diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js index c0df1266fcb..8264f8f2688 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-node.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js @@ -196,7 +196,7 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { this.setLabel(data.label); if( "post_job_actions" in data ) { // Won't be present in response for data inputs - var pja_in = $.parseJSON(data.post_job_actions); + var pja_in = data.post_job_actions; this.post_job_actions = pja_in ? pja_in : {}; } node.nodeView.renderToolErrors(); diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view.js b/client/galaxy/scripts/mvc/workflow/workflow-view.js index e4d1cbe48ea..2ba1c461c9a 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-view.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-view.js @@ -671,7 +671,7 @@ define([ $.each(this.workflow.nodes, function ( k, node ){ if ( node.config_form && node.config_form.inputs ) { Utils.deepeach( node.config_form.inputs, function( d ) { - if ( typeof( d.value ) == 'string' ) { + if ( typeof d.value == 'string' ) { var form_matches = d.value.match( parameter_re ); if ( form_matches ) { matches = matches.concat( form_matches ); @@ -690,13 +690,13 @@ define([ }); } }); - if (matches){ - $.each(matches, function(k, element){ - if ($.inArray(element, workflow_parameters) === -1){ - workflow_parameters.push(element); - } - }); - } + } + if (matches){ + $.each(matches, function(k, element){ + if ($.inArray(element, workflow_parameters) === -1){ + workflow_parameters.push(element); + } + }); } }); if (workflow_parameters && workflow_parameters.length !== 0){ diff --git a/lib/galaxy/jobs/actions/post.py b/lib/galaxy/jobs/actions/post.py index 00309452c8b..d51024670f2 100644 --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -380,7 +380,7 @@ class ActionBox(object): else: # Not pja stuff. pass - 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\ No newline at end of file diff --git a/static/scripts/mvc/workflow/workflow-node.js b/static/scripts/mvc/workflow/workflow-node.js index 4798651d30e..b48f1c4cefc 100644 --- a/static/scripts/mvc/workflow/workflow-node.js +++ b/static/scripts/mvc/workflow/workflow-node.js @@ -1,2 +1,2 @@ -define(["mvc/workflow/workflow-view-node"],function(a){var b=Backbone.Model.extend({initialize:function(a,b){this.app=a,this.element=b.element,this.input_terminals={},this.output_terminals={},this.errors={},this.workflow_outputs=[]},getWorkflowOutput:function(a){return _.findWhere(this.workflow_outputs,{output_name:a})},isWorkflowOutput:function(a){return void 0!=this.getWorkflowOutput(a)},removeWorkflowOutput:function(a){for(;this.isWorkflowOutput(a);)this.workflow_outputs.splice(this.getWorkflowOutput(a),1)},addWorkflowOutput:function(a,b){if(!this.isWorkflowOutput(a)){var c={output_name:a};return b&&(c.label=b),this.workflow_outputs.push(c),!0}return!1},labelWorkflowOutput:function(a,b){var c=!1,d=null;if(this.isWorkflowOutput(a)){var e=this.getWorkflowOutput(a);d=e.label,e.label=b,c=d!=b}else c=this.addWorkflowOutput(a,b);return c&&(this.app.workflow.updateOutputLabel(d,b),this.markChanged(),this.nodeView.redrawWorkflowOutputs()),c},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(a){var b=[];return $.each(a,function(a,c){c.connectors.length>0&&b.push(c)}),b},hasConnectedOutputTerminals:function(){var a=this.output_terminals;for(var b in a)if(a[b].connectors.length>0)return!0;return!1},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var a=this.input_terminals;for(var b in a){var c=a[b];if(c.connectors.length>0&&c.isMappedOver())return!0}return!1},_connectedMappedTerminals:function(a){var b=[];return $.each(a,function(a,c){var d=c.mapOver();d.isCollection&&c.connectors.length>0&&b.push(c)}),b},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(a){var b=[];return $.each(a,function(a,c){var d=c.mapOver();d.isCollection&&b.push(c)}),b},hasMappedOverInputTerminals:function(){var a=!1;return _.each(this.input_terminals,function(b){var c=b.mapOver();c.isCollection&&(a=!0)}),a},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()}),$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()}),$.each(this.output_terminals,function(a,b){b.destroy()}),this.app.workflow.remove_node(this),$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);!function(b){b.removeChild(a),b.appendChild(a)}(a.parentNode),$(a).removeClass("toolForm-active")},setLabel:function(a){this.app.workflow.updateNodeLabel(this.label,a),this.label=a||null},init_field_data:function(b){b.type&&(this.type=b.type),this.name=b.name,this.config_form=b.config_form,this.tool_state=b.tool_state,this.errors=b.errors,this.tooltip=b.tooltip?b.tooltip:"",this.annotation=b.annotation,this.post_job_actions=b.post_job_actions?b.post_job_actions:{},this.setLabel(b.label),this.uuid=b.uuid,this.workflow_outputs=b.workflow_outputs?b.workflow_outputs:[];var c=this,d=new a({el:this.element[0],node:c});c.nodeView=d,$.each(b.data_inputs,function(a,b){d.addDataInput(b)}),b.data_inputs.length>0&&b.data_outputs.length>0&&d.addRule(),$.each(b.data_outputs,function(a,b){d.addDataOutput(b)}),d.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(a){var b=this;if(nodeView=b.nodeView,this.tool_state=a.tool_state,this.config_form=a.config_form,this.errors=a.errors,this.annotation=a.annotation,this.setLabel(a.label),"post_job_actions"in a){var c=$.parseJSON(a.post_job_actions);this.post_job_actions=c?c:{}}b.nodeView.renderToolErrors();var d=nodeView.$("div.inputs"),e=nodeView.newInputsDiv(),f={};_.each(a.data_inputs,function(a){var c=b.nodeView.addDataInput(a,e);f[a.name]=c}),_.each(_.difference(_.values(nodeView.terminalViews),_.values(f)),function(a){a.el.terminal.destroy()}),nodeView.terminalViews=f,b.nodeView.render(),1==a.data_outputs.length&&"collection_type"in a.data_outputs[0]&&nodeView.updateDataOutput(a.data_outputs[0]),d.replaceWith(e),"workflow_outputs"in a&&(this.workflow_outputs=workflow_outputs?workflow_outputs:[]),this.markChanged(),this.redraw()},error:function(a){var b=$(this.element).find(".toolFormBody");b.find("div").remove();var c="
"+a+"
";this.config_form=c,b.html(c),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});return b}); +define(["mvc/workflow/workflow-view-node"],function(a){var b=Backbone.Model.extend({initialize:function(a,b){this.app=a,this.element=b.element,this.input_terminals={},this.output_terminals={},this.errors={},this.workflow_outputs=[]},getWorkflowOutput:function(a){return _.findWhere(this.workflow_outputs,{output_name:a})},isWorkflowOutput:function(a){return void 0!=this.getWorkflowOutput(a)},removeWorkflowOutput:function(a){for(;this.isWorkflowOutput(a);)this.workflow_outputs.splice(this.getWorkflowOutput(a),1)},addWorkflowOutput:function(a,b){if(!this.isWorkflowOutput(a)){var c={output_name:a};return b&&(c.label=b),this.workflow_outputs.push(c),!0}return!1},labelWorkflowOutput:function(a,b){var c=!1,d=null;if(this.isWorkflowOutput(a)){var e=this.getWorkflowOutput(a);d=e.label,e.label=b,c=d!=b}else c=this.addWorkflowOutput(a,b);return c&&(this.app.workflow.updateOutputLabel(d,b),this.markChanged(),this.nodeView.redrawWorkflowOutputs()),c},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(a){var b=[];return $.each(a,function(a,c){c.connectors.length>0&&b.push(c)}),b},hasConnectedOutputTerminals:function(){var a=this.output_terminals;for(var b in a)if(a[b].connectors.length>0)return!0;return!1},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var a=this.input_terminals;for(var b in a){var c=a[b];if(c.connectors.length>0&&c.isMappedOver())return!0}return!1},_connectedMappedTerminals:function(a){var b=[];return $.each(a,function(a,c){var d=c.mapOver();d.isCollection&&c.connectors.length>0&&b.push(c)}),b},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(a){var b=[];return $.each(a,function(a,c){var d=c.mapOver();d.isCollection&&b.push(c)}),b},hasMappedOverInputTerminals:function(){var a=!1;return _.each(this.input_terminals,function(b){var c=b.mapOver();c.isCollection&&(a=!0)}),a},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()}),$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()}),$.each(this.output_terminals,function(a,b){b.destroy()}),this.app.workflow.remove_node(this),$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);!function(b){b.removeChild(a),b.appendChild(a)}(a.parentNode),$(a).removeClass("toolForm-active")},setLabel:function(a){this.app.workflow.updateNodeLabel(this.label,a),this.label=a||null},init_field_data:function(b){b.type&&(this.type=b.type),this.name=b.name,this.config_form=b.config_form,this.tool_state=b.tool_state,this.errors=b.errors,this.tooltip=b.tooltip?b.tooltip:"",this.annotation=b.annotation,this.post_job_actions=b.post_job_actions?b.post_job_actions:{},this.setLabel(b.label),this.uuid=b.uuid,this.workflow_outputs=b.workflow_outputs?b.workflow_outputs:[];var c=this,d=new a({el:this.element[0],node:c});c.nodeView=d,$.each(b.data_inputs,function(a,b){d.addDataInput(b)}),b.data_inputs.length>0&&b.data_outputs.length>0&&d.addRule(),$.each(b.data_outputs,function(a,b){d.addDataOutput(b)}),d.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(a){var b=this;if(nodeView=b.nodeView,this.tool_state=a.tool_state,this.config_form=a.config_form,this.errors=a.errors,this.annotation=a.annotation,this.setLabel(a.label),"post_job_actions"in a){var c=a.post_job_actions;this.post_job_actions=c?c:{}}b.nodeView.renderToolErrors();var d=nodeView.$("div.inputs"),e=nodeView.newInputsDiv(),f={};_.each(a.data_inputs,function(a){var c=b.nodeView.addDataInput(a,e);f[a.name]=c}),_.each(_.difference(_.values(nodeView.terminalViews),_.values(f)),function(a){a.el.terminal.destroy()}),nodeView.terminalViews=f,b.nodeView.render(),1==a.data_outputs.length&&"collection_type"in a.data_outputs[0]&&nodeView.updateDataOutput(a.data_outputs[0]),d.replaceWith(e),"workflow_outputs"in a&&(this.workflow_outputs=workflow_outputs?workflow_outputs:[]),this.markChanged(),this.redraw()},error:function(a){var b=$(this.element).find(".toolFormBody");b.find("div").remove();var c="
"+a+"
";this.config_form=c,b.html(c),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});return b}); //# sourceMappingURL=../../../maps/mvc/workflow/workflow-node.js.map \ No newline at end of file diff --git a/static/scripts/mvc/workflow/workflow-view.js b/static/scripts/mvc/workflow/workflow-view.js index 8d3340569c3..76f70328598 100644 --- a/static/scripts/mvc/workflow/workflow-view.js +++ b/static/scripts/mvc/workflow/workflow-view.js @@ -1,2 +1,2 @@ -define("mvc/workflow/workflow-globals",{}),define(["utils/utils","mvc/workflow/workflow-globals","mvc/workflow/workflow-manager","mvc/workflow/workflow-canvas","mvc/workflow/workflow-node","mvc/tool/tool-form-workflow","mvc/form/form-view","mvc/ui/ui-misc","utils/async-save-text","libs/toastr","ui/editable-text"],function(a,b,c,d,e,f,g,h,i){function j(a){var b=$("#galaxy_tools").contents();if(0===b.length&&(b=$(document)),$(this).removeClass("search_active"),b.find(".toolTitle").removeClass("search_match"),b.find(".toolSectionBody").hide(),b.find(".toolTitle").show(),b.find(".toolPanelLabel").show(),b.find(".toolSectionWrapper").each(function(){"recently_used_wrapper"!==$(this).attr("id")?$(this).show():$(this).hasClass("user_pref_visible")&&$(this).show()}),b.find("#search-no-results").hide(),b.find("#search-spinner").hide(),a){var c=b.find("#tool-search-query");c.val("search tools")}}return NODE_ICONS={tool:"fa-wrench",data_input:"fa-file-o",data_collection_input:"fa-folder-o",subworkflow:"fa-sitemap fa-rotate-270",pause:"fa-pause"},add_node_icon=function(a,b){var c=NODE_ICONS[b];if(c){var d=$(' ').addClass(c);a.before(d)}},Backbone.View.extend({initialize:function(a){function c(){var a=$('

');window.show_modal("Save As a New Workflow",a,{OK:function(){var a=$("#workflow_rename").val().length>0?$("#workflow_rename").val():"SavedAs_"+h.workflow.name,b=$("#wf_annotation").val().length>0?$("#wf_annotation").val():"";$.ajax({url:h.urls.workflow_save_as,type:"POST",data:{workflow_name:a,workflow_annotation:b,workflow_data:function(){return JSON.stringify(h.workflow.to_simple())}}}).done(function(a){window.onbeforeunload=void 0,window.location="/workflow/editor?id="+a,hide_modal()}).fail(function(){hide_modal(),alert("Saving this workflow failed. Please contact this site's administrator.")})},Cancel:hide_modal})}function e(){h.workflow.layout(),h.workflow.fit_canvas_to_nodes(),h.scroll_to_nodes(),h.canvas_manager.draw_overview()}function f(){$.jStorage.set("overview-off",!1),$("#overview-border").css("right","0px"),$("#close-viewport").css("background-position","0px 0px")}function g(){$.jStorage.set("overview-off",!0),$("#overview-border").css("right","20000px"),$("#close-viewport").css("background-position","12px 0px")}var h=b.app=this;this.options=a,this.urls=a&&a.urls||{},this.active_ajax_call=!1;var k=function(){h.workflow.check_changes_in_active_form(),workflow&&h.workflow.has_changes?(do_close=function(){window.onbeforeunload=void 0,window.document.location=h.urls.workflow_index},window.show_modal("Close workflow editor","There are unsaved changes to your workflow which will be lost.",{Cancel:hide_modal,"Save Changes":function(){l(null,do_close)}},{"Don't Save":do_close})):window.document.location=h.urls.workflow_index},l=function(a,b){if(show_message("Saving workflow","progress"),h.workflow.check_changes_in_active_form(),!h.workflow.has_changes)return hide_modal(),void(b&&b());h.workflow.rectify_workflow_outputs();var c=function(a){$.ajax({url:h.urls.save_workflow,type:"POST",data:{id:h.options.id,workflow_data:function(){return JSON.stringify(h.workflow.to_simple())},_:"true"},dataType:"json",success:function(b){var c=$("
").text(b.message);if(b.errors){c.addClass("warningmark");var d=$("