mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
157939aa8f
Details: - Add a new workflow module describing subworkflows. - Add workflow list to editor side panel - with options to link in a subworkflow module or copy the target workflow into the workflow being editted node for node. - Update workflow, workflow step, and workflow invocation models to track subworkflow connections and execution. - Extend workflow outputs with concepts of labels (and UUIDs while I'm there) to match workflow inputs. This allow us to have something to label outputs with in the workflow editor and to reference in the format 2 workflow description language. - Extend workflow editor UI to allow labeling workflow outputs (and enforce that these are unique across a workflow). - Extend workflow invocation and progress tracking to allow invoking a subworkflow as part of another workflow invocation. - Extend workflow import and export code to allow a nested representation of workflows. - Update format 2 workflow description to allow testing nested workflows. Most relevant new and modified test cases can be run using the following commands: ``` ./run_tests.sh -api test/api/test_workflows.py:WorkflowsApiTestCase.test_run_subworkflow_simple ./run_tests.sh -api test/api/test_workflows_from_yaml.py:WorkflowsFromYamlApiTestCase.test_subworkflow_simple ./run_tests.sh -api test/api/test_workflows_from_yaml.py:WorkflowsFromYamlApiTestCase.test_outputs nosetests test/unit/test_galaxy_mapping.py nosetests test/unit/workflows/test_workflow_progress.py ```
2 lines
4.5 KiB
JavaScript
2 lines
4.5 KiB
JavaScript
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.tool_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.form_html=b.form_html,this.tool_state=b.tool_state,this.tool_errors=b.tool_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.form_html=a.form_html,this.tool_errors=a.tool_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="<div style='color: red; text-style: italic;'>"+a+"</div>";this.form_html=c,b.html(c),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});return b});
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