galaxy-commits February 2015

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commit/galaxy-central: guerler: ToolForm: Add optional tool state format
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/175feec6a9d3/ Changeset: 175feec6a9d3 User: guerler Date: 2015-02-04 04:40:36+00:00 Summary: ToolForm: Add optional tool state format Affected #: 9 files diff -r 4e990792d37479e8fb4f6fec272efb51764c5252 -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -317,6 +317,11 @@ // add to field list this.app.field_list[id] = field; + // fix default value if missing + if (input_def.default_value === undefined) { + input_def.default_value = input_def.value; + } + // create input field wrapper var input_element = new InputElement(this.app, { label : input_def.label, diff -r 4e990792d37479e8fb4f6fec272efb51764c5252 -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -123,14 +123,15 @@ } // validate field value - if (field.skip || (field.validate && !field.validate())) { - if (self.app.options.use_defaults) { - value = input.default_value; - } else { - value = null; - } + if (field.skip) { + continue; } - + + // validate field value + if (field.validate && !field.validate()) { + value = null; + } + // ignore certain values if (input.ignore === undefined || (value !== null && input.ignore != value)) { // add value to submission diff -r 4e990792d37479e8fb4f6fec272efb51764c5252 -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2293,7 +2293,7 @@ job_params = job.get_param_values( trans.app, ignore_errors = True ) job_messages = self.check_and_update_param_values( job_params, trans, update_values=False ) tool_message = self._compare_tool_version(trans, job) - params_to_incoming( kwd, self.inputs, job_params, trans.app ) + params_to_incoming( kwd, self.inputs, job_params, trans.app, to_html=False ) except Exception, exception: trans.response.status = 500 return { 'error': str( exception ) } @@ -2463,7 +2463,7 @@ sanitize(tool_dict, 'default_value') # use default value - if not tool_dict['value']: + if tool_dict['value'] is None: tool_dict['value'] = tool_dict['default_value'] # backup final input dictionary diff -r 4e990792d37479e8fb4f6fec272efb51764c5252 -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 lib/galaxy/tools/parameters/__init__.py --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -105,7 +105,7 @@ return rval -def params_to_incoming( incoming, inputs, input_values, app, name_prefix="" ): +def params_to_incoming( incoming, inputs, input_values, app, name_prefix="", to_html=True ): """ Given a tool's parameter definition (`inputs`) and a specific set of parameter `input_values` objects, populate `incoming` with the html values. @@ -117,12 +117,15 @@ for i, d in enumerate( input_values[ input.name ] ): index = d['__index__'] new_name_prefix = name_prefix + "%s_%d|" % ( input.name, index ) - params_to_incoming( incoming, input.inputs, d, app, new_name_prefix ) + params_to_incoming( incoming, input.inputs, d, app, new_name_prefix, to_html=to_html) elif isinstance( input, Conditional ): values = input_values[ input.name ] current = values["__current_case__"] new_name_prefix = name_prefix + input.name + "|" incoming[ new_name_prefix + input.test_param.name ] = values[ input.test_param.name ] - params_to_incoming( incoming, input.cases[current].inputs, values, app, new_name_prefix ) + params_to_incoming( incoming, input.cases[current].inputs, values, app, new_name_prefix, to_html=to_html ) else: - incoming[ name_prefix + input.name ] = input.to_html_value( input_values.get( input.name ), app ) + value = input_values.get( input.name ) + if to_html: + value = input.to_html_value( value, app ) + incoming[ name_prefix + input.name ] = value diff -r 4e990792d37479e8fb4f6fec272efb51764c5252 -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -317,6 +317,11 @@ // add to field list this.app.field_list[id] = field; + // fix default value if missing + if (input_def.default_value === undefined) { + input_def.default_value = input_def.value; + } + // create input field wrapper var input_element = new InputElement(this.app, { label : input_def.label, diff -r 4e990792d37479e8fb4f6fec272efb51764c5252 -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -123,14 +123,15 @@ } // validate field value - if (field.skip || (field.validate && !field.validate())) { - if (self.app.options.use_defaults) { - value = input.default_value; - } else { - value = null; - } + if (field.skip) { + continue; } - + + // validate field value + if (field.validate && !field.validate()) { + value = null; + } + // ignore certain values if (input.ignore === undefined || (value !== null && input.ignore != value)) { // add value to submission diff -r 4e990792d37479e8fb4f6fec272efb51764c5252 -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls="ui-table-plain";i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;function n(i,u){var t=p.id+"-section-"+(q++);var v=null;if(u){v=function(){l.del(t);l.retitle(p.title);s.app.trigger("refresh")}}var w=new g(s.app,{inputs:i});l.add({id:t,title:p.title,$el:w.$el,ondel:v});l.retitle(p.title)}var l=new c.View({title_new:p.title,max:p.max,onnew:function(){n(p.inputs,true);s.app.trigger("refresh")}});var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o,m>=j)}var k=new f(this.app,{label:p.title,help:p.help,field:l});k.$el.addClass("ui-table-form-section");this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);l.append($("<div/>").addClass("ui-table-form-info").html(i.help));var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});if(i.expand){l.$header.trigger("click")}this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;var j=this._createField(i);this.app.field_list[l]=j;var k=new f(this.app,{label:i.label,default_value:i.default_value,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(!this.app.options.is_dynamic){i.info="Data input '"+i.name+"' ("+e.textify(i.extensions.toString())+")";i.value=null;return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,optional:i.optional,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(!this.app.options.is_dynamic&&j.is_dynamic){return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){if(!this.app.options.is_dynamic&&i.is_dynamic){return this._fieldText(i)}var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){if(i.options){i.area=i.multiple;if(!e.validate(i.value)){i.value=""}else{if(i.value instanceof Array){i.value=value.toString()}else{i.value=String(i.value).replace(/[\[\]'"\s]/g,"");if(i.multiple){i.value=i.value.replace(/,/g,"\n")}}}}var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls="ui-table-plain";i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;function n(i,u){var t=p.id+"-section-"+(q++);var v=null;if(u){v=function(){l.del(t);l.retitle(p.title);s.app.trigger("refresh")}}var w=new g(s.app,{inputs:i});l.add({id:t,title:p.title,$el:w.$el,ondel:v});l.retitle(p.title)}var l=new c.View({title_new:p.title,max:p.max,onnew:function(){n(p.inputs,true);s.app.trigger("refresh")}});var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o,m>=j)}var k=new f(this.app,{label:p.title,help:p.help,field:l});k.$el.addClass("ui-table-form-section");this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);l.append($("<div/>").addClass("ui-table-form-info").html(i.help));var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});if(i.expand){l.$header.trigger("click")}this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;var j=this._createField(i);this.app.field_list[l]=j;if(i.default_value===undefined){i.default_value=i.value}var k=new f(this.app,{label:i.label,default_value:i.default_value,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(!this.app.options.is_dynamic){i.info="Data input '"+i.name+"' ("+e.textify(i.extensions.toString())+")";i.value=null;return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,optional:i.optional,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(!this.app.options.is_dynamic&&j.is_dynamic){return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){if(!this.app.options.is_dynamic&&i.is_dynamic){return this._fieldText(i)}var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){if(i.options){i.area=i.multiple;if(!e.validate(i.value)){i.value=""}else{if(i.value instanceof Array){i.value=value.toString()}else{i.value=String(i.value).replace(/[\[\]'"\s]/g,"");if(i.multiple){i.value=i.value.replace(/,/g,"\n")}}}}var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file diff -r 4e990792d37479e8fb4f6fec272efb51764c5252 -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(g[u.type]){v=g[u.type](v)}if(t.skip||(t.validate&&!t.validate())){if(b.app.options.use_defaults){v=u.default_value}else{v=null}}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(g[u.type]){v=g[u.type](v)}if(t.skip){continue}if(t.validate&&!t.validate()){v=null}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})}); \ No newline at end of file diff -r 4e990792d37479e8fb4f6fec272efb51764c5252 -r 175feec6a9d3028812548d62f99fbaa8b69b18e1 templates/webapps/galaxy/workflow/editor_tool_form.mako --- a/templates/webapps/galaxy/workflow/editor_tool_form.mako +++ b/templates/webapps/galaxy/workflow/editor_tool_form.mako @@ -9,7 +9,7 @@ incoming = { '__is_dynamic__' : False } - params_to_incoming( incoming, tool.inputs, module.state.inputs, trans.app ) + params_to_incoming( incoming, tool.inputs, module.state.inputs, trans.app, to_html=False) self.form_config = tool.to_json(trans, **incoming) self.form_config.update({ 'id' : tool.id, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Fix unit tests for ddbe0d1.
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4e990792d374/ Changeset: 4e990792d374 User: jmchilton Date: 2015-02-04 01:09:46+00:00 Summary: Fix unit tests for ddbe0d1. Affected #: 1 file diff -r 655ddcb3e5a8a5eda97a031b3803d053caa5e963 -r 4e990792d37479e8fb4f6fec272efb51764c5252 test/unit/tools/test_evaluation.py --- a/test/unit/tools/test_evaluation.py +++ b/test/unit/tools/test_evaluation.py @@ -29,6 +29,7 @@ # To Test: # - param_file handling. +TEST_TOOL_DIRECTORY = "/path/to/the/tool" class ToolEvaluatorTestCase(TestCase, UsesApp): @@ -245,6 +246,9 @@ else: return super(TestComputeEnviornment, self).unstructured_path_rewriter() + def tool_directory( self ): + return TEST_TOOL_DIRECTORY + class MockTool( object ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Browser test: use new object param style in history api tests
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/655ddcb3e5a8/ Changeset: 655ddcb3e5a8 User: carlfeberhard Date: 2015-02-03 21:54:39+00:00 Summary: Browser test: use new object param style in history api tests Affected #: 1 file diff -r b9dd3817bdabd5c61990af589d31c1097b3c5de6 -r 655ddcb3e5a8a5eda97a031b3803d053caa5e963 test/casperjs/api-history-tests.js --- a/test/casperjs/api-history-tests.js +++ b/test/casperjs/api-history-tests.js @@ -99,7 +99,7 @@ "Id of last history (from index) DOES NOT appear: " + newFirstHistory.id ); this.test.comment( 'calling index with delete=true should include the deleted history' ); - newFirstHistory = this.api.histories.index( true )[0]; + newFirstHistory = this.api.histories.index({ deleted: true })[0]; //this.debug( 'newFirstHistory:\n' + this.jsonStr( newFirstHistory ) ); this.test.assert( newFirstHistory.id === createdHistory.id, "Id of last history (from index) DOES appear using index( deleted=true ): " + newFirstHistory.id ); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: API, tests: add datasets API tests in test/API and casperjs sections; Browser tests: add datasets api, allow api to send extra params for history show & index
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b9dd3817bdab/ Changeset: b9dd3817bdab User: carlfeberhard Date: 2015-02-03 21:11:10+00:00 Summary: API, tests: add datasets API tests in test/API and casperjs sections; Browser tests: add datasets api, allow api to send extra params for history show & index Affected #: 3 files diff -r 5aa058b09609351defd3161754b23a27ea9bef99 -r b9dd3817bdabd5c61990af589d31c1097b3c5de6 test/api/test_datasets.py --- /dev/null +++ b/test/api/test_datasets.py @@ -0,0 +1,41 @@ +import textwrap + +from base import api +from .helpers import TestsDatasets + +class DatasetsApiTestCase( api.ApiTestCase, TestsDatasets ): + + def setUp( self ): + super( DatasetsApiTestCase, self ).setUp() + self.history_id = self._new_history() + + def test_index( self ): + index_response = self._get( "datasets" ) + print index_response + print dir( index_response ) + self._assert_status_code_is( index_response, 501 ) + + def test_show( self ): + hda1 = self._new_dataset( self.history_id ) + show_response = self._get( "datasets/%s" % ( hda1[ "id" ] ) ) + self._assert_status_code_is( show_response, 200 ) + self.__assert_matches_hda( hda1, show_response.json() ) + + def __assert_matches_hda( self, input_hda, query_hda ): + self._assert_has_keys( query_hda, "id", "name" ) + assert input_hda[ "name" ] == query_hda[ "name" ] + assert input_hda[ "id" ] == query_hda[ "id" ] + + def test_display( self ): + contents = textwrap.dedent( """\ + 1 2 3 4 + A B C D + 10 20 30 40 + """ ) + hda1 = self._new_dataset( self.history_id, content=contents ) + display_response = self._get( "histories/%s/contents/%s/display" % ( self.history_id, hda1[ "id" ] ), { + 'raw' : 'True' + }) + self._assert_status_code_is( display_response, 200 ) + #TODO: doesn't work + #assert display_response.text == contents diff -r 5aa058b09609351defd3161754b23a27ea9bef99 -r b9dd3817bdabd5c61990af589d31c1097b3c5de6 test/casperjs/api-dataset-tests.js --- /dev/null +++ b/test/casperjs/api-dataset-tests.js @@ -0,0 +1,59 @@ +var require = patchRequire( require ), + spaceghost = require( 'spaceghost' ).fromCasper( casper ), + xpath = require( 'casper' ).selectXPath, + utils = require( 'utils' ), + format = utils.format; + +spaceghost.test.begin( 'Test the HDA API', 0, function suite( test ){ + spaceghost.start(); + + // =================================================================== SET UP + var email = spaceghost.user.getRandomEmail(), + password = '123456'; + if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; + } + + var detailKeys = [ + // the following are always present regardless of datatype + 'id', 'name', 'api_type', 'model_class', + 'history_id', 'hid', + 'accessible', 'deleted', 'visible', 'purged', + 'state', 'data_type', 'file_ext', 'file_size', + 'misc_info', 'misc_blurb', + 'download_url', 'visualizations', 'display_apps', 'display_types', + 'genome_build' + ]; + + spaceghost.user.loginOrRegisterUser( email, password ); + spaceghost.openHomePage(); + spaceghost.api.tools.thenUploadToCurrent({ filepath: '../../test-data/1.bed' }); + + spaceghost.then( function(){ + // ------------------------------------------------------------------------------------------- INDEX + this.test.comment( 'index should error with not implemented' ); + this.api.assertRaises( function(){ + this.api.datasets.index(); + }, 501, 'not implemented', 'throws unimplemented' ); + + // ------------------------------------------------------------------------------------------- SHOW + this.test.comment( 'show should get an HDA details object' ); + var history = this.api.histories.show( 'most_recently_used', { keys : 'id,hdas' } ), + hdaId = history.hdas[0], + show = this.api.datasets.show( hdaId ); + this.debug( this.jsonStr( history ) ); + this.debug( this.jsonStr( show ) ); + this.test.assert( this.hasKeys( show, detailKeys ), 'Has the proper keys' ); + + // ------------------------------------------------------------------------------------------- DISPLAY + this.test.comment( 'show should get an HDA details object' ); + var fileContents = this.api.datasets.display( history.id, hdaId, { raw: 'True' }); + this.test.assert( fileContents.split( '\n' ).length === 66, '1.bed has 66 lines' ); + }); + + + // =================================================================== + spaceghost.run( function(){ test.done(); }); +}); + diff -r 5aa058b09609351defd3161754b23a27ea9bef99 -r b9dd3817bdabd5c61990af589d31c1097b3c5de6 test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -13,6 +13,7 @@ this.configuration = new ConfigurationAPI( this ); this.histories = new HistoriesAPI( this ); this.hdas = new HDAAPI( this ); + this.datasets = new DatasetsAPI( this ); this.tools = new ToolsAPI( this ); this.workflows = new WorkflowsAPI( this ); this.users = new UsersAPI( this ); @@ -80,7 +81,10 @@ ( resp.responseJSON? this.spaceghost.jsonStr( resp.responseJSON ) : resp.responseText ) ); throw new APIError( resp.responseText, resp.status ); } - return JSON.parse( resp.responseText ); + if( options.dataType === undefined || options.dataType === 'json' ){ + return JSON.parse( resp.responseText ); + } + return resp.responseText; }; // =================================================================== TESTING @@ -217,22 +221,34 @@ update : '/api/histories/%s', }; -HistoriesAPI.prototype.index = function index( deleted ){ - this.api.spaceghost.info( 'histories.index: ' + (( deleted )?( 'w deleted' ):( '(wo deleted)' )) ); - - deleted = deleted || false; +HistoriesAPI.prototype.index = function index( params ){ + var spaceghost = this.api.spaceghost; + spaceghost.info( 'histories.index:\n' + spaceghost.jsonStr( params ) ); + if( params === undefined ){ + params = { deleted: false }; + } + if( params.deleted === undefined ){ + params.deleted = false; + } + spaceghost.debug( 'params (now):' + spaceghost.jsonStr( params ) ); return this.api._ajax( this.urlTpls.index, { - data : { deleted: deleted } + data : params }); }; -HistoriesAPI.prototype.show = function show( id, deleted ){ - this.api.spaceghost.info( 'histories.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); - - id = ( id === 'most_recently_used' || id === 'current' )?( id ):( this.api.ensureId( id ) ); - deleted = deleted || false; +HistoriesAPI.prototype.show = function show( id, params ){ + var spaceghost = this.api.spaceghost; + this.api.spaceghost.info( 'histories.show: ' + id + '\n' + spaceghost.jsonStr( params ) ); + id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); + if( params === undefined ){ + params = { deleted: false }; + } + if( params.deleted === undefined ){ + params.deleted = false; + } + spaceghost.debug( 'params (now):' + spaceghost.jsonStr( params ) ); return this.api._ajax( utils.format( this.urlTpls.show, id ), { - data : { deleted: deleted } + data : params }); }; @@ -365,8 +381,55 @@ //TODO: delete_ +// =================================================================== HDAS +var DatasetsAPI = function DatasetsAPI( api ){ + this.api = api; +}; +DatasetsAPI.prototype.toString = function toString(){ + return this.api + '.DatasetsAPI'; +}; + +// ------------------------------------------------------------------- +DatasetsAPI.prototype.urlTpls = { + index : '/api/datasets', + show : '/api/datasets/%s', + // wut. + display : '/api/histories/%s/contents/%s/display' +}; + +DatasetsAPI.prototype.index = function index(){ + this.api.spaceghost.info( 'datasets.index: ' ); + var data = {}; + + return this.api._ajax( utils.format( this.urlTpls.index ), { + data : data + }); +}; + +DatasetsAPI.prototype.show = function show( id ){ + this.api.spaceghost.info( 'datasets.show: ' + [ id ] ); + var data = {}; + + return this.api._ajax( utils.format( this.urlTpls.show, id ), { + data : data + }); +}; + +DatasetsAPI.prototype.display = function show( historyId, id, params ){ + this.api.spaceghost.info( 'datasets.display: ' + [ historyId, id ] ); + if( params === undefined ){ + params = {}; + } + return this.api._ajax( utils.format( this.urlTpls.display, this.api.ensureId( historyId ), id ), { + data : params, + dataType : 'text' + }); +}; + + + // =================================================================== TOOLS -var ToolsAPI = function HDAAPI( api ){ +var ToolsAPI = function ToolsAPI( api ){ this.api = api; }; ToolsAPI.prototype.toString = function toString(){ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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[galaxyproject/usegalaxy-playbook] b99609: Add 16GB destination on Test.
by GitHub 03 Feb '15

03 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b99609e7179ffbd6a05466f93a3bc29c5cdad125 https://github.com/galaxyproject/usegalaxy-playbook/commit/b99609e7179ffbd6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-03 (Tue, 03 Feb 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Add 16GB destination on Test. Commit: ba5ac03d2c051b739c2269026691d4ccc05748ea https://github.com/galaxyproject/usegalaxy-playbook/commit/ba5ac03d2c051b73… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-03 (Tue, 03 Feb 2015) Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook Commit: 45d9f85fc733f8b948aaf5980bdc1e183a88e007 https://github.com/galaxyproject/usegalaxy-playbook/commit/45d9f85fc733f8b9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-03 (Tue, 03 Feb 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated mutable configs on Test. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/a613651323a6...…

1 0

[galaxyproject/usegalaxy-playbook] a61365: removed an extra line
by GitHub 03 Feb '15

03 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a613651323a6e64975bb254fbc7bd64ed9c822d8 https://github.com/galaxyproject/usegalaxy-playbook/commit/a613651323a6e649… Author: Anton Nekrutenko <anekrut(a)gmail.com> Date: 2015-02-03 (Tue, 03 Feb 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- removed an extra line

1 0

[galaxyproject/usegalaxy-playbook] 5e28db: added picard to slurm_normal_single_16G
by GitHub 03 Feb '15

03 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5e28dbf72786519cee52f7228b35a25e9a0a3c5c https://github.com/galaxyproject/usegalaxy-playbook/commit/5e28dbf72786519c… Author: Anton Nekrutenko <anekrut(a)gmail.com> Date: 2015-02-03 (Tue, 03 Feb 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- added picard to slurm_normal_single_16G

1 0

commit/galaxy-central: guerler: ToolForm: Fix data parameter reset
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5aa058b09609/ Changeset: 5aa058b09609 User: guerler Date: 2015-02-03 19:45:01+00:00 Summary: ToolForm: Fix data parameter reset Affected #: 3 files diff -r ce32e86d525d18ca9922ab69399b87045e031c6e -r 5aa058b09609351defd3161754b23a27ea9bef99 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -210,8 +210,9 @@ console.debug('tools-select-content::value() - Skipped.'); } } else { - this.current = 'single'; - this.select_single.value('__null__'); + this.select_single && this.select_single.value('__null__'); + this.select_multiple && this.select_multiple.value('__null__'); + this.select_collection && this.select_collection.value('__null__'); } this.refresh(); } diff -r ce32e86d525d18ca9922ab69399b87045e031c6e -r 5aa058b09609351defd3161754b23a27ea9bef99 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -210,8 +210,9 @@ console.debug('tools-select-content::value() - Skipped.'); } } else { - this.current = 'single'; - this.select_single.value('__null__'); + this.select_single && this.select_single.value('__null__'); + this.select_multiple && this.select_multiple.value('__null__'); + this.select_collection && this.select_collection.value('__null__'); } this.refresh(); } diff -r ce32e86d525d18ca9922ab69399b87045e031c6e -r 5aa058b09609351defd3161754b23a27ea9bef99 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(l,g){this.app=l;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(g.type=="data_collection"){this.mode="collection"}else{if(g.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(g.extensions);var n="No dataset available.";if(k){n="No "+k+" dataset available."}var m="No dataset list available.";if(k){m="No "+k+" dataset collection available."}if(this.mode=="single"){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({optional:g.optional,error_text:n,onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,error_text:n,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="collection"){j.push({icon:"fa-folder-o",label:"Dataset collection",value:"collection"});this.select_collection=new e.Select.View({error_text:m,optional:g.optional,onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());if(_.size(this.list)>1){this.$el.append(c.wrap(this.button_type.$el))}for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.current="single";this.select_single.value("__null__")}this.refresh()}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(l,g){this.app=l;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(g.type=="data_collection"){this.mode="collection"}else{if(g.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(g.extensions);var n="No dataset available.";if(k){n="No "+k+" dataset available."}var m="No dataset list available.";if(k){m="No "+k+" dataset collection available."}if(this.mode=="single"){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({optional:g.optional,error_text:n,onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,error_text:n,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="collection"){j.push({icon:"fa-folder-o",label:"Dataset collection",value:"collection"});this.select_collection=new e.Select.View({error_text:m,optional:g.optional,onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());if(_.size(this.list)>1){this.$el.append(c.wrap(this.button_type.$el))}for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(h){if(h!==undefined){if(h&&h.values){try{var l=[];for(var g in h.values){l.push(h.values[g].id)}if(h&&h.values.length>0&&h.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}else{this.select_single&&this.select_single.value("__null__");this.select_multiple&&this.select_multiple.value("__null__");this.select_collection&&this.select_collection.value("__null__")}this.refresh()}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var g in j){f.values.push({id:j[g],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Add requires to ensure repoze is on the path (should resolve issue seen on Test but nowhere else that I know of).
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ce32e86d525d/ Changeset: ce32e86d525d User: dannon Date: 2015-02-03 18:25:42+00:00 Summary: Add requires to ensure repoze is on the path (should resolve issue seen on Test but nowhere else that I know of). Affected #: 3 files diff -r e75441f1e264318e2004f27b3cc868f237f3b6d2 -r ce32e86d525d18ca9922ab69399b87045e031c6e lib/galaxy/managers/base.py --- a/lib/galaxy/managers/base.py +++ b/lib/galaxy/managers/base.py @@ -29,6 +29,7 @@ pkg_resources.require( "SQLAlchemy >= 0.4" ) import sqlalchemy +pkg_resources.require("repoze.lru") # used by Routes pkg_resources.require("Routes") import routes @@ -853,7 +854,7 @@ 'create_time' : { 'op': ( 'le', 'ge' ) }, 'update_time' : { 'op': ( 'le', 'ge' ) }, }) - + def parse_filters( self, filter_tuple_list ): """ Parse string 3-tuples (attr, op, val) into orm or functional filters. diff -r e75441f1e264318e2004f27b3cc868f237f3b6d2 -r ce32e86d525d18ca9922ab69399b87045e031c6e lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py +++ b/lib/galaxy/web/framework/base.py @@ -12,6 +12,7 @@ import pkg_resources pkg_resources.require("Paste") +pkg_resources.require("repoze.lru") # used by Routes pkg_resources.require("Routes") pkg_resources.require("WebOb") diff -r e75441f1e264318e2004f27b3cc868f237f3b6d2 -r ce32e86d525d18ca9922ab69399b87045e031c6e lib/galaxy/web/framework/helpers/__init__.py --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -13,6 +13,7 @@ from webhelpers import date from webhelpers.html.tags import stylesheet_link, javascript_link +eggs.require( "repoze.lru" ) # used by Routes eggs.require( "Routes" ) from routes import url_for Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Core, authentication: set status code of trans._authenticate_api errors to 403 in _future_expose_api, some readability changes
by commits-noreply＠bitbucket.org 03 Feb '15

03 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e75441f1e264/ Changeset: e75441f1e264 User: carlfeberhard Date: 2015-02-03 17:47:02+00:00 Summary: Core, authentication: set status code of trans._authenticate_api errors to 403 in _future_expose_api, some readability changes Affected #: 1 file diff -r bcaffc4a0a61d3d803cee45435548d0db0e59e54 -r e75441f1e264318e2004f27b3cc868f237f3b6d2 lib/galaxy/web/framework/decorators.py --- a/lib/galaxy/web/framework/decorators.py +++ b/lib/galaxy/web/framework/decorators.py @@ -202,19 +202,20 @@ """ @wraps(func) def decorator( self, trans, *args, **kwargs ): + # errors passed in from trans._authenicate_api if trans.error_message: - # TODO: Document this branch, when can this happen, - # I don't understand it. - return __api_error_response( trans, err_msg=trans.error_message ) + return __api_error_response( trans, status_code=403, err_code=error_codes.USER_NO_API_KEY, + err_msg=trans.error_message ) + if trans.anonymous: + # error if anon and user required + if user_required: + return __api_error_response( trans, status_code=403, err_code=error_codes.USER_NO_API_KEY, + err_msg="API authentication required for this request" ) + # error if anon and no session + if not trans.galaxy_session and user_or_session_required: + return __api_error_response( trans, status_code=403, err_code=error_codes.USER_NO_API_KEY, + err_msg="API authentication required for this request" ) - # error if user required and anon - # error if anon and no session - if ( ( trans.anonymous and user_required ) - or ( trans.anonymous and user_or_session_required and not trans.galaxy_session ) ): - error_code = error_codes.USER_NO_API_KEY - # Use error codes default error message. - err_msg = "API authentication required for this request" - return __api_error_response( trans, err_code=error_code, err_msg=err_msg, status_code=403 ) if trans.request.body: try: kwargs['payload'] = __extract_payload_from_request(trans, func, kwargs) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits February 2015