._buildForm(a.tool_model||a),!e&&f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:!1}),Galaxy.emit.debug("tool-form-base::initialize()","Initial tool model ready.",a),b.resolve()},error:function(a){var d=a&&a.err_msg||"Uncaught error.";f.$el.is(":empty")?f.$el.prepend(new c.Message({message:d,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:d,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form::initialize()","Initial tool model request failed.",a),b.reject()}})},_updateModel:function(b){var c=this,d=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",e={tool_id:this.options.id,tool_version:this.options.version,inputs:$.extend(!0,{},c.data.create())};this.wait(!0),Galaxy.emit.debug("tool-form-base::_updateModel()","Sending current state.",e),a.request({type:"POST",url:d,data:e,success:function(a){c.update(a.tool_model||a),c.options.update&&c.options.update(a),c.wait(!1),Galaxy.emit.debug("tool-form-base::_updateModel()","Received new model.",a),b.resolve()},error:function(a){Galaxy.emit.debug("tool-form-base::_updateModel()","Refresh request failed.",a),b.reject()}})},_operations:function(){var a=this,b=this.options,d=new c.ButtonMenu({icon:"fa-cubes",title:!b.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!b.sustain_version&&b.versions&&b.versions.length>1)for(var f in b.versions){var g=b.versions[f];g!=b.version&&d.addMenu({title:"Switch to "+g,version:g,icon:"fa-cube",onclick:function(){var c=b.id.replace(b.version,this.version),d=this.version;a.deferred.reset(),a.deferred.execute(function(b){a._buildModel(b,{id:c,version:d})})}})}else d.$el.hide();var h=new c.ButtonMenu({icon:"fa-caret-down",title:!b.narrow&&"Options"||null,tooltip:"View available options"});return b.biostar_url&&(h.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/p/new/post/")}}),h.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(b.biostar_url+"/local/search/page/?q="+b.name)}})),h.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+b.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&h.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+b.id+"/download"}}),b.requirements&&b.requirements.length>0&&h.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,a.message.update({message:""})):(this.visible=!0,a.message.update({persistent:!0,message:e.requirements(b),status:"info"}))}}),b.sharable_url&&h.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(b.sharable_url)}}),{menu:h,versions:d}},_footer:function(){var a=this.options,b=$("
").append(e.help(a));if(a.citations){var c=$("
"),d=new f.ToolCitationCollection;d.tool_id=a.id;var h=new g.CitationListView({el:c,collection:d});h.render(),d.fetch(),b.append(c)}return b}})}); //# sourceMappingURL=../../../maps/mvc/tool/tool-form-base.js.map \ No newline at end of file diff --git a/static/scripts/mvc/tool/tool-form-composite.js b/static/scripts/mvc/tool/tool-form-composite.js index d5217e1a31a..dfeec09e69e 100644 --- a/static/scripts/mvc/tool/tool-form-composite.js +++ b/static/scripts/mvc/tool/tool-form-composite.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-view","mvc/form/form-data","mvc/tool/tool-form-base"],function(a,b,c,d,e){var f=Backbone.View.extend({initialize:function(f){var g=this;this.workflow_id=f.id,this.forms=[],this.steps=[],this.setElement('
'),this.$header=$("
").addClass("ui-form-header"),this.$header.append(new b.Label({title:"Workflow: "+f.name}).$el),this.$header.append(new b.Button({title:"Collapse",icon:"fa-angle-double-up",onclick:function(){_.each(g.forms,function(a){a.portlet.collapse()})}}).$el),this.$header.append(new b.Button({title:"Expand all",icon:"fa-angle-double-down",onclick:function(){_.each(g.forms,function(a){a.portlet.expand()})}}).$el),this.$el.append(this.$header),_.each(f.steps,function(b,f){Galaxy.emit.debug("tool-form-composite::initialize()",f+" : Preparing workflow step."),b=a.merge({name:"Step "+(parseInt(f)+1)+": "+b.name,icon:"",help:null,description:b.annotation&&" - "+b.annotation||b.description,citations:null,collapsible:!0,collapsed:f>0,sustain_version:!0,sustain_repeats:!0,sustain_conditionals:!0,narrow:!0,text_enable:"Edit",text_disable:"Undo",cls_enable:"fa fa-edit",cls_disable:"fa fa-undo"},b);var h=null;-1!=["data_input","data_collection_input"].indexOf(b.step_type)?h=new c(a.merge({title:""+b.name+""},b)):"tool"==b.step_type&&(a.deepeach(b.inputs,function(a){a.type&&(a.options&&0==a.options.length&&(a.is_workflow=!0),a.value&&"RuntimeValue"==a.value.__class__?a.value=null:-1!=["data","data_collection"].indexOf(a.type)||g._isWorkflowParameter(a.value)||(a.collapsible_value=a.value,a.collapsible_preview=!0))}),d.matchIds(b.inputs,b.input_connections_by_name,function(a,b){b&&(b.type="hidden",b.value=b.ignore="",b.options=null,b.help=_.reduce(a,function(a,b){return a&&(a+=", "),a+"Output dataset '"+b.output_name+"' from step "+b.order_index},""))}),d.matchContext(b.inputs,"data_ref",function(a,b){a.is_workflow=!b.options||g._isWorkflowParameter(a.value)}),h=new e(b).form),g.forms[f]=h,g.steps[f]=b});var h={},i={},j=0,k=function(a,b,c){var d=a.$("input");0===d.length&&(d=a.$el),d.addClass(c).css({color:b,"border-color":b})};if(_.each(this.steps,function(a,b){_.each(a.inputs,function(a){var c=g._isWorkflowParameter(a.value);if(c){var d=g.forms[b].field_list[a.id],e=g.forms[b].element_list[a.id];h[c]=h[c]||[],h[c].push(d),d.value(c),e.disable(!0),i[c]=i[c]||{type:a.type,is_workflow:a.options,label:c,name:c,color:"hsl( "+100*++j+", 70%, 30% )"},k(d,i[c].color,"ui-form-wp-target")}})}),!_.isEmpty(i)){var l=new c({title:"Workflow Parameters",inputs:i,onchange:function(){_.each(l.data.create(),function(b,c){_.each(h[c],function(d){d.value(a.sanitize(b)||c)})})}});_.each(l.field_list,function(a,b){k(a,l.input_list[b].color,"ui-form-wp-source")}),this.$el.append("

").addClass("ui-margin-top"),this.$el.append(l.$el)}_.each(g.steps,function(a,b){var c=g.forms[b];g.$el.append("

").addClass("ui-margin-top").append(c.$el),a.post_job_actions&&a.post_job_actions.length&&(c.portlet.append($("

").addClass("ui-margin-top")),c.portlet.append($("

").addClass("fa fa-bolt").append(_.reduce(a.post_job_actions,function(a,b){return a+" "+b.short_str},"")))),Galaxy.emit.debug("tool-form-composite::initialize()",b+" : Workflow step state ready.",a)}),this.history_form=null,f.history_id||(this.history_form=new c({inputs:[{type:"conditional",test_param:{name:"new_history",label:"Send results to a new history",type:"boolean",value:"false",help:""},cases:[{value:"true",inputs:[{name:"new_history_name",label:"History name",type:"text",value:f.name}]}]}]}),this.$el.append("

").addClass("ui-margin-top"),this.$el.append(this.history_form.$el)),this.$el.append("

").addClass("ui-margin-top"),this.execute_btn=new b.Button({icon:"fa-check",title:"Run workflow",cls:"btn btn-primary",floating:"clear",onclick:function(){g._execute()}}),this.$el.append(this.execute_btn.$el),$("body").append(this.$el)},_execute:function(){var b=this,c={inputs:{},parameters:{}},d=!0;_.each(this.forms,function(a,e){var f=a.data.create(),g=b.steps[e],h=g.step_id,i=g.step_type,j=g.order_index;c.parameters[h]={},a.trigger("reset");for(var k in f){var l=f[k],m=a.data.match(k),n=(a.field_list[m],a.input_list[m]);-1!=["data_input","data_collection_input"].indexOf(i)?l&&l.values&&l.values.length>0?c.inputs[j]=l.values[0]:d&&(a.highlight(m),d=!1):n.optional||n.is_workflow||null!=l?c.parameters[h][k]=l:(a.highlight(m),d=!1)}}),console.log(JSON.stringify(c)),d?(b._enabled(!1),Galaxy.emit.debug("tools-form-composite::submit()","Validation complete.",c),a.request({type:"POST",url:Galaxy.root+"api/workflows/"+this.workflow_id+"/invocations",data:c,success:function(a){Galaxy.emit.debug("tool-form-composite::submit","Submission successful.",a),parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents(),console.log(a)},error:function(a){if(console.log(a),a&&a.err_data){var b=form.data.matchResponse(a.err_data);for(var c in b){form.highlight(c,b[c]);break}}else Galaxy.modal&&Galaxy.modal.show({title:"Job submission failed",body:a&&a.err_msg||ToolTemplate.error(options.job_def),buttons:{Close:function(){Galaxy.modal.hide()}}})},complete:function(){b._enabled(!0)}})):b._enabled(!0)},_enabled:function(a){a?this.execute_btn.unwait():this.execute_btn.wait(),a?this.history_form.portlet.enable():this.history_form.portlet.disable(),_.each(this.forms,function(b){a?b.portlet.enable():b.portlet.disable()})},_isWorkflowParameter:function(b){return"$"===String(b).substring(0,1)?a.sanitize(b.substring(2,b.length-1)):void 0}});return{View:f}}); +define(["utils/utils","mvc/ui/ui-misc","mvc/form/form-view","mvc/form/form-data","mvc/tool/tool-form-base"],function(a,b,c,d,e){var f=Backbone.View.extend({initialize:function(f){var g=this;this.workflow_id=f.id,this.forms=[],this.steps=[],this.setElement('

'),this.$header=$("
").addClass("ui-form-header"),this.$header.append(new b.Label({title:"Workflow: "+f.name}).$el),this.$header.append(new b.Button({title:"Collapse",icon:"fa-angle-double-up",onclick:function(){_.each(g.forms,function(a){a.portlet.collapse()})}}).$el),this.$header.append(new b.Button({title:"Expand all",icon:"fa-angle-double-down",onclick:function(){_.each(g.forms,function(a){a.portlet.expand()})}}).$el),this.$el.append(this.$header),_.each(f.steps,function(b,f){Galaxy.emit.debug("tool-form-composite::initialize()",f+" : Preparing workflow step."),b=a.merge({name:"Step "+(parseInt(f)+1)+": "+b.name,icon:"",help:null,description:b.annotation&&" - "+b.annotation||b.description,citations:null,collapsible:!0,collapsed:f>0,sustain_version:!0,sustain_repeats:!0,sustain_conditionals:!0,narrow:!0,text_enable:"Edit",text_disable:"Undo",cls_enable:"fa fa-edit",cls_disable:"fa fa-undo"},b);var h=null;-1!=["data_input","data_collection_input"].indexOf(b.step_type)?(h=new c(a.merge({title:""+b.name+""},b)),h.render()):"tool"==b.step_type&&(a.deepeach(b.inputs,function(a){a.type&&(a.options&&0==a.options.length&&(a.is_workflow=!0),a.value&&"RuntimeValue"==a.value.__class__?a.value=null:-1!=["data","data_collection"].indexOf(a.type)||g._isWorkflowParameter(a.value)||(a.collapsible_value=a.value,a.collapsible_preview=!0))}),d.matchIds(b.inputs,b.input_connections_by_name,function(a,b){b&&(b.type="hidden",b.value=b.ignore="",b.options=null,b.help=_.reduce(a,function(a,b){return a&&(a+=", "),a+"Output dataset '"+b.output_name+"' from step "+b.order_index},""))}),d.matchContext(b.inputs,"data_ref",function(a,b){a.is_workflow=!b.options||g._isWorkflowParameter(a.value)}),h=new e(b)),g.forms[f]=h,g.steps[f]=b});var h={},i={},j=0,k=function(a,b,c){var d=a.$("input");0===d.length&&(d=a.$el),d.addClass(c).css({color:b,"border-color":b})};if(_.each(this.steps,function(a,b){_.each(a.inputs,function(a){var c=g._isWorkflowParameter(a.value);if(c){var d=g.forms[b].field_list[a.id],e=g.forms[b].element_list[a.id];h[c]=h[c]||[],h[c].push(d),d.value(c),e.disable(!0),i[c]=i[c]||{type:a.type,is_workflow:a.options,label:c,name:c,color:"hsl( "+100*++j+", 70%, 30% )"},k(d,i[c].color,"ui-form-wp-target")}})}),!_.isEmpty(i)){var l=new c({title:"Workflow Parameters",inputs:i,onchange:function(){_.each(l.data.create(),function(b,c){_.each(h[c],function(d){d.value(a.sanitize(b)||c)})})}});l.render(),_.each(l.field_list,function(a,b){k(a,l.input_list[b].color,"ui-form-wp-source")}),this.$el.append("

").addClass("ui-margin-top"),this.$el.append(l.$el)}_.each(g.steps,function(a,b){var c=g.forms[b];g.$el.append("

").addClass("ui-margin-top").append(c.$el),a.post_job_actions&&a.post_job_actions.length&&(c.portlet.append($("

").addClass("ui-margin-top")),c.portlet.append($("

").addClass("fa fa-bolt").append(_.reduce(a.post_job_actions,function(a,b){return a+" "+b.short_str},"")))),Galaxy.emit.debug("tool-form-composite::initialize()",b+" : Workflow step state ready.",a)}),this.history_form=null,f.history_id||(this.history_form=new c({inputs:[{type:"conditional",test_param:{name:"new_history",label:"Send results to a new history",type:"boolean",value:"false",help:""},cases:[{value:"true",inputs:[{name:"new_history_name",label:"History name",type:"text",value:f.name}]}]}]}),this.$el.append("

").addClass("ui-margin-top"),this.$el.append(this.history_form.render().$el)),this.$el.append("

").addClass("ui-margin-top"),this.execute_btn=new b.Button({icon:"fa-check",title:"Run workflow",cls:"btn btn-primary",floating:"clear",onclick:function(){g._execute()}}),this.$el.append(this.execute_btn.$el),$("body").append(this.$el)},_execute:function(){var b=this,c={inputs:{},parameters:{}},d=!0;_.each(this.forms,function(a,e){var f=a.data.create(),g=b.steps[e],h=g.step_id,i=g.step_type,j=g.order_index;c.parameters[h]={},a.trigger("reset");for(var k in f){var l=f[k],m=a.data.match(k),n=(a.field_list[m],a.input_list[m]);-1!=["data_input","data_collection_input"].indexOf(i)?l&&l.values&&l.values.length>0?c.inputs[j]=l.values[0]:d&&(a.highlight(m),d=!1):n.optional||n.is_workflow||null!=l?c.parameters[h][k]=l:(a.highlight(m),d=!1)}}),console.log(JSON.stringify(c)),d?(b._enabled(!1),Galaxy.emit.debug("tools-form-composite::submit()","Validation complete.",c),a.request({type:"POST",url:Galaxy.root+"api/workflows/"+this.workflow_id+"/invocations",data:c,success:function(a){Galaxy.emit.debug("tool-form-composite::submit","Submission successful.",a),parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents(),console.log(a)},error:function(a){if(console.log(a),a&&a.err_data){var b=form.data.matchResponse(a.err_data);for(var c in b){form.highlight(c,b[c]);break}}else Galaxy.modal&&Galaxy.modal.show({title:"Job submission failed",body:a&&a.err_msg||ToolTemplate.error(options.job_def),buttons:{Close:function(){Galaxy.modal.hide()}}})},complete:function(){b._enabled(!0)}})):b._enabled(!0)},_enabled:function(a){a?this.execute_btn.unwait():this.execute_btn.wait(),a?this.history_form.portlet.enable():this.history_form.portlet.disable(),_.each(this.forms,function(b){a?b.portlet.enable():b.portlet.disable()})},_isWorkflowParameter:function(b){return"$"===String(b).substring(0,1)?a.sanitize(b.substring(2,b.length-1)):void 0}});return{View:f}}); //# sourceMappingURL=../../../maps/mvc/tool/tool-form-composite.js.map \ No newline at end of file diff --git a/static/scripts/mvc/tool/tool-form-workflow.js b/static/scripts/mvc/tool/tool-form-workflow.js index 69d4d306f1e..71cbe721ea6 100644 --- a/static/scripts/mvc/tool/tool-form-workflow.js +++ b/static/scripts/mvc/tool/tool-form-workflow.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/tool/tool-form-base"],function(a,b){var c=b.extend({initialize:function(c){var d=this;return this.node=c.node,this.node?(this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,sustain_version:!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(b){b.type&&(-1!=["data","data_collection"].indexOf(b.type)?(b.type="hidden",b.info="Data input '"+b.name+"' ("+a.textify(b.extensions&&b.extensions.toString())+")",b.value=null):(b.collapsible_value={__class__:"RuntimeValue"},b.is_workflow=b.options&&0==b.options.length||-1!=["integer","float"].indexOf(b.type)))}),a.deepeach(c.inputs,function(a){"conditional"==a.type&&(a.test_param.collapsible_value=void 0)}),this._makeSections(c),void b.prototype.initialize.call(this,c)):void Galaxy.emit.debug("tool-form-workflow::initialize()","Node not found in workflow.")},_makeSections:function(b){var c=b.inputs,d=b.datatypes;c[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 e=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(e){c[a.uid()]={name:"pja__"+e+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+e])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},c[a.uid()]={name:"pja__"+e+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+e])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var f in this.node.output_terminals)c[a.uid()]=this._makeSection(f,d)}},_makeSection:function(a,b){function c(b,d){d=d||[],d.push(b);for(var e in b.inputs){var f=b.inputs[e];if(f.action){if(f.name="pja__"+a+"__"+f.action,f.pja_arg&&(f.name+="__"+f.pja_arg),f.payload)for(var h in f.payload){var i=f.payload[h];f.payload[f.name+"__"+h]=i,delete i}var j=g.post_job_actions[f.action+a];if(j){for(var k in d)d[k].expanded=!0;f.value=f.pja_arg?j.action_arguments&&j.action_arguments[f.pja_arg]||f.value:"true"}}f.inputs&&c(f,d.slice(0))}}var d=[],e=[];for(key in b)d.push({0:b[key],1:b[key]});for(key in this.node.input_terminals)e.push(this.node.input_terminals[key].name);d.sort(function(a,b){return a.label>b.label?1:a.labelhere for more information. Valid inputs are: '+e.join(", ")+"."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:d,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"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",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},g=this;return c(f),f}});return{View:c}}); +define(["utils/utils","mvc/tool/tool-form-base"],function(a,b){var c=b.extend({initialize:function(c){var d=this;return this.node=c.node,this.node?(this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,sustain_version:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(b){b.type&&(-1!=["data","data_collection"].indexOf(b.type)?(b.type="hidden",b.info="Data input '"+b.name+"' ("+a.textify(b.extensions&&b.extensions.toString())+")",b.value=null):(b.collapsible_value={__class__:"RuntimeValue"},b.is_workflow=b.options&&0==b.options.length||-1!=["integer","float"].indexOf(b.type)))}),a.deepeach(c.inputs,function(a){"conditional"==a.type&&(a.test_param.collapsible_value=void 0)}),this._makeSections(c),void b.prototype.initialize.call(this,c)):void Galaxy.emit.debug("tool-form-workflow::initialize()","Node not found in workflow.")},_makeSections:function(b){var c=b.inputs,d=b.datatypes;c[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 e=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(e){c[a.uid()]={name:"pja__"+e+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+e])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},c[a.uid()]={name:"pja__"+e+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+e])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var f in this.node.output_terminals)c[a.uid()]=this._makeSection(f,d)}},_makeSection:function(a,b){function c(b,d){d=d||[],d.push(b);for(var e in b.inputs){var f=b.inputs[e];if(f.action){if(f.name="pja__"+a+"__"+f.action,f.pja_arg&&(f.name+="__"+f.pja_arg),f.payload)for(var h in f.payload){var i=f.payload[h];f.payload[f.name+"__"+h]=i,delete i}var j=g.post_job_actions[f.action+a];if(j){for(var k in d)d[k].expanded=!0;f.value=f.pja_arg?j.action_arguments&&j.action_arguments[f.pja_arg]||f.value:"true"}}f.inputs&&c(f,d.slice(0))}}var d=[],e=[];for(key in b)d.push({0:b[key],1:b[key]});for(key in this.node.input_terminals)e.push(this.node.input_terminals[key].name);d.sort(function(a,b){return a.label>b.label?1:a.labelhere for more information. Valid inputs are: '+e.join(", ")+"."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:d,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"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",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},g=this;return c(f),f}});return{View:c}}); //# sourceMappingURL=../../../maps/mvc/tool/tool-form-workflow.js.map \ No newline at end of file diff --git a/static/scripts/mvc/tool/tool-form.js b/static/scripts/mvc/tool/tool-form.js index 3883ce699b9..b6ffb78246b 100644 --- a/static/scripts/mvc/tool/tool-form.js +++ b/static/scripts/mvc/tool/tool-form.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/tool/tool-form-base","mvc/tool/tool-template"],function(a,b,c,d){var e=c.extend({initialize:function(d){var e=this;c.prototype.initialize.call(this,a.merge({customize:function(a){a.buttons={execute:execute_btn=new b.Button({icon:"fa-check",tooltip:"Execute: "+a.name+" ("+a.version+")",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){execute_btn.wait(),e.form.portlet.disable(),e.submit(a,function(){execute_btn.unwait(),e.form.portlet.enable()})}})},a.job_id&&a.job_remap&&(a.inputs.rerun_remap_job_id={label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",a.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."})}},d))},submit:function(b,c){var e=this,f={tool_id:b.id,tool_version:b.version,inputs:this.form.data.create()};return this.form.trigger("reset"),e.validate(f)?(Galaxy.emit.debug("tool-form::submit()","Validation complete.",f),void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:f,success:function(a){c&&c(),e.form.$el.replaceWith(d.success(a)),parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(a){if(c&&c(),Galaxy.emit.debug("tool-form::submit","Submission failed.",a),a&&a.err_data){var b=e.form.data.matchResponse(a.err_data);for(var g in b){e.form.highlight(g,b[g]);break}}else e.form.modal.show({title:"Job submission failed",body:a&&a.err_msg||d.error(f),buttons:{Close:function(){e.form.modal.hide()}}})}})):(Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(c&&c()))},validate:function(a){var b=a.inputs,c=-1,d=null;for(var e in b){var f=b[e],g=this.form.data.match(e),h=this.form.field_list[g],i=this.form.input_list[g];if(g&&i&&h){if(!i.optional&&null==f)return this.form.highlight(g),!1;if(f&&f.batch){var j=f.values.length,k=j>0&&f.values[0]&&f.values[0].src;if(k)if(null===d)d=k;else if(d!==k)return this.form.highlight(g,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===c)c=j;else if(c!==j)return this.form.highlight(g,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+j+" selection(s) while a previous field contains "+c+"."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0}});return{View:e}}); +define(["utils/utils","mvc/ui/ui-misc","mvc/tool/tool-form-base","mvc/tool/tool-template"],function(a,b,c,d){var e=c.extend({initialize:function(d){var e=this;c.prototype.initialize.call(this,a.merge({customize:function(a){a.buttons={execute:execute_btn=new b.Button({icon:"fa-check",tooltip:"Execute: "+a.name+" ("+a.version+")",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){execute_btn.wait(),e.portlet.disable(),e.submit(a,function(){execute_btn.unwait(),e.portlet.enable()})}})},a.job_id&&a.job_remap&&(a.inputs.rerun_remap_job_id={label:"Resume dependencies from this job",name:"rerun_remap_job_id",type:"select",display:"radio",ignore:"__ignore__",value:"__ignore__",options:[["Yes",a.job_id],["No","__ignore__"]],help:"The previous run of this tool failed and other tools were waiting for it to finish successfully. Use this option to resume those tools using the new output(s) of this tool run."})}},d))},submit:function(b,c){var e=this,f={tool_id:b.id,tool_version:b.version,inputs:this.data.create()};return this.trigger("reset"),e.validate(f)?(Galaxy.emit.debug("tool-form::submit()","Validation complete.",f),void a.request({type:"POST",url:galaxy_config.root+"api/tools",data:f,success:function(a){c&&c(),e.$el.empty().append(d.success(a)),parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.refreshContents()},error:function(a){if(c&&c(),Galaxy.emit.debug("tool-form::submit","Submission failed.",a),a&&a.err_data){var b=e.data.matchResponse(a.err_data);for(var g in b){e.highlight(g,b[g]);break}}else e.modal.show({title:"Job submission failed",body:a&&a.err_msg||d.error(f),buttons:{Close:function(){e.modal.hide()}}})}})):(Galaxy.emit.debug("tool-form::submit()","Submission canceled. Validation failed."),void(c&&c()))},validate:function(a){var b=a.inputs,c=-1,d=null;for(var e in b){var f=b[e],g=this.data.match(e),h=this.field_list[g],i=this.input_list[g];if(g&&i&&h){if(!i.optional&&null==f)return this.highlight(g),!1;if(f&&f.batch){var j=f.values.length,k=j>0&&f.values[0]&&f.values[0].src;if(k)if(null===d)d=k;else if(d!==k)return this.highlight(g,"Please select either dataset or dataset list fields for all batch mode fields."),!1;if(-1===c)c=j;else if(c!==j)return this.highlight(g,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains "+j+" selection(s) while a previous field contains "+c+"."),!1}}else Galaxy.emit.debug("tool-form::validate()","Retrieving input objects failed.")}return!0}});return{View:e}}); //# sourceMappingURL=../../../maps/mvc/tool/tool-form.js.map \ No newline at end of file