From 0a506dc561f9bf73a241db727723f1a24ff401f3 Mon Sep 17 00:00:00 2001 From: guerler Date: Sat, 2 May 2015 16:00:38 -0400 Subject: [PATCH 1/4] Workflow editor adjustments --- client/galaxy/scripts/mvc/form/form-data.js | 2 +- client/galaxy/scripts/mvc/tools/tools-form-workflow.js | 7 ++++++- static/maps/mvc/form/form-data.js.map | 2 +- static/maps/mvc/tools/tools-form-workflow.js.map | 2 +- static/scripts/mvc/form/form-data.js | 2 +- static/scripts/mvc/tools/tools-form-workflow.js | 2 +- 6 files changed, 11 insertions(+), 6 deletions(-) diff --git a/client/galaxy/scripts/mvc/form/form-data.js b/client/galaxy/scripts/mvc/form/form-data.js index 0562d97fbf9..194b431eb75 100644 --- a/client/galaxy/scripts/mvc/form/form-data.js +++ b/client/galaxy/scripts/mvc/form/form-data.js @@ -98,7 +98,7 @@ return Backbone.Model.extend({ break; // handle sections case 'section': - convert(job_input_id, node); + convert(input.flat && job_input_id || '', node); break; default: // get field diff --git a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js index fd8c8a5ce0d..c8dbdfc88fe 100644 --- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js @@ -41,7 +41,11 @@ define(['utils/utils', 'mvc/tools/tools-form-base'], Utils.deepeach(options.inputs, function(item) { if (item.type) { if (item.type == 'conditional') { - item.test_param.optional = false; + item.test_param.collapsible = false; + } else { + if ((['data', 'data_collection']).indexOf(item.type) == -1) { + item.collapsible = true; + } } } }); @@ -140,6 +144,7 @@ define(['utils/utils', 'mvc/tools/tools-form-base'], var input_config = { title : 'Add Actions: \'' + output_id + '\'', type : 'section', + flat : true, inputs : [{ action : 'RenameDatasetAction', argument : 'newname', diff --git a/static/maps/mvc/form/form-data.js.map b/static/maps/mvc/form/form-data.js.map index 7522cbb5ded..57976deb231 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\ No newline at end of file diff --git a/static/scripts/mvc/form/form-data.js b/static/scripts/mvc/form/form-data.js index 3e74c8c30a6..95fadcd57f4 100644 --- a/static/scripts/mvc/form/form-data.js +++ b/static/scripts/mvc/form/form-data.js @@ -1,2 +1,2 @@ -define(["utils/utils"],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},checksum:function(){var a="";for(var b in this.app.field_list){var c=this.app.field_list[b];a+=JSON.stringify(c.value&&c.value())}return a},create:function(){function a(a,b,d){c.map_dict[a]=b,e[a]=d}function b(d,e){for(var f in e){var g=e[f];if(g.input){var h=g.input,i=d;switch(""!=d&&(i+="|"),i+=h.name,h.type){case"repeat":var j="section-",k=[],l=null;for(var m in g){var n=m.indexOf(j);-1!=n&&(n+=j.length,k.push(parseInt(m.substr(n))),l||(l=m.substr(0,n)))}k.sort(function(a,b){return a-b});var f=0;for(var o in k)b(i+"_"+f++,g[l+k[o]]);break;case"conditional":var p=c.app.field_list[h.id].value();a(i+"|"+h.test_param.name,h.id,p);var q=c.matchCase(h,p);-1!=q&&b(i,e[h.id+"-section-"+q]);break;case"section":b(i,g);break;default:var r=c.app.field_list[h.id];if(r&&r.value){var p=r.value();if((void 0===h.ignore||h.ignore!=p)&&(a(i,h.id,p),h.payload))for(var s in h.payload)a(s,h.id,h.payload[s])}}}}}var c=this,d={};this._iterate(this.app.section.$el,d);var e={};return this.map_dict={},b("",d),e},match:function(a){return this.map_dict&&this.map_dict[a]},matchCase:function(a,b){"boolean"==a.test_param.type&&(b="true"==b?a.test_param.truevalue||"true":a.test_param.falsevalue||"false");for(var c in a.cases)if(a.cases[c].value==b)return c;return-1},matchModel:function(a,b){function c(a,d){for(var f in d){var g=d[f],h=g.name;switch(""!=a&&(h=a+"|"+h),g.type){case"repeat":for(var i in g.cache)c(h+"_"+i,g.cache[i]);break;case"conditional":var j=g.test_param&&g.test_param.value,k=e.matchCase(g,j);-1!=k&&c(h,g.cases[k].inputs);break;case"section":c(h,g.inputs);break;default:var l=e.map_dict[h];l&&b(l,g)}}}var d={},e=this;return c("",a.inputs),d},matchResponse:function(a){function b(a,e){if("string"==typeof e){var f=d.map_dict[a];f&&(c[f]=e)}else for(var g in e){var h=g;if(""!==a){var i="|";e instanceof Array&&(i="_"),h=a+i+h}b(h,e[g])}}var c={},d=this;return b("",a),c},_iterate:function(a,b){var c=this,d=$(a).children();d.each(function(){var a=this,d=$(a).attr("id");if($(a).hasClass("section-row")){b[d]={};var e=c.app.input_list[d];e&&(b[d]={input:e}),c._iterate(a,b[d])}else c._iterate(a,b)})}})}); +define(["utils/utils"],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},checksum:function(){var a="";for(var b in this.app.field_list){var c=this.app.field_list[b];a+=JSON.stringify(c.value&&c.value())}return a},create:function(){function a(a,b,d){c.map_dict[a]=b,e[a]=d}function b(d,e){for(var f in e){var g=e[f];if(g.input){var h=g.input,i=d;switch(""!=d&&(i+="|"),i+=h.name,h.type){case"repeat":var j="section-",k=[],l=null;for(var m in g){var n=m.indexOf(j);-1!=n&&(n+=j.length,k.push(parseInt(m.substr(n))),l||(l=m.substr(0,n)))}k.sort(function(a,b){return a-b});var f=0;for(var o in k)b(i+"_"+f++,g[l+k[o]]);break;case"conditional":var p=c.app.field_list[h.id].value();a(i+"|"+h.test_param.name,h.id,p);var q=c.matchCase(h,p);-1!=q&&b(i,e[h.id+"-section-"+q]);break;case"section":b(h.flat&&i||"",g);break;default:var r=c.app.field_list[h.id];if(r&&r.value){var p=r.value();if((void 0===h.ignore||h.ignore!=p)&&(a(i,h.id,p),h.payload))for(var s in h.payload)a(s,h.id,h.payload[s])}}}}}var c=this,d={};this._iterate(this.app.section.$el,d);var e={};return this.map_dict={},b("",d),e},match:function(a){return this.map_dict&&this.map_dict[a]},matchCase:function(a,b){"boolean"==a.test_param.type&&(b="true"==b?a.test_param.truevalue||"true":a.test_param.falsevalue||"false");for(var c in a.cases)if(a.cases[c].value==b)return c;return-1},matchModel:function(a,b){function c(a,d){for(var f in d){var 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index 6aa13b34246..27d8a9c37bb 100644 --- a/static/scripts/mvc/tools/tools-form-workflow.js +++ b/static/scripts/mvc/tools/tools-form-workflow.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){if(this.node=workflow.active_node,!this.node)return void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&"conditional"==a.type&&(a.test_param.optional=!1)});var d=this;a.get({url:galaxy_config.root+"api/datatypes",cache:!0,success:function(a){d.datatypes=a,d._makeSections(c.inputs),b.prototype.initialize.call(d,c)}})},_makeSections:function(b){b[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var c=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(c){b[a.uid()]={name:"pja__"+c+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+c])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},b[a.uid()]={name:"pja__"+c+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+c])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var d in this.node.output_terminals)b[a.uid()]=this._makeSection(d)}},_makeSection:function(a){function b(c,d){d=d||[],d.push(c);for(var f in c.inputs){var g=c.inputs[f];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=e.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expand=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&b(g,d.slice(0))}}var c=[];for(key in this.datatypes)c.push({0:this.datatypes[key],1:this.datatypes[key]});c.sort(function(a,b){return a.label>b.label?1:a.labelhere for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:c,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},e=this;return b(d),d}});return{View:c}}); +define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){if(this.node=workflow.active_node,!this.node)return void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&("conditional"==a.type?a.test_param.collapsible=!1:-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0))});var d=this;a.get({url:galaxy_config.root+"api/datatypes",cache:!0,success:function(a){d.datatypes=a,d._makeSections(c.inputs),b.prototype.initialize.call(d,c)}})},_makeSections:function(b){b[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var c=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(c){b[a.uid()]={name:"pja__"+c+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+c])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},b[a.uid()]={name:"pja__"+c+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+c])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var d in this.node.output_terminals)b[a.uid()]=this._makeSection(d)}},_makeSection:function(a){function b(c,d){d=d||[],d.push(c);for(var f in c.inputs){var g=c.inputs[f];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=e.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expand=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&b(g,d.slice(0))}}var c=[];for(key in this.datatypes)c.push({0:this.datatypes[key],1:this.datatypes[key]});c.sort(function(a,b){return a.label>b.label?1:a.labelhere for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:c,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},e=this;return b(d),d}});return{View:c}}); //# sourceMappingURL=../../../maps/mvc/tools/tools-form-workflow.js.map \ No newline at end of file From 32eb1ea0fc05b47d9d5700c3c067e0088b1b93dc Mon Sep 17 00:00:00 2001 From: guerler Date: Mon, 4 May 2015 14:32:10 -0400 Subject: [PATCH 2/4] Fix flat sections --- client/galaxy/scripts/mvc/form/form-data.js | 2 +- client/galaxy/scripts/mvc/tools/tools-form-workflow.js | 1 + static/maps/mvc/form/form-data.js.map | 2 +- static/maps/mvc/tools/tools-form-workflow.js.map | 2 +- static/scripts/mvc/form/form-data.js | 2 +- static/scripts/mvc/tools/tools-form-workflow.js | 2 +- 6 files changed, 6 insertions(+), 5 deletions(-) diff --git a/client/galaxy/scripts/mvc/form/form-data.js b/client/galaxy/scripts/mvc/form/form-data.js index 194b431eb75..cc7f7dceabe 100644 --- a/client/galaxy/scripts/mvc/form/form-data.js +++ b/client/galaxy/scripts/mvc/form/form-data.js @@ -98,7 +98,7 @@ return Backbone.Model.extend({ break; // handle sections case 'section': - convert(input.flat && job_input_id || '', node); + convert(!input.flat && job_input_id || '', node); break; default: // get field diff --git a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js index c8dbdfc88fe..4935ed6bb5f 100644 --- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js @@ -173,6 +173,7 @@ define(['utils/utils', 'mvc/tools/tools-form-base'], },{ title : 'Assign columns', type : 'section', + flat : true, inputs : [{ action : 'ColumnSetAction', argument : 'chromCol', diff --git a/static/maps/mvc/form/form-data.js.map b/static/maps/mvc/form/form-data.js.map index 57976deb231..ea0f95980ee 100644 --- a/static/maps/mvc/form/form-data.js.map +++ b/static/maps/mvc/form/form-data.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/static/scripts/mvc/form/form-data.js b/static/scripts/mvc/form/form-data.js index 95fadcd57f4..f6b2b9be17d 100644 --- a/static/scripts/mvc/form/form-data.js +++ b/static/scripts/mvc/form/form-data.js @@ -1,2 +1,2 @@ -define(["utils/utils"],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},checksum:function(){var a="";for(var b in this.app.field_list){var c=this.app.field_list[b];a+=JSON.stringify(c.value&&c.value())}return a},create:function(){function a(a,b,d){c.map_dict[a]=b,e[a]=d}function b(d,e){for(var f in e){var g=e[f];if(g.input){var h=g.input,i=d;switch(""!=d&&(i+="|"),i+=h.name,h.type){case"repeat":var j="section-",k=[],l=null;for(var m in g){var n=m.indexOf(j);-1!=n&&(n+=j.length,k.push(parseInt(m.substr(n))),l||(l=m.substr(0,n)))}k.sort(function(a,b){return a-b});var f=0;for(var o in k)b(i+"_"+f++,g[l+k[o]]);break;case"conditional":var p=c.app.field_list[h.id].value();a(i+"|"+h.test_param.name,h.id,p);var q=c.matchCase(h,p);-1!=q&&b(i,e[h.id+"-section-"+q]);break;case"section":b(h.flat&&i||"",g);break;default:var r=c.app.field_list[h.id];if(r&&r.value){var p=r.value();if((void 0===h.ignore||h.ignore!=p)&&(a(i,h.id,p),h.payload))for(var s in h.payload)a(s,h.id,h.payload[s])}}}}}var c=this,d={};this._iterate(this.app.section.$el,d);var e={};return this.map_dict={},b("",d),e},match:function(a){return this.map_dict&&this.map_dict[a]},matchCase:function(a,b){"boolean"==a.test_param.type&&(b="true"==b?a.test_param.truevalue||"true":a.test_param.falsevalue||"false");for(var c in a.cases)if(a.cases[c].value==b)return c;return-1},matchModel:function(a,b){function c(a,d){for(var f in d){var g=d[f],h=g.name;switch(""!=a&&(h=a+"|"+h),g.type){case"repeat":for(var i in g.cache)c(h+"_"+i,g.cache[i]);break;case"conditional":var j=g.test_param&&g.test_param.value,k=e.matchCase(g,j);-1!=k&&c(h,g.cases[k].inputs);break;case"section":c(h,g.inputs);break;default:var l=e.map_dict[h];l&&b(l,g)}}}var d={},e=this;return c("",a.inputs),d},matchResponse:function(a){function b(a,e){if("string"==typeof e){var f=d.map_dict[a];f&&(c[f]=e)}else for(var g in e){var h=g;if(""!==a){var i="|";e instanceof Array&&(i="_"),h=a+i+h}b(h,e[g])}}var c={},d=this;return b("",a),c},_iterate:function(a,b){var c=this,d=$(a).children();d.each(function(){var a=this,d=$(a).attr("id");if($(a).hasClass("section-row")){b[d]={};var e=c.app.input_list[d];e&&(b[d]={input:e}),c._iterate(a,b[d])}else c._iterate(a,b)})}})}); +define(["utils/utils"],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},checksum:function(){var a="";for(var b in this.app.field_list){var c=this.app.field_list[b];a+=JSON.stringify(c.value&&c.value())}return a},create:function(){function a(a,b,d){c.map_dict[a]=b,e[a]=d}function b(d,e){for(var f in e){var g=e[f];if(g.input){var h=g.input,i=d;switch(""!=d&&(i+="|"),i+=h.name,h.type){case"repeat":var j="section-",k=[],l=null;for(var m in g){var n=m.indexOf(j);-1!=n&&(n+=j.length,k.push(parseInt(m.substr(n))),l||(l=m.substr(0,n)))}k.sort(function(a,b){return a-b});var f=0;for(var o in k)b(i+"_"+f++,g[l+k[o]]);break;case"conditional":var p=c.app.field_list[h.id].value();a(i+"|"+h.test_param.name,h.id,p);var q=c.matchCase(h,p);-1!=q&&b(i,e[h.id+"-section-"+q]);break;case"section":b(!h.flat&&i||"",g);break;default:var r=c.app.field_list[h.id];if(r&&r.value){var p=r.value();if((void 0===h.ignore||h.ignore!=p)&&(a(i,h.id,p),h.payload))for(var s in h.payload)a(s,h.id,h.payload[s])}}}}}var c=this,d={};this._iterate(this.app.section.$el,d);var e={};return this.map_dict={},b("",d),e},match:function(a){return this.map_dict&&this.map_dict[a]},matchCase:function(a,b){"boolean"==a.test_param.type&&(b="true"==b?a.test_param.truevalue||"true":a.test_param.falsevalue||"false");for(var c in a.cases)if(a.cases[c].value==b)return c;return-1},matchModel:function(a,b){function c(a,d){for(var f in d){var g=d[f],h=g.name;switch(""!=a&&(h=a+"|"+h),g.type){case"repeat":for(var i in g.cache)c(h+"_"+i,g.cache[i]);break;case"conditional":var j=g.test_param&&g.test_param.value,k=e.matchCase(g,j);-1!=k&&c(h,g.cases[k].inputs);break;case"section":c(h,g.inputs);break;default:var l=e.map_dict[h];l&&b(l,g)}}}var d={},e=this;return c("",a.inputs),d},matchResponse:function(a){function b(a,e){if("string"==typeof e){var f=d.map_dict[a];f&&(c[f]=e)}else for(var g in e){var h=g;if(""!==a){var i="|";e instanceof Array&&(i="_"),h=a+i+h}b(h,e[g])}}var c={},d=this;return b("",a),c},_iterate:function(a,b){var c=this,d=$(a).children();d.each(function(){var a=this,d=$(a).attr("id");if($(a).hasClass("section-row")){b[d]={};var e=c.app.input_list[d];e&&(b[d]={input:e}),c._iterate(a,b[d])}else c._iterate(a,b)})}})}); //# sourceMappingURL=../../../maps/mvc/form/form-data.js.map \ No newline at end of file diff --git a/static/scripts/mvc/tools/tools-form-workflow.js b/static/scripts/mvc/tools/tools-form-workflow.js index 27d8a9c37bb..d8dff6ab849 100644 --- a/static/scripts/mvc/tools/tools-form-workflow.js +++ b/static/scripts/mvc/tools/tools-form-workflow.js @@ -1,2 +1,2 @@ -define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){if(this.node=workflow.active_node,!this.node)return void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&("conditional"==a.type?a.test_param.collapsible=!1:-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0))});var d=this;a.get({url:galaxy_config.root+"api/datatypes",cache:!0,success:function(a){d.datatypes=a,d._makeSections(c.inputs),b.prototype.initialize.call(d,c)}})},_makeSections:function(b){b[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var c=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(c){b[a.uid()]={name:"pja__"+c+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+c])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},b[a.uid()]={name:"pja__"+c+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+c])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var d in this.node.output_terminals)b[a.uid()]=this._makeSection(d)}},_makeSection:function(a){function b(c,d){d=d||[],d.push(c);for(var f in c.inputs){var g=c.inputs[f];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=e.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expand=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&b(g,d.slice(0))}}var c=[];for(key in this.datatypes)c.push({0:this.datatypes[key],1:this.datatypes[key]});c.sort(function(a,b){return a.label>b.label?1:a.labelhere for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:c,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},e=this;return b(d),d}});return{View:c}}); +define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){if(this.node=workflow.active_node,!this.node)return void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&("conditional"==a.type?a.test_param.collapsible=!1:-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0))});var d=this;a.get({url:galaxy_config.root+"api/datatypes",cache:!0,success:function(a){d.datatypes=a,d._makeSections(c.inputs),b.prototype.initialize.call(d,c)}})},_makeSections:function(b){b[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var c=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(c){b[a.uid()]={name:"pja__"+c+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+c])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},b[a.uid()]={name:"pja__"+c+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+c])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var d in this.node.output_terminals)b[a.uid()]=this._makeSection(d)}},_makeSection:function(a){function b(c,d){d=d||[],d.push(c);for(var f in c.inputs){var g=c.inputs[f];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=e.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expand=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&b(g,d.slice(0))}}var c=[];for(key in this.datatypes)c.push({0:this.datatypes[key],1:this.datatypes[key]});c.sort(function(a,b){return a.label>b.label?1:a.labelhere for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:c,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},e=this;return b(d),d}});return{View:c}}); //# sourceMappingURL=../../../maps/mvc/tools/tools-form-workflow.js.map \ No newline at end of file From 08d76ee0cf5a14c2818a6b11a1f6639746bc5391 Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 7 May 2015 02:07:53 -0400 Subject: [PATCH 3/4] Fix automated section expansion for post job actions --- client/galaxy/scripts/mvc/tools/tools-form-workflow.js | 2 +- static/maps/mvc/tools/tools-form-workflow.js.map | 2 +- static/scripts/mvc/tools/tools-form-workflow.js | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js index 4935ed6bb5f..672cf8f784c 100644 --- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js @@ -242,7 +242,7 @@ define(['utils/utils', 'mvc/tools/tools-form-base'], if (d) { // mark as expanded for (var j in head_list) { - head_list[j].expand = true; + head_list[j].expanded = true; } // update input field value diff --git a/static/maps/mvc/tools/tools-form-workflow.js.map b/static/maps/mvc/tools/tools-form-workflow.js.map index 3a6c3cc1468..ed0fd421d41 100644 --- a/static/maps/mvc/tools/tools-form-workflow.js.map +++ b/static/maps/mvc/tools/tools-form-workflow.js.map @@ -1 +1 @@ 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Blank fields are ignored."}]},e=this;return b(d),d}});return{View:c}}); +define(["utils/utils","mvc/tools/tools-form-base"],function(a,b){var c=b.extend({initialize:function(c){if(this.node=workflow.active_node,!this.node)return void console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");this.post_job_actions=this.node.post_job_actions||{},c=a.merge(c,{text_enable:"Set in Advance",text_disable:"Set at Runtime",is_workflow:!0,narrow:!0,initial_errors:!0,cls:"ui-portlet-narrow",update_url:galaxy_config.root+"api/workflows/build_module",update:function(a){d.node.update_field_data(a),d.form.errors(a&&a.tool_model)}}),a.deepeach(c.inputs,function(a){a.type&&("conditional"==a.type?a.test_param.collapsible=!1:-1==["data","data_collection"].indexOf(a.type)&&(a.collapsible=!0))});var d=this;a.get({url:galaxy_config.root+"api/datatypes",cache:!0,success:function(a){d.datatypes=a,d._makeSections(c.inputs),b.prototype.initialize.call(d,c)}})},_makeSections:function(b){b[a.uid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:!0,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var c=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(c){b[a.uid()]={name:"pja__"+c+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+c])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}},b[a.uid()]={name:"pja__"+c+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+c])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var d in this.node.output_terminals)b[a.uid()]=this._makeSection(d)}},_makeSection:function(a){function b(c,d){d=d||[],d.push(c);for(var f in c.inputs){var g=c.inputs[f];if(g.action){if(g.name="pja__"+a+"__"+g.action,g.argument&&(g.name+="__"+g.argument),g.payload)for(var h in g.payload){var i=g.payload[h];g.payload[g.name+"__"+h]=i,delete i}var j=e.post_job_actions[g.action+a];if(j){for(var k in d)d[k].expanded=!0;g.value=g.argument?j.action_arguments&&j.action_arguments[g.argument]||g.value:"true"}}g.inputs&&b(g,d.slice(0))}}var c=[];for(key in this.datatypes)c.push({0:this.datatypes[key],1:this.datatypes[key]});c.sort(function(a,b){return a.label>b.label?1:a.labelhere for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:c,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]},e=this;return b(d),d}});return{View:c}}); //# sourceMappingURL=../../../maps/mvc/tools/tools-form-workflow.js.map \ No newline at end of file From ea40e6b47ec8c4ad31348f9081188bd10db4648c Mon Sep 17 00:00:00 2001 From: guerler Date: Thu, 7 May 2015 05:14:36 -0400 Subject: [PATCH 4/4] Fix annotations --- lib/galaxy/webapps/galaxy/api/workflows.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py index 57196020f60..f0e7aa9e6f5 100644 --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -316,8 +316,8 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn """ tool_id = payload.get( 'tool_id', None ) tool_version = payload.get( 'tool_version', None ) - tool_inputs = payload.get( 'inputs', None ) - annotation = payload.get( 'annotation', '' ) + tool_inputs = payload.get( 'inputs', {} ) + annotation = payload.get( 'annotation', tool_inputs.get('annotation', '') ) # load tool tool = self._get_tool( tool_id, tool_version=tool_version, user=trans.user )