From c0fd3c7c6ddef01b0546b485a1a4e88d215042e2 Mon Sep 17 00:00:00 2001 From: guerler Date: Wed, 19 Apr 2017 15:54:05 -0400 Subject: [PATCH 1/2] Display input parameters default value for runtime values --- client/galaxy/scripts/mvc/tool/tool-form-composite.js | 5 +++-- lib/galaxy/tools/__init__.py | 4 +++- static/maps/mvc/tool/tool-form-composite.js.map | 2 +- static/scripts/mvc/tool/tool-form-composite.js | 2 +- 4 files changed, 8 insertions(+), 5 deletions(-) diff --git a/client/galaxy/scripts/mvc/tool/tool-form-composite.js b/client/galaxy/scripts/mvc/tool/tool-form-composite.js index ca5783bd077..3c2398db6e9 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form-composite.js +++ b/client/galaxy/scripts/mvc/tool/tool-form-composite.js @@ -157,9 +157,10 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view' input.options && ( ( input.options.length == 0 && !data_resolved ) || input.wp_linked ) && ( input.is_workflow = true ); data_ref && ( input.is_workflow = ( data_ref.step_linked && !self._isDataStep( data_ref.step_linked ) ) || input.wp_linked ); ( is_data_input || ( input.value && input.value.__class__ == 'RuntimeValue' && !input.step_linked ) ) && ( step.collapsed = false ); - input.value && input.value.__class__ == 'RuntimeValue' && ( input.value = null ); input.flavor = 'workflow'; - if ( !is_data_input && input.type !== 'hidden' && !input.wp_linked ) { + if ( input.value && input.value.__class__ == 'RuntimeValue' ) { + input.value = input.default_value; + } else if ( !is_data_input && input.type !== 'hidden' && !input.wp_linked ) { if ( input.optional || ( !Utils.isEmpty( input.value ) && input.value !== '' ) ) { input.collapsible_value = input.value; input.collapsible_preview = true; diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index b84709615f6..905f6396e8d 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1830,8 +1830,10 @@ class Tool( object, Dictifiable ): populate_model( input.inputs, group_state, tool_dict[ 'inputs' ], other_values ) else: try: + initial_value = input.get_initial_value( request_context, other_values ) tool_dict = input.to_dict( request_context, other_values=other_values ) - tool_dict[ 'value' ] = input.value_to_basic( state_inputs.get( input.name, input.get_initial_value( request_context, other_values ) ), self.app, use_security=True ) + tool_dict[ 'value' ] = input.value_to_basic( state_inputs.get( input.name, initial_value ), self.app, use_security=True ) + tool_dict[ 'default_value' ] = input.value_to_basic( initial_value, self.app, use_security=True ) tool_dict[ 'text_value' ] = input.value_to_display_text( tool_dict[ 'value' ] ) except Exception as e: tool_dict = input.to_dict( request_context ) diff --git a/static/maps/mvc/tool/tool-form-composite.js.map b/static/maps/mvc/tool/tool-form-composite.js.map index b66abf8d75b..a793b629a56 100644 --- a/static/maps/mvc/tool/tool-form-composite.js.map +++ b/static/maps/mvc/tool/tool-form-composite.js.map @@ -1 +1 @@ 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\ 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 3c07d2e8a3e..ee211fc8683 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","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/form/form-data","mvc/tool/tool-form-base","mvc/ui/ui-modal","mvc/webhooks","mvc/workflow/workflow-icons"],function(a,b,c,d,e,f,g,h,i){var j=Backbone.View.extend({initialize:function(a){var c=this;this.modal=parent.Galaxy.modal||new g.View,this.model=a&&a.model||new Backbone.Model(a),this.deferred=new b,this.setElement($("
").addClass("ui-form-composite").append(this.$message=$("
")).append(this.$header=$("
")).append(this.$steps=$("
"))),$("body").append(this.$el),this._configure(),this.render(),this._refresh(),this.$el.on("click",function(){c._refresh()}),this.$steps.scroll(function(){c._refresh()}),$(window).resize(function(){c._refresh()})},_refresh:function(){var a=_.reduce(this.$el.children(),function(a,b){return a+$(b).outerHeight()},0)-this.$steps.height()+25;this.$steps.css("height",$(window).height()-a)},_configure:function(){function b(a,b){for(var e=/\$\{(.+?)\}/g;match=e.exec(String(a));){var f=match[1];b(c.wp_inputs[f]=c.wp_inputs[f]||{label:f,name:f,type:"text",color:"hsl( "+100*++d+", 70%, 30% )",style:"ui-form-wp-source",links:[]})}}var c=this;this.forms=[],this.steps=[],this.links=[],this.parms=[],_.each(this.model.get("steps"),function(b,d){Galaxy.emit.debug("tool-form-composite::initialize()",d+" : Preparing workflow step.");var e=i[b.step_type],f=parseInt(d+1)+": "+(b.step_label||b.step_name);b.annotation&&(f+=" - "+b.annotation),b.step_version&&(f+=" (Galaxy Version "+b.step_version+")"),b=a.merge({index:d,title:_.escape(f),icon:e||"",help:null,citations:null,collapsible:!0,collapsed:d>0&&!c._isDataStep(b),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",errors:b.messages,initial_errors:!0,cls:"ui-portlet-narrow",hide_operations:!0,needs_refresh:!1,always_refresh:"tool"!=b.step_type},b),c.steps[d]=b,c.links[d]=[],c.parms[d]={}}),_.each(this.steps,function(a,b){e.visitInputs(a.inputs,function(a,d){c.parms[b][d]=a})}),_.each(this.steps,function(a,b){_.each(a.output_connections,function(a){_.each(c.steps,function(d){d.step_index===a.input_step_index&&c.links[b].push(d)})})}),_.each(this.steps,function(a,b){_.each(c.steps,function(d,e){var f={};_.each(a.output_connections,function(a){d.step_index===a.input_step_index&&(f[a.input_name]=a)}),_.each(c.parms[e],function(c,d){var e=f[d];e&&(c.type="hidden",c.help=c.step_linked?c.help+", ":"",c.help+="Output dataset '"+e.output_name+"' from step "+(parseInt(b)+1),c.step_linked=c.step_linked||[],c.step_linked.push(a))})})});var d=0;this.wp_inputs={},_.each(this.steps,function(a,d){_.each(c.parms[d],function(c){b(c.value,function(b){b.links.push(a),c.wp_linked=!0,c.type="text",c.backdrop=!0,c.style="ui-form-wp-target"})}),_.each(a.post_job_actions,function(a){_.each(a.action_arguments,function(a){b(a,function(){})})})}),_.each(this.steps,function(b){if("tool"==b.step_type){var d=!0;e.visitInputs(b.inputs,function(e,f,g){var h=-1!=["data","data_collection"].indexOf(e.type),i=g[e.data_ref];e.step_linked&&!c._isDataStep(e.step_linked)&&(d=!1),e.options&&(0==e.options.length&&!d||e.wp_linked)&&(e.is_workflow=!0),i&&(e.is_workflow=i.step_linked&&!c._isDataStep(i.step_linked)||e.wp_linked),(h||e.value&&"RuntimeValue"==e.value.__class__&&!e.step_linked)&&(b.collapsed=!1),e.value&&"RuntimeValue"==e.value.__class__&&(e.value=null),e.flavor="workflow",h||"hidden"===e.type||e.wp_linked||(e.optional||!a.isEmpty(e.value)&&""!==e.value)&&(e.collapsible_value=e.value,e.collapsible_preview=!0)})}})},render:function(){var a=this;this.deferred.reset(),this._renderHeader(),this._renderMessage(),this._renderParameters(),this._renderHistory(),_.each(this.steps,function(b){a._renderStep(b)})},_renderHeader:function(){var a=this;this.execute_btn=new c.Button({icon:"fa-check",title:"Run workflow",cls:"btn btn-primary",onclick:function(){a._execute()}}),this.$header.addClass("ui-form-header").empty().append(new c.Label({title:"Workflow: "+this.model.get("name")}).$el).append(this.execute_btn.$el)},_renderMessage:function(){this.$message.empty(),this.model.get("has_upgrade_messages")&&this.$message.append(new c.Message({message:"Some tools in this workflow may have changed since it was last saved or some errors were found. The workflow may still run, but any new options will have default values. Please review the messages below to make a decision about whether the changes will affect your analysis.",status:"warning",persistent:!0,fade:!1}).$el);var a=this.model.get("step_version_changes");a&&a.length>0&&this.$message.append(new c.Message({message:"Some tools are being executed with different versions compared to those available when this workflow was last saved because the other versions are not or no longer available on this Galaxy instance. To upgrade your workflow and dismiss this message simply edit the workflow and re-save it.",status:"warning",persistent:!0,fade:!1}).$el)},_renderParameters:function(){var a=this;this.wp_form=null,_.isEmpty(this.wp_inputs)||(this.wp_form=new d({title:"Workflow Parameters",inputs:this.wp_inputs,cls:"ui-portlet-narrow",onchange:function(){_.each(a.wp_form.input_list,function(b){_.each(b.links,function(b){a._refreshStep(b)})})}}),this._append(this.$steps.empty(),this.wp_form.$el))},_renderHistory:function(){this.history_form=new d({cls:"ui-portlet-narrow",title:"History Options",inputs:[{type:"conditional",name:"new_history",test_param:{name:"check",label:"Send results to a new history",type:"boolean",value:"false",help:""},cases:[{value:"true",inputs:[{name:"name",label:"History name",type:"text",value:this.model.get("name")}]}]}]}),this._append(this.$steps,this.history_form.$el)},_renderStep:function(b){var c=this,e=null;this.deferred.execute(function(g){if(c.$steps.addClass("ui-steps"),"tool"==b.step_type)b.postchange=function(c,d){var e={tool_id:b.id,tool_version:b.version,inputs:$.extend(!0,{},d.data.create())};d.wait(!0),Galaxy.emit.debug("tool-form-composite::postchange()","Sending current state.",e),a.request({type:"POST",url:Galaxy.root+"api/tools/"+b.id+"/build",data:e,success:function(a){d.update(a),d.wait(!1),Galaxy.emit.debug("tool-form-composite::postchange()","Received new model.",a),c.resolve()},error:function(a){Galaxy.emit.debug("tool-form-composite::postchange()","Refresh request failed.",a),c.reject()}})},e=new f(b),b.post_job_actions&&b.post_job_actions.length&&e.portlet.append($("
").addClass("ui-form-element-disabled").append($("
").addClass("ui-form-title").html("Job Post Actions")).append($("
").addClass("ui-form-preview").html(_.reduce(b.post_job_actions,function(a,b){return a+" "+b.short_str},""))));else{var h=-1!=["data_input","data_collection_input"].indexOf(b.step_type);_.each(b.inputs,function(a){a.flavor="module",a.hide_label=h}),e=new d(a.merge({title:b.title,onchange:function(){_.each(c.links[b.index],function(a){c._refreshStep(a)})},inputs:b.inputs&&b.inputs.length>0?b.inputs:[{type:"hidden",name:"No options available.",ignore:null}]},b))}c.forms[b.index]=e,c._append(c.$steps,e.$el),b.needs_refresh&&c._refreshStep(b),e.portlet[c.show_progress?"disable":"enable"](),c.show_progress&&c.execute_btn.model.set({wait:!0,wait_text:"Preparing...",percentage:100*(b.index+1)/c.steps.length}),Galaxy.emit.debug("tool-form-composite::initialize()",b.index+" : Workflow step state ready.",b),setTimeout(function(){g.resolve()},0)})},_refreshStep:function(a){var b=this,c=this.forms[a.index];c?(_.each(b.parms[a.index],function(a,d){if(a.step_linked||a.wp_linked){var e=c.field_list[c.data.match(d)];if(e){var f=void 0;if(a.step_linked)f={values:[]},_.each(a.step_linked,function(a){b._isDataStep(a)&&(value=b.forms[a.index].data.create().input,value&&_.each(value.values,function(a){f.values.push(a)}))}),!a.multiple&&f.values.length>0&&(f={values:[f.values[0]]});else if(a.wp_linked){f=a.value;for(var g=/\$\{(.+?)\}/g;match=g.exec(a.value);){var h=b.wp_form.field_list[b.wp_form.data.match(match[1])],i=h&&h.value();i&&(f=f.replace(new RegExp("\\"+match[0],"g"),i))}}void 0!==f&&e.value(f)}}}),c.trigger("change")):a.needs_refresh=!0},_refreshHistory:function(){var a=this,b=parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.model;this._refresh_history&&clearTimeout(this._refresh_history),b&&b.refresh().success(function(){0===b.numOfUnfinishedShownContents()&&(a._refresh_history=setTimeout(function(){a._refreshHistory()},b.UPDATE_DELAY))})},_execute:function(){var a=this;this.show_progress=!0,this._enabled(!1),this.deferred.execute(function(b){setTimeout(function(){b.resolve(),a._submit()},0)})},_submit:function(){var b=this,c=this.history_form.data.create(),d={new_history_name:c["new_history|name"]?c["new_history|name"]:null,history_id:c["new_history|name"]?null:this.model.get("history_id"),replacement_params:this.wp_form?this.wp_form.data.create():{},parameters:{},parameters_normalized:!0,batch:!0},e=!0;for(var f in this.forms){var g=this.forms[f],i=g.data.create(),j=b.steps[f],k=j.step_index;g.trigger("reset");for(var l in i){var m=i[l],n=g.data.match(l),o=(g.field_list[n],g.input_list[n]);if(!o.step_linked){if(e=this._isDataStep(j)?m&&m.values&&m.values.length>0:o.optional||o.is_workflow&&""!==m||!o.is_workflow&&null!==m,!e){g.highlight(n);break}d.parameters[k]=d.parameters[k]||{},d.parameters[k][l]=i[l]}}if(!e)break}e?(Galaxy.emit.debug("tool-form-composite::submit()","Validation complete.",d),a.request({type:"POST",url:Galaxy.root+"api/workflows/"+this.model.id+"/invocations",data:d,success:function(a){if(Galaxy.emit.debug("tool-form-composite::submit","Submission successful.",a),b.$el.children().hide(),b.$el.append(b._templateSuccess(a)),$.isArray(a)&&a.length>0){b.$el.append($("
",{id:"webhook-view"}));{new h.WebhookView({urlRoot:Galaxy.root+"api/webhooks/workflow"})}}b._refreshHistory()},error:function(a){Galaxy.emit.debug("tool-form-composite::submit","Submission failed.",a);var c=!1;if(a&&a.err_data)for(var e in b.forms){var f=b.forms[e],g=a.err_data[f.model.get("step_index")];if(g){var h=f.data.matchResponse(g);for(var i in h){f.highlight(i,h[i]),c=!0;break}}}c||b.modal.show({title:"Workflow submission failed",body:b._templateError(d,a&&a.err_msg),buttons:{Close:function(){b.modal.hide()}}})},complete:function(){b._enabled(!0)}})):(b._enabled(!0),Galaxy.emit.debug("tool-form-composite::submit()","Validation failed.",d))},_append:function(a,b){a.append("

").append(b)},_enabled:function(a){this.execute_btn.model.set({wait:!a,wait_text:"Sending...",percentage:-1}),this.wp_form&&this.wp_form.portlet[a?"enable":"disable"](),this.history_form&&this.history_form.portlet[a?"enable":"disable"](),_.each(this.forms,function(b){b&&b.portlet[a?"enable":"disable"]()})},_isDataStep:function(a){lst=$.isArray(a)?a:[a];for(var b=0;b0?$("

").addClass("donemessagelarge").append($("

").html("Successfully invoked workflow "+a.sanitize(this.model.get("name"))+""+(b.length>1?" "+b.length+" times":"")+".")).append($("

").append("").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")):this._templateError(b,"Invalid success response. No invocations found.")},_templateError:function(a,b){return $("

").addClass("errormessagelarge").append($("

").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(JSON.stringify(b)||""))).append($("

").text(JSON.stringify(a,null,4)))}});return{View:j}});
+define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/form/form-data","mvc/tool/tool-form-base","mvc/ui/ui-modal","mvc/webhooks","mvc/workflow/workflow-icons"],function(a,b,c,d,e,f,g,h,i){var j=Backbone.View.extend({initialize:function(a){var c=this;this.modal=parent.Galaxy.modal||new g.View,this.model=a&&a.model||new Backbone.Model(a),this.deferred=new b,this.setElement($("
").addClass("ui-form-composite").append(this.$message=$("
")).append(this.$header=$("
")).append(this.$steps=$("
"))),$("body").append(this.$el),this._configure(),this.render(),this._refresh(),this.$el.on("click",function(){c._refresh()}),this.$steps.scroll(function(){c._refresh()}),$(window).resize(function(){c._refresh()})},_refresh:function(){var a=_.reduce(this.$el.children(),function(a,b){return a+$(b).outerHeight()},0)-this.$steps.height()+25;this.$steps.css("height",$(window).height()-a)},_configure:function(){function b(a,b){for(var e=/\$\{(.+?)\}/g;match=e.exec(String(a));){var f=match[1];b(c.wp_inputs[f]=c.wp_inputs[f]||{label:f,name:f,type:"text",color:"hsl( "+100*++d+", 70%, 30% )",style:"ui-form-wp-source",links:[]})}}var c=this;this.forms=[],this.steps=[],this.links=[],this.parms=[],_.each(this.model.get("steps"),function(b,d){Galaxy.emit.debug("tool-form-composite::initialize()",d+" : Preparing workflow step.");var e=i[b.step_type],f=parseInt(d+1)+": "+(b.step_label||b.step_name);b.annotation&&(f+=" - "+b.annotation),b.step_version&&(f+=" (Galaxy Version "+b.step_version+")"),b=a.merge({index:d,title:_.escape(f),icon:e||"",help:null,citations:null,collapsible:!0,collapsed:d>0&&!c._isDataStep(b),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",errors:b.messages,initial_errors:!0,cls:"ui-portlet-narrow",hide_operations:!0,needs_refresh:!1,always_refresh:"tool"!=b.step_type},b),c.steps[d]=b,c.links[d]=[],c.parms[d]={}}),_.each(this.steps,function(a,b){e.visitInputs(a.inputs,function(a,d){c.parms[b][d]=a})}),_.each(this.steps,function(a,b){_.each(a.output_connections,function(a){_.each(c.steps,function(d){d.step_index===a.input_step_index&&c.links[b].push(d)})})}),_.each(this.steps,function(a,b){_.each(c.steps,function(d,e){var f={};_.each(a.output_connections,function(a){d.step_index===a.input_step_index&&(f[a.input_name]=a)}),_.each(c.parms[e],function(c,d){var e=f[d];e&&(c.type="hidden",c.help=c.step_linked?c.help+", ":"",c.help+="Output dataset '"+e.output_name+"' from step "+(parseInt(b)+1),c.step_linked=c.step_linked||[],c.step_linked.push(a))})})});var d=0;this.wp_inputs={},_.each(this.steps,function(a,d){_.each(c.parms[d],function(c){b(c.value,function(b){b.links.push(a),c.wp_linked=!0,c.type="text",c.backdrop=!0,c.style="ui-form-wp-target"})}),_.each(a.post_job_actions,function(a){_.each(a.action_arguments,function(a){b(a,function(){})})})}),_.each(this.steps,function(b){if("tool"==b.step_type){var d=!0;e.visitInputs(b.inputs,function(e,f,g){var h=-1!=["data","data_collection"].indexOf(e.type),i=g[e.data_ref];e.step_linked&&!c._isDataStep(e.step_linked)&&(d=!1),e.options&&(0==e.options.length&&!d||e.wp_linked)&&(e.is_workflow=!0),i&&(e.is_workflow=i.step_linked&&!c._isDataStep(i.step_linked)||e.wp_linked),(h||e.value&&"RuntimeValue"==e.value.__class__&&!e.step_linked)&&(b.collapsed=!1),e.flavor="workflow",e.value&&"RuntimeValue"==e.value.__class__?e.value=e.default_value:h||"hidden"===e.type||e.wp_linked||(e.optional||!a.isEmpty(e.value)&&""!==e.value)&&(e.collapsible_value=e.value,e.collapsible_preview=!0)})}})},render:function(){var a=this;this.deferred.reset(),this._renderHeader(),this._renderMessage(),this._renderParameters(),this._renderHistory(),_.each(this.steps,function(b){a._renderStep(b)})},_renderHeader:function(){var a=this;this.execute_btn=new c.Button({icon:"fa-check",title:"Run workflow",cls:"btn btn-primary",onclick:function(){a._execute()}}),this.$header.addClass("ui-form-header").empty().append(new c.Label({title:"Workflow: "+this.model.get("name")}).$el).append(this.execute_btn.$el)},_renderMessage:function(){this.$message.empty(),this.model.get("has_upgrade_messages")&&this.$message.append(new c.Message({message:"Some tools in this workflow may have changed since it was last saved or some errors were found. The workflow may still run, but any new options will have default values. Please review the messages below to make a decision about whether the changes will affect your analysis.",status:"warning",persistent:!0,fade:!1}).$el);var a=this.model.get("step_version_changes");a&&a.length>0&&this.$message.append(new c.Message({message:"Some tools are being executed with different versions compared to those available when this workflow was last saved because the other versions are not or no longer available on this Galaxy instance. To upgrade your workflow and dismiss this message simply edit the workflow and re-save it.",status:"warning",persistent:!0,fade:!1}).$el)},_renderParameters:function(){var a=this;this.wp_form=null,_.isEmpty(this.wp_inputs)||(this.wp_form=new d({title:"Workflow Parameters",inputs:this.wp_inputs,cls:"ui-portlet-narrow",onchange:function(){_.each(a.wp_form.input_list,function(b){_.each(b.links,function(b){a._refreshStep(b)})})}}),this._append(this.$steps.empty(),this.wp_form.$el))},_renderHistory:function(){this.history_form=new d({cls:"ui-portlet-narrow",title:"History Options",inputs:[{type:"conditional",name:"new_history",test_param:{name:"check",label:"Send results to a new history",type:"boolean",value:"false",help:""},cases:[{value:"true",inputs:[{name:"name",label:"History name",type:"text",value:this.model.get("name")}]}]}]}),this._append(this.$steps,this.history_form.$el)},_renderStep:function(b){var c=this,e=null;this.deferred.execute(function(g){if(c.$steps.addClass("ui-steps"),"tool"==b.step_type)b.postchange=function(c,d){var e={tool_id:b.id,tool_version:b.version,inputs:$.extend(!0,{},d.data.create())};d.wait(!0),Galaxy.emit.debug("tool-form-composite::postchange()","Sending current state.",e),a.request({type:"POST",url:Galaxy.root+"api/tools/"+b.id+"/build",data:e,success:function(a){d.update(a),d.wait(!1),Galaxy.emit.debug("tool-form-composite::postchange()","Received new model.",a),c.resolve()},error:function(a){Galaxy.emit.debug("tool-form-composite::postchange()","Refresh request failed.",a),c.reject()}})},e=new f(b),b.post_job_actions&&b.post_job_actions.length&&e.portlet.append($("
").addClass("ui-form-element-disabled").append($("
").addClass("ui-form-title").html("Job Post Actions")).append($("
").addClass("ui-form-preview").html(_.reduce(b.post_job_actions,function(a,b){return a+" "+b.short_str},""))));else{var h=-1!=["data_input","data_collection_input"].indexOf(b.step_type);_.each(b.inputs,function(a){a.flavor="module",a.hide_label=h}),e=new d(a.merge({title:b.title,onchange:function(){_.each(c.links[b.index],function(a){c._refreshStep(a)})},inputs:b.inputs&&b.inputs.length>0?b.inputs:[{type:"hidden",name:"No options available.",ignore:null}]},b))}c.forms[b.index]=e,c._append(c.$steps,e.$el),b.needs_refresh&&c._refreshStep(b),e.portlet[c.show_progress?"disable":"enable"](),c.show_progress&&c.execute_btn.model.set({wait:!0,wait_text:"Preparing...",percentage:100*(b.index+1)/c.steps.length}),Galaxy.emit.debug("tool-form-composite::initialize()",b.index+" : Workflow step state ready.",b),setTimeout(function(){g.resolve()},0)})},_refreshStep:function(a){var b=this,c=this.forms[a.index];c?(_.each(b.parms[a.index],function(a,d){if(a.step_linked||a.wp_linked){var e=c.field_list[c.data.match(d)];if(e){var f=void 0;if(a.step_linked)f={values:[]},_.each(a.step_linked,function(a){b._isDataStep(a)&&(value=b.forms[a.index].data.create().input,value&&_.each(value.values,function(a){f.values.push(a)}))}),!a.multiple&&f.values.length>0&&(f={values:[f.values[0]]});else if(a.wp_linked){f=a.value;for(var g=/\$\{(.+?)\}/g;match=g.exec(a.value);){var h=b.wp_form.field_list[b.wp_form.data.match(match[1])],i=h&&h.value();i&&(f=f.replace(new RegExp("\\"+match[0],"g"),i))}}void 0!==f&&e.value(f)}}}),c.trigger("change")):a.needs_refresh=!0},_refreshHistory:function(){var a=this,b=parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.model;this._refresh_history&&clearTimeout(this._refresh_history),b&&b.refresh().success(function(){0===b.numOfUnfinishedShownContents()&&(a._refresh_history=setTimeout(function(){a._refreshHistory()},b.UPDATE_DELAY))})},_execute:function(){var a=this;this.show_progress=!0,this._enabled(!1),this.deferred.execute(function(b){setTimeout(function(){b.resolve(),a._submit()},0)})},_submit:function(){var b=this,c=this.history_form.data.create(),d={new_history_name:c["new_history|name"]?c["new_history|name"]:null,history_id:c["new_history|name"]?null:this.model.get("history_id"),replacement_params:this.wp_form?this.wp_form.data.create():{},parameters:{},parameters_normalized:!0,batch:!0},e=!0;for(var f in this.forms){var g=this.forms[f],i=g.data.create(),j=b.steps[f],k=j.step_index;g.trigger("reset");for(var l in i){var m=i[l],n=g.data.match(l),o=(g.field_list[n],g.input_list[n]);if(!o.step_linked){if(e=this._isDataStep(j)?m&&m.values&&m.values.length>0:o.optional||o.is_workflow&&""!==m||!o.is_workflow&&null!==m,!e){g.highlight(n);break}d.parameters[k]=d.parameters[k]||{},d.parameters[k][l]=i[l]}}if(!e)break}e?(Galaxy.emit.debug("tool-form-composite::submit()","Validation complete.",d),a.request({type:"POST",url:Galaxy.root+"api/workflows/"+this.model.id+"/invocations",data:d,success:function(a){if(Galaxy.emit.debug("tool-form-composite::submit","Submission successful.",a),b.$el.children().hide(),b.$el.append(b._templateSuccess(a)),$.isArray(a)&&a.length>0){b.$el.append($("
",{id:"webhook-view"}));{new h.WebhookView({urlRoot:Galaxy.root+"api/webhooks/workflow"})}}b._refreshHistory()},error:function(a){Galaxy.emit.debug("tool-form-composite::submit","Submission failed.",a);var c=!1;if(a&&a.err_data)for(var e in b.forms){var f=b.forms[e],g=a.err_data[f.model.get("step_index")];if(g){var h=f.data.matchResponse(g);for(var i in h){f.highlight(i,h[i]),c=!0;break}}}c||b.modal.show({title:"Workflow submission failed",body:b._templateError(d,a&&a.err_msg),buttons:{Close:function(){b.modal.hide()}}})},complete:function(){b._enabled(!0)}})):(b._enabled(!0),Galaxy.emit.debug("tool-form-composite::submit()","Validation failed.",d))},_append:function(a,b){a.append("
").append(b)},_enabled:function(a){this.execute_btn.model.set({wait:!a,wait_text:"Sending...",percentage:-1}),this.wp_form&&this.wp_form.portlet[a?"enable":"disable"](),this.history_form&&this.history_form.portlet[a?"enable":"disable"](),_.each(this.forms,function(b){b&&b.portlet[a?"enable":"disable"]()})},_isDataStep:function(a){lst=$.isArray(a)?a:[a];for(var b=0;b0?$("
").addClass("donemessagelarge").append($("
").html("Successfully invoked workflow "+a.sanitize(this.model.get("name"))+""+(b.length>1?" "+b.length+" times":"")+".")).append($("
").append("").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")):this._templateError(b,"Invalid success response. No invocations found.")},_templateError:function(a,b){return $("
").addClass("errormessagelarge").append($("
").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(JSON.stringify(b)||""))).append($("
").text(JSON.stringify(a,null,4)))}});return{View:j}});
 //# sourceMappingURL=../../../maps/mvc/tool/tool-form-composite.js.map
\ No newline at end of file

From fba860f689d1af5e6727a946e20e1521f83620ed Mon Sep 17 00:00:00 2001
From: guerler 
Date: Wed, 19 Apr 2017 15:57:36 -0400
Subject: [PATCH 2/2] Use local flag to handle runtime values

---
 client/galaxy/scripts/mvc/tool/tool-form-composite.js | 6 +++---
 static/maps/mvc/tool/tool-form-composite.js.map       | 2 +-
 static/scripts/mvc/tool/tool-form-composite.js        | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/client/galaxy/scripts/mvc/tool/tool-form-composite.js b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
index 3c2398db6e9..ed627bdbf62 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form-composite.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form-composite.js
@@ -151,16 +151,16 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
                 if ( step.step_type == 'tool' ) {
                     var data_resolved = true;
                     FormData.visitInputs( step.inputs, function ( input, name, context ) {
+                        var is_runtime_value = input.value && input.value.__class__ == 'RuntimeValue';
                         var is_data_input = ([ 'data', 'data_collection' ]).indexOf( input.type ) != -1;
                         var data_ref = context[ input.data_ref ];
                         input.step_linked && !self._isDataStep( input.step_linked ) && ( data_resolved = false );
                         input.options && ( ( input.options.length == 0 && !data_resolved ) || input.wp_linked ) && ( input.is_workflow = true );
                         data_ref && ( input.is_workflow = ( data_ref.step_linked && !self._isDataStep( data_ref.step_linked ) ) || input.wp_linked );
                         ( is_data_input || ( input.value && input.value.__class__ == 'RuntimeValue' && !input.step_linked ) ) && ( step.collapsed = false );
+                        is_runtime_value && ( input.value = input.default_value );
                         input.flavor = 'workflow';
-                        if ( input.value && input.value.__class__ == 'RuntimeValue' ) {
-                            input.value = input.default_value;
-                        } else if ( !is_data_input && input.type !== 'hidden' && !input.wp_linked ) {
+                        if ( !is_runtime_value && !is_data_input && input.type !== 'hidden' && !input.wp_linked ) {
                             if ( input.optional || ( !Utils.isEmpty( input.value ) && input.value !== '' ) ) {
                                 input.collapsible_value = input.value;
                                 input.collapsible_preview = true;
diff --git a/static/maps/mvc/tool/tool-form-composite.js.map b/static/maps/mvc/tool/tool-form-composite.js.map
index a793b629a56..a1183c6dcc6 100644
--- a/static/maps/mvc/tool/tool-form-composite.js.map
+++ b/static/maps/mvc/tool/tool-form-composite.js.map
@@ -1 +1 @@
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\ 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 ee211fc8683..0a19d4cb2e9 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","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/form/form-data","mvc/tool/tool-form-base","mvc/ui/ui-modal","mvc/webhooks","mvc/workflow/workflow-icons"],function(a,b,c,d,e,f,g,h,i){var j=Backbone.View.extend({initialize:function(a){var c=this;this.modal=parent.Galaxy.modal||new g.View,this.model=a&&a.model||new Backbone.Model(a),this.deferred=new b,this.setElement($("
").addClass("ui-form-composite").append(this.$message=$("
")).append(this.$header=$("
")).append(this.$steps=$("
"))),$("body").append(this.$el),this._configure(),this.render(),this._refresh(),this.$el.on("click",function(){c._refresh()}),this.$steps.scroll(function(){c._refresh()}),$(window).resize(function(){c._refresh()})},_refresh:function(){var a=_.reduce(this.$el.children(),function(a,b){return a+$(b).outerHeight()},0)-this.$steps.height()+25;this.$steps.css("height",$(window).height()-a)},_configure:function(){function b(a,b){for(var e=/\$\{(.+?)\}/g;match=e.exec(String(a));){var f=match[1];b(c.wp_inputs[f]=c.wp_inputs[f]||{label:f,name:f,type:"text",color:"hsl( "+100*++d+", 70%, 30% )",style:"ui-form-wp-source",links:[]})}}var c=this;this.forms=[],this.steps=[],this.links=[],this.parms=[],_.each(this.model.get("steps"),function(b,d){Galaxy.emit.debug("tool-form-composite::initialize()",d+" : Preparing workflow step.");var e=i[b.step_type],f=parseInt(d+1)+": "+(b.step_label||b.step_name);b.annotation&&(f+=" - "+b.annotation),b.step_version&&(f+=" (Galaxy Version "+b.step_version+")"),b=a.merge({index:d,title:_.escape(f),icon:e||"",help:null,citations:null,collapsible:!0,collapsed:d>0&&!c._isDataStep(b),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",errors:b.messages,initial_errors:!0,cls:"ui-portlet-narrow",hide_operations:!0,needs_refresh:!1,always_refresh:"tool"!=b.step_type},b),c.steps[d]=b,c.links[d]=[],c.parms[d]={}}),_.each(this.steps,function(a,b){e.visitInputs(a.inputs,function(a,d){c.parms[b][d]=a})}),_.each(this.steps,function(a,b){_.each(a.output_connections,function(a){_.each(c.steps,function(d){d.step_index===a.input_step_index&&c.links[b].push(d)})})}),_.each(this.steps,function(a,b){_.each(c.steps,function(d,e){var f={};_.each(a.output_connections,function(a){d.step_index===a.input_step_index&&(f[a.input_name]=a)}),_.each(c.parms[e],function(c,d){var e=f[d];e&&(c.type="hidden",c.help=c.step_linked?c.help+", ":"",c.help+="Output dataset '"+e.output_name+"' from step "+(parseInt(b)+1),c.step_linked=c.step_linked||[],c.step_linked.push(a))})})});var d=0;this.wp_inputs={},_.each(this.steps,function(a,d){_.each(c.parms[d],function(c){b(c.value,function(b){b.links.push(a),c.wp_linked=!0,c.type="text",c.backdrop=!0,c.style="ui-form-wp-target"})}),_.each(a.post_job_actions,function(a){_.each(a.action_arguments,function(a){b(a,function(){})})})}),_.each(this.steps,function(b){if("tool"==b.step_type){var d=!0;e.visitInputs(b.inputs,function(e,f,g){var h=-1!=["data","data_collection"].indexOf(e.type),i=g[e.data_ref];e.step_linked&&!c._isDataStep(e.step_linked)&&(d=!1),e.options&&(0==e.options.length&&!d||e.wp_linked)&&(e.is_workflow=!0),i&&(e.is_workflow=i.step_linked&&!c._isDataStep(i.step_linked)||e.wp_linked),(h||e.value&&"RuntimeValue"==e.value.__class__&&!e.step_linked)&&(b.collapsed=!1),e.flavor="workflow",e.value&&"RuntimeValue"==e.value.__class__?e.value=e.default_value:h||"hidden"===e.type||e.wp_linked||(e.optional||!a.isEmpty(e.value)&&""!==e.value)&&(e.collapsible_value=e.value,e.collapsible_preview=!0)})}})},render:function(){var a=this;this.deferred.reset(),this._renderHeader(),this._renderMessage(),this._renderParameters(),this._renderHistory(),_.each(this.steps,function(b){a._renderStep(b)})},_renderHeader:function(){var a=this;this.execute_btn=new c.Button({icon:"fa-check",title:"Run workflow",cls:"btn btn-primary",onclick:function(){a._execute()}}),this.$header.addClass("ui-form-header").empty().append(new c.Label({title:"Workflow: "+this.model.get("name")}).$el).append(this.execute_btn.$el)},_renderMessage:function(){this.$message.empty(),this.model.get("has_upgrade_messages")&&this.$message.append(new c.Message({message:"Some tools in this workflow may have changed since it was last saved or some errors were found. The workflow may still run, but any new options will have default values. Please review the messages below to make a decision about whether the changes will affect your analysis.",status:"warning",persistent:!0,fade:!1}).$el);var a=this.model.get("step_version_changes");a&&a.length>0&&this.$message.append(new c.Message({message:"Some tools are being executed with different versions compared to those available when this workflow was last saved because the other versions are not or no longer available on this Galaxy instance. To upgrade your workflow and dismiss this message simply edit the workflow and re-save it.",status:"warning",persistent:!0,fade:!1}).$el)},_renderParameters:function(){var a=this;this.wp_form=null,_.isEmpty(this.wp_inputs)||(this.wp_form=new d({title:"Workflow Parameters",inputs:this.wp_inputs,cls:"ui-portlet-narrow",onchange:function(){_.each(a.wp_form.input_list,function(b){_.each(b.links,function(b){a._refreshStep(b)})})}}),this._append(this.$steps.empty(),this.wp_form.$el))},_renderHistory:function(){this.history_form=new d({cls:"ui-portlet-narrow",title:"History Options",inputs:[{type:"conditional",name:"new_history",test_param:{name:"check",label:"Send results to a new history",type:"boolean",value:"false",help:""},cases:[{value:"true",inputs:[{name:"name",label:"History name",type:"text",value:this.model.get("name")}]}]}]}),this._append(this.$steps,this.history_form.$el)},_renderStep:function(b){var c=this,e=null;this.deferred.execute(function(g){if(c.$steps.addClass("ui-steps"),"tool"==b.step_type)b.postchange=function(c,d){var e={tool_id:b.id,tool_version:b.version,inputs:$.extend(!0,{},d.data.create())};d.wait(!0),Galaxy.emit.debug("tool-form-composite::postchange()","Sending current state.",e),a.request({type:"POST",url:Galaxy.root+"api/tools/"+b.id+"/build",data:e,success:function(a){d.update(a),d.wait(!1),Galaxy.emit.debug("tool-form-composite::postchange()","Received new model.",a),c.resolve()},error:function(a){Galaxy.emit.debug("tool-form-composite::postchange()","Refresh request failed.",a),c.reject()}})},e=new f(b),b.post_job_actions&&b.post_job_actions.length&&e.portlet.append($("
").addClass("ui-form-element-disabled").append($("
").addClass("ui-form-title").html("Job Post Actions")).append($("
").addClass("ui-form-preview").html(_.reduce(b.post_job_actions,function(a,b){return a+" "+b.short_str},""))));else{var h=-1!=["data_input","data_collection_input"].indexOf(b.step_type);_.each(b.inputs,function(a){a.flavor="module",a.hide_label=h}),e=new d(a.merge({title:b.title,onchange:function(){_.each(c.links[b.index],function(a){c._refreshStep(a)})},inputs:b.inputs&&b.inputs.length>0?b.inputs:[{type:"hidden",name:"No options available.",ignore:null}]},b))}c.forms[b.index]=e,c._append(c.$steps,e.$el),b.needs_refresh&&c._refreshStep(b),e.portlet[c.show_progress?"disable":"enable"](),c.show_progress&&c.execute_btn.model.set({wait:!0,wait_text:"Preparing...",percentage:100*(b.index+1)/c.steps.length}),Galaxy.emit.debug("tool-form-composite::initialize()",b.index+" : Workflow step state ready.",b),setTimeout(function(){g.resolve()},0)})},_refreshStep:function(a){var b=this,c=this.forms[a.index];c?(_.each(b.parms[a.index],function(a,d){if(a.step_linked||a.wp_linked){var e=c.field_list[c.data.match(d)];if(e){var f=void 0;if(a.step_linked)f={values:[]},_.each(a.step_linked,function(a){b._isDataStep(a)&&(value=b.forms[a.index].data.create().input,value&&_.each(value.values,function(a){f.values.push(a)}))}),!a.multiple&&f.values.length>0&&(f={values:[f.values[0]]});else if(a.wp_linked){f=a.value;for(var g=/\$\{(.+?)\}/g;match=g.exec(a.value);){var h=b.wp_form.field_list[b.wp_form.data.match(match[1])],i=h&&h.value();i&&(f=f.replace(new RegExp("\\"+match[0],"g"),i))}}void 0!==f&&e.value(f)}}}),c.trigger("change")):a.needs_refresh=!0},_refreshHistory:function(){var a=this,b=parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.model;this._refresh_history&&clearTimeout(this._refresh_history),b&&b.refresh().success(function(){0===b.numOfUnfinishedShownContents()&&(a._refresh_history=setTimeout(function(){a._refreshHistory()},b.UPDATE_DELAY))})},_execute:function(){var a=this;this.show_progress=!0,this._enabled(!1),this.deferred.execute(function(b){setTimeout(function(){b.resolve(),a._submit()},0)})},_submit:function(){var b=this,c=this.history_form.data.create(),d={new_history_name:c["new_history|name"]?c["new_history|name"]:null,history_id:c["new_history|name"]?null:this.model.get("history_id"),replacement_params:this.wp_form?this.wp_form.data.create():{},parameters:{},parameters_normalized:!0,batch:!0},e=!0;for(var f in this.forms){var g=this.forms[f],i=g.data.create(),j=b.steps[f],k=j.step_index;g.trigger("reset");for(var l in i){var m=i[l],n=g.data.match(l),o=(g.field_list[n],g.input_list[n]);if(!o.step_linked){if(e=this._isDataStep(j)?m&&m.values&&m.values.length>0:o.optional||o.is_workflow&&""!==m||!o.is_workflow&&null!==m,!e){g.highlight(n);break}d.parameters[k]=d.parameters[k]||{},d.parameters[k][l]=i[l]}}if(!e)break}e?(Galaxy.emit.debug("tool-form-composite::submit()","Validation complete.",d),a.request({type:"POST",url:Galaxy.root+"api/workflows/"+this.model.id+"/invocations",data:d,success:function(a){if(Galaxy.emit.debug("tool-form-composite::submit","Submission successful.",a),b.$el.children().hide(),b.$el.append(b._templateSuccess(a)),$.isArray(a)&&a.length>0){b.$el.append($("
",{id:"webhook-view"}));{new h.WebhookView({urlRoot:Galaxy.root+"api/webhooks/workflow"})}}b._refreshHistory()},error:function(a){Galaxy.emit.debug("tool-form-composite::submit","Submission failed.",a);var c=!1;if(a&&a.err_data)for(var e in b.forms){var f=b.forms[e],g=a.err_data[f.model.get("step_index")];if(g){var h=f.data.matchResponse(g);for(var i in h){f.highlight(i,h[i]),c=!0;break}}}c||b.modal.show({title:"Workflow submission failed",body:b._templateError(d,a&&a.err_msg),buttons:{Close:function(){b.modal.hide()}}})},complete:function(){b._enabled(!0)}})):(b._enabled(!0),Galaxy.emit.debug("tool-form-composite::submit()","Validation failed.",d))},_append:function(a,b){a.append("
").append(b)},_enabled:function(a){this.execute_btn.model.set({wait:!a,wait_text:"Sending...",percentage:-1}),this.wp_form&&this.wp_form.portlet[a?"enable":"disable"](),this.history_form&&this.history_form.portlet[a?"enable":"disable"](),_.each(this.forms,function(b){b&&b.portlet[a?"enable":"disable"]()})},_isDataStep:function(a){lst=$.isArray(a)?a:[a];for(var b=0;b0?$("
").addClass("donemessagelarge").append($("
").html("Successfully invoked workflow "+a.sanitize(this.model.get("name"))+""+(b.length>1?" "+b.length+" times":"")+".")).append($("
").append("").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")):this._templateError(b,"Invalid success response. No invocations found.")},_templateError:function(a,b){return $("
").addClass("errormessagelarge").append($("
").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(JSON.stringify(b)||""))).append($("
").text(JSON.stringify(a,null,4)))}});return{View:j}});
+define(["utils/utils","utils/deferred","mvc/ui/ui-misc","mvc/form/form-view","mvc/form/form-data","mvc/tool/tool-form-base","mvc/ui/ui-modal","mvc/webhooks","mvc/workflow/workflow-icons"],function(a,b,c,d,e,f,g,h,i){var j=Backbone.View.extend({initialize:function(a){var c=this;this.modal=parent.Galaxy.modal||new g.View,this.model=a&&a.model||new Backbone.Model(a),this.deferred=new b,this.setElement($("
").addClass("ui-form-composite").append(this.$message=$("
")).append(this.$header=$("
")).append(this.$steps=$("
"))),$("body").append(this.$el),this._configure(),this.render(),this._refresh(),this.$el.on("click",function(){c._refresh()}),this.$steps.scroll(function(){c._refresh()}),$(window).resize(function(){c._refresh()})},_refresh:function(){var a=_.reduce(this.$el.children(),function(a,b){return a+$(b).outerHeight()},0)-this.$steps.height()+25;this.$steps.css("height",$(window).height()-a)},_configure:function(){function b(a,b){for(var e=/\$\{(.+?)\}/g;match=e.exec(String(a));){var f=match[1];b(c.wp_inputs[f]=c.wp_inputs[f]||{label:f,name:f,type:"text",color:"hsl( "+100*++d+", 70%, 30% )",style:"ui-form-wp-source",links:[]})}}var c=this;this.forms=[],this.steps=[],this.links=[],this.parms=[],_.each(this.model.get("steps"),function(b,d){Galaxy.emit.debug("tool-form-composite::initialize()",d+" : Preparing workflow step.");var e=i[b.step_type],f=parseInt(d+1)+": "+(b.step_label||b.step_name);b.annotation&&(f+=" - "+b.annotation),b.step_version&&(f+=" (Galaxy Version "+b.step_version+")"),b=a.merge({index:d,title:_.escape(f),icon:e||"",help:null,citations:null,collapsible:!0,collapsed:d>0&&!c._isDataStep(b),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",errors:b.messages,initial_errors:!0,cls:"ui-portlet-narrow",hide_operations:!0,needs_refresh:!1,always_refresh:"tool"!=b.step_type},b),c.steps[d]=b,c.links[d]=[],c.parms[d]={}}),_.each(this.steps,function(a,b){e.visitInputs(a.inputs,function(a,d){c.parms[b][d]=a})}),_.each(this.steps,function(a,b){_.each(a.output_connections,function(a){_.each(c.steps,function(d){d.step_index===a.input_step_index&&c.links[b].push(d)})})}),_.each(this.steps,function(a,b){_.each(c.steps,function(d,e){var f={};_.each(a.output_connections,function(a){d.step_index===a.input_step_index&&(f[a.input_name]=a)}),_.each(c.parms[e],function(c,d){var e=f[d];e&&(c.type="hidden",c.help=c.step_linked?c.help+", ":"",c.help+="Output dataset '"+e.output_name+"' from step "+(parseInt(b)+1),c.step_linked=c.step_linked||[],c.step_linked.push(a))})})});var d=0;this.wp_inputs={},_.each(this.steps,function(a,d){_.each(c.parms[d],function(c){b(c.value,function(b){b.links.push(a),c.wp_linked=!0,c.type="text",c.backdrop=!0,c.style="ui-form-wp-target"})}),_.each(a.post_job_actions,function(a){_.each(a.action_arguments,function(a){b(a,function(){})})})}),_.each(this.steps,function(b){if("tool"==b.step_type){var d=!0;e.visitInputs(b.inputs,function(e,f,g){var h=e.value&&"RuntimeValue"==e.value.__class__,i=-1!=["data","data_collection"].indexOf(e.type),j=g[e.data_ref];e.step_linked&&!c._isDataStep(e.step_linked)&&(d=!1),e.options&&(0==e.options.length&&!d||e.wp_linked)&&(e.is_workflow=!0),j&&(e.is_workflow=j.step_linked&&!c._isDataStep(j.step_linked)||e.wp_linked),(i||e.value&&"RuntimeValue"==e.value.__class__&&!e.step_linked)&&(b.collapsed=!1),h&&(e.value=e.default_value),e.flavor="workflow",h||i||"hidden"===e.type||e.wp_linked||(e.optional||!a.isEmpty(e.value)&&""!==e.value)&&(e.collapsible_value=e.value,e.collapsible_preview=!0)})}})},render:function(){var a=this;this.deferred.reset(),this._renderHeader(),this._renderMessage(),this._renderParameters(),this._renderHistory(),_.each(this.steps,function(b){a._renderStep(b)})},_renderHeader:function(){var a=this;this.execute_btn=new c.Button({icon:"fa-check",title:"Run workflow",cls:"btn btn-primary",onclick:function(){a._execute()}}),this.$header.addClass("ui-form-header").empty().append(new c.Label({title:"Workflow: "+this.model.get("name")}).$el).append(this.execute_btn.$el)},_renderMessage:function(){this.$message.empty(),this.model.get("has_upgrade_messages")&&this.$message.append(new c.Message({message:"Some tools in this workflow may have changed since it was last saved or some errors were found. The workflow may still run, but any new options will have default values. Please review the messages below to make a decision about whether the changes will affect your analysis.",status:"warning",persistent:!0,fade:!1}).$el);var a=this.model.get("step_version_changes");a&&a.length>0&&this.$message.append(new c.Message({message:"Some tools are being executed with different versions compared to those available when this workflow was last saved because the other versions are not or no longer available on this Galaxy instance. To upgrade your workflow and dismiss this message simply edit the workflow and re-save it.",status:"warning",persistent:!0,fade:!1}).$el)},_renderParameters:function(){var a=this;this.wp_form=null,_.isEmpty(this.wp_inputs)||(this.wp_form=new d({title:"Workflow Parameters",inputs:this.wp_inputs,cls:"ui-portlet-narrow",onchange:function(){_.each(a.wp_form.input_list,function(b){_.each(b.links,function(b){a._refreshStep(b)})})}}),this._append(this.$steps.empty(),this.wp_form.$el))},_renderHistory:function(){this.history_form=new d({cls:"ui-portlet-narrow",title:"History Options",inputs:[{type:"conditional",name:"new_history",test_param:{name:"check",label:"Send results to a new history",type:"boolean",value:"false",help:""},cases:[{value:"true",inputs:[{name:"name",label:"History name",type:"text",value:this.model.get("name")}]}]}]}),this._append(this.$steps,this.history_form.$el)},_renderStep:function(b){var c=this,e=null;this.deferred.execute(function(g){if(c.$steps.addClass("ui-steps"),"tool"==b.step_type)b.postchange=function(c,d){var e={tool_id:b.id,tool_version:b.version,inputs:$.extend(!0,{},d.data.create())};d.wait(!0),Galaxy.emit.debug("tool-form-composite::postchange()","Sending current state.",e),a.request({type:"POST",url:Galaxy.root+"api/tools/"+b.id+"/build",data:e,success:function(a){d.update(a),d.wait(!1),Galaxy.emit.debug("tool-form-composite::postchange()","Received new model.",a),c.resolve()},error:function(a){Galaxy.emit.debug("tool-form-composite::postchange()","Refresh request failed.",a),c.reject()}})},e=new f(b),b.post_job_actions&&b.post_job_actions.length&&e.portlet.append($("
").addClass("ui-form-element-disabled").append($("
").addClass("ui-form-title").html("Job Post Actions")).append($("
").addClass("ui-form-preview").html(_.reduce(b.post_job_actions,function(a,b){return a+" "+b.short_str},""))));else{var h=-1!=["data_input","data_collection_input"].indexOf(b.step_type);_.each(b.inputs,function(a){a.flavor="module",a.hide_label=h}),e=new d(a.merge({title:b.title,onchange:function(){_.each(c.links[b.index],function(a){c._refreshStep(a)})},inputs:b.inputs&&b.inputs.length>0?b.inputs:[{type:"hidden",name:"No options available.",ignore:null}]},b))}c.forms[b.index]=e,c._append(c.$steps,e.$el),b.needs_refresh&&c._refreshStep(b),e.portlet[c.show_progress?"disable":"enable"](),c.show_progress&&c.execute_btn.model.set({wait:!0,wait_text:"Preparing...",percentage:100*(b.index+1)/c.steps.length}),Galaxy.emit.debug("tool-form-composite::initialize()",b.index+" : Workflow step state ready.",b),setTimeout(function(){g.resolve()},0)})},_refreshStep:function(a){var b=this,c=this.forms[a.index];c?(_.each(b.parms[a.index],function(a,d){if(a.step_linked||a.wp_linked){var e=c.field_list[c.data.match(d)];if(e){var f=void 0;if(a.step_linked)f={values:[]},_.each(a.step_linked,function(a){b._isDataStep(a)&&(value=b.forms[a.index].data.create().input,value&&_.each(value.values,function(a){f.values.push(a)}))}),!a.multiple&&f.values.length>0&&(f={values:[f.values[0]]});else if(a.wp_linked){f=a.value;for(var g=/\$\{(.+?)\}/g;match=g.exec(a.value);){var h=b.wp_form.field_list[b.wp_form.data.match(match[1])],i=h&&h.value();i&&(f=f.replace(new RegExp("\\"+match[0],"g"),i))}}void 0!==f&&e.value(f)}}}),c.trigger("change")):a.needs_refresh=!0},_refreshHistory:function(){var a=this,b=parent.Galaxy&&parent.Galaxy.currHistoryPanel&&parent.Galaxy.currHistoryPanel.model;this._refresh_history&&clearTimeout(this._refresh_history),b&&b.refresh().success(function(){0===b.numOfUnfinishedShownContents()&&(a._refresh_history=setTimeout(function(){a._refreshHistory()},b.UPDATE_DELAY))})},_execute:function(){var a=this;this.show_progress=!0,this._enabled(!1),this.deferred.execute(function(b){setTimeout(function(){b.resolve(),a._submit()},0)})},_submit:function(){var b=this,c=this.history_form.data.create(),d={new_history_name:c["new_history|name"]?c["new_history|name"]:null,history_id:c["new_history|name"]?null:this.model.get("history_id"),replacement_params:this.wp_form?this.wp_form.data.create():{},parameters:{},parameters_normalized:!0,batch:!0},e=!0;for(var f in this.forms){var g=this.forms[f],i=g.data.create(),j=b.steps[f],k=j.step_index;g.trigger("reset");for(var l in i){var m=i[l],n=g.data.match(l),o=(g.field_list[n],g.input_list[n]);if(!o.step_linked){if(e=this._isDataStep(j)?m&&m.values&&m.values.length>0:o.optional||o.is_workflow&&""!==m||!o.is_workflow&&null!==m,!e){g.highlight(n);break}d.parameters[k]=d.parameters[k]||{},d.parameters[k][l]=i[l]}}if(!e)break}e?(Galaxy.emit.debug("tool-form-composite::submit()","Validation complete.",d),a.request({type:"POST",url:Galaxy.root+"api/workflows/"+this.model.id+"/invocations",data:d,success:function(a){if(Galaxy.emit.debug("tool-form-composite::submit","Submission successful.",a),b.$el.children().hide(),b.$el.append(b._templateSuccess(a)),$.isArray(a)&&a.length>0){b.$el.append($("
",{id:"webhook-view"}));{new h.WebhookView({urlRoot:Galaxy.root+"api/webhooks/workflow"})}}b._refreshHistory()},error:function(a){Galaxy.emit.debug("tool-form-composite::submit","Submission failed.",a);var c=!1;if(a&&a.err_data)for(var e in b.forms){var f=b.forms[e],g=a.err_data[f.model.get("step_index")];if(g){var h=f.data.matchResponse(g);for(var i in h){f.highlight(i,h[i]),c=!0;break}}}c||b.modal.show({title:"Workflow submission failed",body:b._templateError(d,a&&a.err_msg),buttons:{Close:function(){b.modal.hide()}}})},complete:function(){b._enabled(!0)}})):(b._enabled(!0),Galaxy.emit.debug("tool-form-composite::submit()","Validation failed.",d))},_append:function(a,b){a.append("
").append(b)},_enabled:function(a){this.execute_btn.model.set({wait:!a,wait_text:"Sending...",percentage:-1}),this.wp_form&&this.wp_form.portlet[a?"enable":"disable"](),this.history_form&&this.history_form.portlet[a?"enable":"disable"](),_.each(this.forms,function(b){b&&b.portlet[a?"enable":"disable"]()})},_isDataStep:function(a){lst=$.isArray(a)?a:[a];for(var b=0;b0?$("
").addClass("donemessagelarge").append($("
").html("Successfully invoked workflow "+a.sanitize(this.model.get("name"))+""+(b.length>1?" "+b.length+" times":"")+".")).append($("
").append("").text("You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.")):this._templateError(b,"Invalid success response. No invocations found.")},_templateError:function(a,b){return $("
").addClass("errormessagelarge").append($("
").text("The server could not complete the request. Please contact the Galaxy Team if this error persists. "+(JSON.stringify(b)||""))).append($("
").text(JSON.stringify(a,null,4)))}});return{View:j}});
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