galaxy-commits August 2013

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commit/galaxy-central: jgoecks: Add version command information to Cuff* tools.
by commits-noreply＠bitbucket.org 23 Aug '13

23 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e2bca7e8fe7e/ Changeset: e2bca7e8fe7e User: jgoecks Date: 2013-08-23 16:49:06 Summary: Add version command information to Cuff* tools. Affected #: 3 files diff -r fa8c4978733072137f708190e65d46c6cb616b0b -r e2bca7e8fe7e0f3022c1e1afb4a6eed54dec2bcf tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml +++ b/tools/ngs_rna/cuffcompare_wrapper.xml @@ -4,6 +4,7 @@ <requirements><requirement type="package">cufflinks</requirement></requirements> + <version_command>cuffcompare 2>&1 | head -n 1</version_command><command interpreter="python"> cuffcompare_wrapper.py diff -r fa8c4978733072137f708190e65d46c6cb616b0b -r e2bca7e8fe7e0f3022c1e1afb4a6eed54dec2bcf tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -4,6 +4,7 @@ <requirements><requirement type="package">cufflinks</requirement></requirements> + <version_command>cuffdiff 2>&1 | head -n 1</version_command><command> cuffdiff --FDR=$fdr diff -r fa8c4978733072137f708190e65d46c6cb616b0b -r e2bca7e8fe7e0f3022c1e1afb4a6eed54dec2bcf tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -4,6 +4,7 @@ <requirements><requirement type="package">cufflinks</requirement></requirements> + <version_command>cufflinks 2>&1 | head -n 1</version_command><command interpreter="python"> cufflinks_wrapper.py --input=$input 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: 2 new changesets
by commits-noreply＠bitbucket.org 23 Aug '13

23 Aug '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fa8c49787330/ Changeset: fa8c49787330 User: dan Date: 2013-08-23 15:07:28 Summary: Fix for ToolParameterValueWrapper.get_display_text() due to inconsistent behavior between Python2.7 and lower for empty strings. expected quoted empty string: $ python2.7 Python 2.7.5 (default, Aug 1 2013, 00:59:24) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import pipes >>> print pipes.quote('') '' >>> repr( pipes.quote('') ) '"\'\'"' >>> python < 2.7: $ python2.6 Python 2.6.1 (r261:67515, Aug 2 2010, 20:10:18) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import pipes >>> print pipes.quote('') >>> repr( pipes.quote('') ) "''" >>> Affected #: 1 file diff -r c0073a8c820c43b419dfdcc8d88ba157e214f610 -r fa8c4978733072137f708190e65d46c6cb616b0b lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -3284,7 +3284,14 @@ def __nonzero__( self ): return bool( self.value ) def get_display_text( self, quote=True ): - return pipes.quote( self.input.value_to_display_text( self.value, self.input.tool.app ) ) + """ + Returns a string containing the value that would be displayed to the user in the tool interface. + When quote is True (default), the string is escaped for e.g. command-line usage. + """ + rval = self.input.value_to_display_text( self.value, self.input.tool.app ) or '' + if quote: + return pipes.quote( rval ) or "''" #pipes.quote in Python < 2.7 returns an empty string instead of the expected quoted empty string + return rval class RawObjectWrapper( ToolParameterValueWrapper ): """ https://bitbucket.org/galaxy/galaxy-central/commits/de04c251c6ca/ Changeset: de04c251c6ca Branch: stable User: dan Date: 2013-08-23 15:07:28 Summary: Fix for ToolParameterValueWrapper.get_display_text() due to inconsistent behavior between Python2.7 and lower for empty strings. expected quoted empty string: $ python2.7 Python 2.7.5 (default, Aug 1 2013, 00:59:24) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import pipes >>> print pipes.quote('') '' >>> repr( pipes.quote('') ) '"\'\'"' >>> python < 2.7: $ python2.6 Python 2.6.1 (r261:67515, Aug 2 2010, 20:10:18) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import pipes >>> print pipes.quote('') >>> repr( pipes.quote('') ) "''" >>> Affected #: 1 file diff -r 29ab5a6d75a778cd4989adf881c47916607b9acb -r de04c251c6cae5760fd13c83030a6aab78ae0c4e lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -3258,7 +3258,14 @@ def __nonzero__( self ): return bool( self.value ) def get_display_text( self, quote=True ): - return pipes.quote( self.input.value_to_display_text( self.value, self.input.tool.app ) ) + """ + Returns a string containing the value that would be displayed to the user in the tool interface. + When quote is True (default), the string is escaped for e.g. command-line usage. + """ + rval = self.input.value_to_display_text( self.value, self.input.tool.app ) or '' + if quote: + return pipes.quote( rval ) or "''" #pipes.quote in Python < 2.7 returns an empty string instead of the expected quoted empty string + return rval class RawObjectWrapper( ToolParameterValueWrapper ): """ 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: jgoecks: Fixes for 8ed926e: (1) enable labels to be displayed outside of sections in tool panel and(b) revert class for label divs. Pack script.
by commits-noreply＠bitbucket.org 23 Aug '13

23 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c0073a8c820c/ Changeset: c0073a8c820c User: jgoecks Date: 2013-08-23 00:13:57 Summary: Fixes for 8ed926e: (1) enable labels to be displayed outside of sections in tool panel and(b) revert class for label divs. Pack script. Affected #: 3 files diff -r 24f4f507fdecf214e9090f215fe309249a29252d -r c0073a8c820c43b419dfdcc8d88ba157e214f610 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -93,6 +93,15 @@ class ToolNotFoundException( Exception ): pass +def dictify_helper( obj, kwargs ): + """ Helper function that provides the appropriate kwargs to dictify an object. """ + + # Label.dictify cannot have kwargs. + if isinstance( obj, ToolSectionLabel ): + kwargs = {} + + return obj.dictify( **kwargs ) + class ToolBox( object, DictifiableMixin ): """Container for a collection of tools""" @@ -722,8 +731,12 @@ # Produce panel. rval = [] + kwargs = dict( + trans = trans, + link_details = True + ) for elt in panel_elts: - rval.append( elt.dictify( trans, link_details=True ) ) + rval.append( dictify_helper( elt, kwargs ) ) else: tools = [] for id, tool in self.tools_by_id.items(): @@ -816,11 +829,12 @@ section_dict = super( ToolSection, self ).dictify() section_elts = [] - for key, val in self.elems.items(): - if isinstance( val, ToolSectionLabel ): - section_elts.append( val.dictify() ) - else: - section_elts.append( val.dictify( trans, link_details=link_details ) ) + kwargs = dict( + trans = trans, + link_details = link_details + ) + for elt in self.elems.values(): + section_elts.append( dictify_helper( elt, kwargs ) ) section_dict[ 'elems' ] = section_elts return section_dict diff -r 24f4f507fdecf214e9090f215fe309249a29252d -r c0073a8c820c43b419dfdcc8d88ba157e214f610 static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -499,7 +499,7 @@ */ var ToolSectionLabelView = BaseView.extend({ tagName: 'div', - className: 'ToolSectionLabel', + className: 'toolPanelLabel', render: function() { this.$el.append( $("<span/>").text(this.model.attributes.text) ); diff -r 24f4f507fdecf214e9090f215fe309249a29252d -r c0073a8c820c43b419dfdcc8d88ba157e214f610 static/scripts/packed/mvc/tools.js --- a/static/scripts/packed/mvc/tools.js +++ b/static/scripts/packed/mvc/tools.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/backbone-relational"],function(t,a,u){var f={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},get_samples:function(){var w=this.get("type"),v=null;if(w==="number"){v=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(w==="select"){v=t.map(this.get("options"),function(x){return x[0]})}}return v},set_value:function(v){this.set("value",v||"")}},{TYPE_DICT:{number:d},create:function(v){var w=e.TYPE_DICT[v.type]||e;return new w(v)}});var d=e.extend({defaults:t.extend({},e.prototype.defaults,{min:null,max:null}),initialize:function(){e.prototype.initialize.call(this);if(this.attributes.min){this.attributes.min=parseInt(this.attributes.min,10)}if(this.attributes.max){this.attributes.max=parseInt(this.attributes.max,10)}},set_value:function(v){this.set("value",parseInt(v,10))}});var h=Backbone.RelationalModel.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[]},initialize:function(v){this.attributes.inputs=new Backbone.Collection(t.map(v.inputs,function(w){return e.create(w)}))},urlRoot:galaxy_config.root+"api/tools",copy:function(w){var x=new h(this.toJSON());if(w){var v=new Backbone.Collection();x.get("inputs").each(function(y){if(y.get_samples()){v.push(y)}});x.set("inputs",v)}return x},apply_search_results:function(v){(t.indexOf(v,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(v,w){this.get("inputs").find(function(x){return x.get("name")===v}).set("value",w)},set_input_values:function(w){var v=this;t.each(t.keys(w),function(x){v.set_input_value(x,w[x])})},run:function(){return this._run()},rerun:function(w,v){return this._run({action:"rerun",target_dataset_id:w.id,regions:v})},get_inputs_dict:function(){var v={};this.get("inputs").each(function(w){v[w.get("name")]=w.get("value")});return v},_run:function(x){var y=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},x);var w=$.Deferred(),v=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(y),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(z){return z!=="pending"}});$.when(v.go()).then(function(z){w.resolve(new u.DatasetCollection().reset(z))});return w}});t.extend(h.prototype,f);var n=Backbone.View.extend({});var k=Backbone.Collection.extend({model:h});var r=Backbone.Model.extend(f);var i=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){t.each(this.attributes.elems,function(v){v.show()});this.show();this.set("open",false)},apply_search_results:function(w){var x=true,v;t.each(this.attributes.elems,function(y){if(y instanceof r){v=y;v.hide()}else{if(y instanceof h){if(y.apply_search_results(w)){x=false;if(v){v.show()}}}}});if(x){this.hide()}else{this.show();this.set("open",true)}}});t.extend(i.prototype,f);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var x=this.attributes.query;if(x.length<this.attributes.min_chars_for_search){this.set("results",null);return}var w=x+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var v=this;this.timer=setTimeout(function(){$.get(v.attributes.search_url,{query:w},function(y){v.set("results",y);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});t.extend(c.prototype,f);var l=Backbone.Model.extend({initialize:function(v){this.attributes.tool_search=v.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=v.tools;this.attributes.layout=new Backbone.Collection(this.parse(v.layout))},parse:function(w){var v=this,x=function(A){var z=A.model_class;if(z.indexOf("Tool")===z.length-4){return v.attributes.tools.get(A.id)}else{if(z==="ToolSection"){var y=t.map(A.elems,x);A.elems=y;return new i(A)}else{if(z==="ToolSectionLabel"){return new r(A)}}}};return t.map(w,x)},clear_search_results:function(){this.get("layout").each(function(v){if(v instanceof i){v.clear_search_results()}else{v.show()}})},apply_search_results:function(){var w=this.get("tool_search").get("results");if(w===null){this.clear_search_results();return}var v=null;this.get("layout").each(function(x){if(x instanceof r){v=x;v.hide()}else{if(x instanceof h){if(x.apply_search_results(w)){if(v){v.show()}}}else{v=null;x.apply_search_results(w)}}})}});var p=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var j=p.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var b=p.extend({tagName:"div",className:"ToolSectionLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var o=p.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){p.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var v=this.$el.find(".toolSectionBody");t.each(this.model.attributes.elems,function(w){if(w instanceof h){var x=new j({model:w,className:"toolTitle"});x.render();v.append(x.$el)}else{if(w instanceof r){var y=new b({model:w});y.render();v.append(y.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var m=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find(".tooltip").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(v){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===v.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var s=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var v=this;var w=new m({model:this.model.get("tool_search")});w.render();v.$el.append(w.$el);this.model.get("layout").each(function(y){if(y instanceof i){var x=new o({model:y});x.render();v.$el.append(x.$el)}else{if(y instanceof h){var z=new j({model:y,className:"toolTitleNoSection"});z.render();v.$el.append(z.$el)}else{if(y instanceof r){var A=new b({model:y});A.render();v.$el.append(A.$el)}}}});v.$el.find("a.tool-link").click(function(z){var y=$(this).attr("class").split(/\s+/)[0],x=v.model.get("tools").get(y);v.trigger("tool_link_click",z,x)});return this},handle_search_results:function(){var v=this.model.get("tool_search").get("results");if(v&&v.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var q=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var g=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new s({collection:this.collection});this.tool_form_view=new q()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var v=this;this.tool_panel_view.on("tool_link_click",function(x,w){x.preventDefault();v.show_tool(w)})},show_tool:function(w){var v=this;w.fetch().done(function(){v.tool_form_view.model=w;v.tool_form_view.render();v.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,Tool:h,ToolCollection:k,ToolSearch:c,ToolPanel:l,ToolPanelView:s,ToolFormView:q}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util","mvc/data","libs/backbone/backbone-relational"],function(t,a,u){var f={hidden:false,show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}};var e=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new e(this.toJSON())},get_samples:function(){var w=this.get("type"),v=null;if(w==="number"){v=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(w==="select"){v=t.map(this.get("options"),function(x){return x[0]})}}return v},set_value:function(v){this.set("value",v||"")}},{TYPE_DICT:{number:d},create:function(v){var w=e.TYPE_DICT[v.type]||e;return new w(v)}});var d=e.extend({defaults:t.extend({},e.prototype.defaults,{min:null,max:null}),initialize:function(){e.prototype.initialize.call(this);if(this.attributes.min){this.attributes.min=parseInt(this.attributes.min,10)}if(this.attributes.max){this.attributes.max=parseInt(this.attributes.max,10)}},set_value:function(v){this.set("value",parseInt(v,10))}});var h=Backbone.RelationalModel.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[]},initialize:function(v){this.attributes.inputs=new Backbone.Collection(t.map(v.inputs,function(w){return e.create(w)}))},urlRoot:galaxy_config.root+"api/tools",copy:function(w){var x=new h(this.toJSON());if(w){var v=new Backbone.Collection();x.get("inputs").each(function(y){if(y.get_samples()){v.push(y)}});x.set("inputs",v)}return x},apply_search_results:function(v){(t.indexOf(v,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(v,w){this.get("inputs").find(function(x){return x.get("name")===v}).set("value",w)},set_input_values:function(w){var v=this;t.each(t.keys(w),function(x){v.set_input_value(x,w[x])})},run:function(){return this._run()},rerun:function(w,v){return this._run({action:"rerun",target_dataset_id:w.id,regions:v})},get_inputs_dict:function(){var v={};this.get("inputs").each(function(w){v[w.get("name")]=w.get("value")});return v},_run:function(x){var y=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},x);var w=$.Deferred(),v=new a.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(y),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(z){return z!=="pending"}});$.when(v.go()).then(function(z){w.resolve(new u.DatasetCollection().reset(z))});return w}});t.extend(h.prototype,f);var n=Backbone.View.extend({});var k=Backbone.Collection.extend({model:h});var r=Backbone.Model.extend(f);var i=Backbone.Model.extend({defaults:{elems:[],open:false},clear_search_results:function(){t.each(this.attributes.elems,function(v){v.show()});this.show();this.set("open",false)},apply_search_results:function(w){var x=true,v;t.each(this.attributes.elems,function(y){if(y instanceof r){v=y;v.hide()}else{if(y instanceof h){if(y.apply_search_results(w)){x=false;if(v){v.show()}}}}});if(x){this.hide()}else{this.show();this.set("open",true)}}});t.extend(i.prototype,f);var c=Backbone.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var x=this.attributes.query;if(x.length<this.attributes.min_chars_for_search){this.set("results",null);return}var w=x+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var v=this;this.timer=setTimeout(function(){$.get(v.attributes.search_url,{query:w},function(y){v.set("results",y);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});t.extend(c.prototype,f);var l=Backbone.Model.extend({initialize:function(v){this.attributes.tool_search=v.tool_search;this.attributes.tool_search.on("change:results",this.apply_search_results,this);this.attributes.tools=v.tools;this.attributes.layout=new Backbone.Collection(this.parse(v.layout))},parse:function(w){var v=this,x=function(A){var z=A.model_class;if(z.indexOf("Tool")===z.length-4){return v.attributes.tools.get(A.id)}else{if(z==="ToolSection"){var y=t.map(A.elems,x);A.elems=y;return new i(A)}else{if(z==="ToolSectionLabel"){return new r(A)}}}};return t.map(w,x)},clear_search_results:function(){this.get("layout").each(function(v){if(v instanceof i){v.clear_search_results()}else{v.show()}})},apply_search_results:function(){var w=this.get("tool_search").get("results");if(w===null){this.clear_search_results();return}var v=null;this.get("layout").each(function(x){if(x instanceof r){v=x;v.hide()}else{if(x instanceof h){if(x.apply_search_results(w)){if(v){v.show()}}}else{v=null;x.apply_search_results(w)}}})}});var p=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var j=p.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var b=p.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.text));return this}});var o=p.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){p.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var v=this.$el.find(".toolSectionBody");t.each(this.model.attributes.elems,function(w){if(w instanceof h){var x=new j({model:w,className:"toolTitle"});x.render();v.append(x.$el)}else{if(w instanceof r){var y=new b({model:w});y.render();v.append(y.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var m=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}this.$el.find(".tooltip").tooltip();return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(v){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===v.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var s=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var v=this;var w=new m({model:this.model.get("tool_search")});w.render();v.$el.append(w.$el);this.model.get("layout").each(function(y){if(y instanceof i){var x=new o({model:y});x.render();v.$el.append(x.$el)}else{if(y instanceof h){var z=new j({model:y,className:"toolTitleNoSection"});z.render();v.$el.append(z.$el)}else{if(y instanceof r){var A=new b({model:y});A.render();v.$el.append(A.$el)}}}});v.$el.find("a.tool-link").click(function(z){var y=$(this).attr("class").split(/\s+/)[0],x=v.model.get("tools").get(y);v.trigger("tool_link_click",z,x)});return this},handle_search_results:function(){var v=this.model.get("tool_search").get("results");if(v&&v.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var q=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var g=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new s({collection:this.collection});this.tool_form_view=new q()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var v=this;this.tool_panel_view.on("tool_link_click",function(x,w){x.preventDefault();v.show_tool(w)})},show_tool:function(w){var v=this;w.fetch().done(function(){v.tool_form_view.model=w;v.tool_form_view.render();v.tool_form_view.$el.show();$("#left").width("650px")})}});return{ToolParameter:e,IntegerToolParameter:d,Tool:h,ToolCollection:k,ToolSearch:c,ToolPanel:l,ToolPanelView:s,ToolFormView:q}}); \ 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: Dave Bouvier: Fix for running a tool migration script that specifies one or more repositories with complex tool dependencies.
by commits-noreply＠bitbucket.org 23 Aug '13

23 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/24f4f507fdec/ Changeset: 24f4f507fdec User: Dave Bouvier Date: 2013-08-22 20:44:56 Summary: Fix for running a tool migration script that specifies one or more repositories with complex tool dependencies. Affected #: 2 files diff -r 185232cef732d9b79aad686ca0aa556bb7c63614 -r 24f4f507fdecf214e9090f215fe309249a29252d lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -19,6 +19,7 @@ from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import xml_util +import tool_shed.galaxy_install.tool_dependencies.common_util as cu import pkg_resources @@ -1123,6 +1124,7 @@ if not toolshed: # Default to the current tool shed. toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' ) + cleaned_toolshed = cu.clean_tool_shed_url( toolshed ) name = repository_elem.get( 'name' ) owner = repository_elem.get( 'owner' ) changeset_revision = repository_elem.get( 'changeset_revision' ) @@ -1135,7 +1137,7 @@ # generating metadata for an installed repository. See if we can locate the installed repository via the changeset_revision defined in the # repository_elem (it may be outdated). If we're successful in locating an installed repository with the attributes defined in the # repository_elem, we know it is valid. - repository = suc.get_repository_for_dependency_relationship( app, toolshed, name, owner, changeset_revision ) + repository = suc.get_repository_for_dependency_relationship( app, cleaned_toolshed, name, owner, changeset_revision ) if repository: return repository_dependency_tup, is_valid, error_message else: @@ -1144,7 +1146,7 @@ if text: updated_changeset_revisions = util.listify( text ) for updated_changeset_revision in updated_changeset_revisions: - repository = suc.get_repository_for_dependency_relationship( app, toolshed, name, owner, updated_changeset_revision ) + repository = suc.get_repository_for_dependency_relationship( app, cleaned_toolshed, name, owner, updated_changeset_revision ) if repository: return repository_dependency_tup, is_valid, error_message # We'll currently default to setting the repository dependency definition as invalid if an installed repository cannot be found. diff -r 185232cef732d9b79aad686ca0aa556bb7c63614 -r 24f4f507fdecf214e9090f215fe309249a29252d lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -872,8 +872,8 @@ # tool shed that is associated with repository_metadata. tool_shed_url = get_url_from_tool_shed( app, tool_shed ) url = url_join( tool_shed_url, - 'repository/next_installable_changeset_revision?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ - ( url_for( '/', qualified=True ), name, owner, changeset_revision ) ) + 'repository/next_installable_changeset_revision?name=%s&owner=%s&changeset_revision=%s' % \ + ( name, owner, changeset_revision ) ) text = common_util.tool_shed_get( app, tool_shed_url, url ) if text: repository = get_tool_shed_repository_by_shed_name_owner_changeset_revision( app=app, 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: greg: Automatically eliminate tool entries from non-shed-related tool panel configs for tools contained in tool shed repositories that were migrated out of the Galaxy distribution.
by commits-noreply＠bitbucket.org 22 Aug '13

22 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/185232cef732/ Changeset: 185232cef732 User: greg Date: 2013-08-22 16:12:08 Summary: Automatically eliminate tool entries from non-shed-related tool panel configs for tools contained in tool shed repositories that were migrated out of the Galaxy distribution. Affected #: 5 files diff -r 097abeb6969e93265135a8d6f3e566b5e913ca8f -r 185232cef732d9b79aad686ca0aa556bb7c63614 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -3,7 +3,9 @@ All of the tools were at some point included in the Galaxy distribution, but are now hosted in the main Galaxy tool shed. """ import os +import shutil import tempfile +import threading from galaxy import util from galaxy.tools import ToolSection from galaxy.util.json import from_json_string @@ -63,7 +65,9 @@ if tool_panel_configs: # The missing_tool_configs_dict contents are something like: # {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]} - tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app, tool_panel_configs, latest_migration_script_number ) + tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app, + tool_panel_configs, + latest_migration_script_number ) else: # It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but # we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in @@ -79,7 +83,9 @@ file_names = ', '.join( self.proprietary_tool_confs ) if missing_tool_configs_dict: for repository_elem in root: - self.install_repository( repository_elem, install_dependencies ) + # Make sure we have a valid repository tag. + if self.__is_valid_repository_tag( repository_elem ): + self.install_repository( repository_elem, install_dependencies ) else: message = "\nNo tools associated with migration stage %s are defined in your " % str( latest_migration_script_number ) message += "file%s named %s,\nso no repositories will be installed on disk.\n" % ( plural, file_names ) @@ -89,6 +95,43 @@ message += "Try again later.\n" print message + def filter_and_persist_proprietary_tool_panel_configs( self, tool_configs_to_filter ): + """Eliminate all entries in all non-shed-related tool panel configs for all tool config file names in the received tool_configs_to_filter.""" + for proprietary_tool_conf in self.proprietary_tool_confs: + persist_required = False + tree, error_message = xml_util.parse_xml( proprietary_tool_conf ) + if tree: + root = tree.getroot() + for elem in root: + if elem.tag == 'tool': + # Tools outside of sections. + file_path = elem.get( 'file', None ) + if file_path: + file_name = suc.strip_path( file_path ) + if file_name in tool_configs_to_filter: + root.remove( elem ) + persist_required = True + elif elem.tag == 'section': + # Tools contained in a section. + for section_elem in elem: + if section_elem.tag == 'tool': + file_path = section_elem.get( 'file', None ) + if file_path: + file_name = suc.strip_path( file_path ) + + if file_name in tool_configs_to_filter: + elem.remove( section_elem ) + persist_required = True + if persist_required: + fh = tempfile.NamedTemporaryFile( 'wb', prefix="tmp-toolshed-fapptpc" ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'wb' ) + tree.write( tmp_filename ) + fh.close() + shutil.move( tmp_filename, os.path.abspath( proprietary_tool_conf ) ) + os.chmod( proprietary_tool_conf, 0644 ) + def get_guid( self, repository_clone_url, relative_install_dir, tool_config ): if self.shed_config_dict.get( 'tool_path' ): relative_install_dir = os.path.join( self.shed_config_dict['tool_path'], relative_install_dir ) @@ -108,9 +151,11 @@ return suc.generate_tool_guid( repository_clone_url, tool ) def get_proprietary_tool_panel_elems( self, latest_tool_migration_script_number ): - # Parse each config in self.proprietary_tool_confs (the default is tool_conf.xml) and generate a list of Elements that are - # either ToolSection elements or Tool elements. These will be used to generate new entries in the migrated_tools_conf.xml - # file for the installed tools. + """ + Parse each config in self.proprietary_tool_confs (the default is tool_conf.xml) and generate a list of Elements that are + either ToolSection elements or Tool elements. These will be used to generate new entries in the migrated_tools_conf.xml + file for the installed tools. + """ tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) ) # Parse the XML and load the file attributes for later checking against the integrated elements from self.proprietary_tool_confs. migrated_tool_configs = [] @@ -183,7 +228,13 @@ return is_displayed, tool_sections def handle_repository_contents( self, tool_shed_repository, repository_clone_url, relative_install_dir, repository_elem, install_dependencies ): - """Generate the metadata for the installed tool shed repository, among other things.""" + """ + Generate the metadata for the installed tool shed repository, among other things. If the installed tool_shed_repository contains tools + that are loaded into the Galaxy tool panel, this method will automatically eliminate all entries for each of the tools defined in the + received repository_elem from all non-shed-related tool panel configuration files since the entries are automatically added to the reserved + migrated_tools_conf.xml file as part of the migration process. + """ + tool_configs_to_filter = [] tool_panel_dict_for_display = odict() if self.tool_path: repo_install_dir = os.path.join( self.tool_path, relative_install_dir ) @@ -197,11 +248,29 @@ is_displayed, tool_sections = self.get_containing_tool_sections( tool_config ) if is_displayed: tool_panel_dict_for_tool_config = tool_util.generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) + # The tool-panel_dict has the following structure. + # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} for k, v in tool_panel_dict_for_tool_config.items(): tool_panel_dict_for_display[ k ] = v + for tool_panel_dict in v: + # Keep track of tool config file names associated with entries that have been made to the migrated_tools_conf.xml file so + # they can be eliminated from all non-shed-related tool panel configs. + tool_config_file = tool_panel_dict.get( 'tool_config', None ) + if tool_config_file: + if tool_config_file not in tool_configs_to_filter: + tool_configs_to_filter.append( tool_config_file ) else: print 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' \ % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) ) + if tool_configs_to_filter: + lock = threading.Lock() + lock.acquire( True ) + try: + self.filter_and_persist_proprietary_tool_panel_configs( tool_configs_to_filter ) + except Exception, e: + log.exception( "Exception attempting to filter and persist non-shed-related tool panel configs:\n%s" % str( e ) ) + finally: + lock.release() metadata_dict, invalid_file_tups = metadata_util.generate_metadata_for_changeset_revision( app=self.app, repository=tool_shed_repository, changeset_revision=tool_shed_repository.changeset_revision, @@ -384,3 +453,13 @@ # Assume that the repository has been installed if we find a .hg directory. return True return False + + def __is_valid_repository_tag( self, elem ): + # <repository name="emboss_datatypes" description="Datatypes for Emboss tools" changeset_revision="a89163f31369" /> + if elem.tag != 'repository': + return False + if not elem.get( 'name' ): + return False + if not elem.get( 'changeset_revision' ): + return False + return True diff -r 097abeb6969e93265135a8d6f3e566b5e913ca8f -r 185232cef732d9b79aad686ca0aa556bb7c63614 lib/tool_shed/galaxy_install/migrate/check.py --- a/lib/tool_shed/galaxy_install/migrate/check.py +++ b/lib/tool_shed/galaxy_install/migrate/check.py @@ -1,13 +1,17 @@ -import sys, os, logging, subprocess +import logging +import os +import subprocess +import sys from galaxy import eggs -import pkg_resources -pkg_resources.require( "SQLAlchemy" ) -pkg_resources.require( "decorator" ) -pkg_resources.require( "Tempita " ) -pkg_resources.require( "sqlalchemy-migrate" ) - -from migrate.versioning import repository, schema -from sqlalchemy import * +eggs.require( "decorator" ) +eggs.require( "Tempita" ) +eggs.require( "SQLAlchemy" ) +eggs.require( "sqlalchemy_migrate" ) +from migrate.versioning import repository +from migrate.versioning import schema +from sqlalchemy import create_engine +from sqlalchemy import MetaData +from sqlalchemy import Table from galaxy.util.odict import odict from galaxy.model.orm import dialect_to_egg from tool_shed.util import common_util @@ -52,7 +56,9 @@ if tool_panel_configs: # The missing_tool_configs_dict contents are something like: # {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]} - tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number ) + tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app, + tool_panel_configs, + latest_tool_migration_script_number ) else: # It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but # we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in @@ -136,8 +142,8 @@ msg += "Tool dependencies can be installed after the repositories have been installed as well.\n\n" msg += "After the installation process finishes, you can start your Galaxy server. As part of this installation process,\n" msg += "entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these\n" - msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these files should be\n" - msg += "removed from your file%s named %s, but only after the installation process finishes.\n\n" % ( plural, tool_panel_config_file_names ) + msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been\n" + msg += "removed from your file%s named %s.\n\n" % ( plural, tool_panel_config_file_names ) for missing_tool_config, tool_dependencies in missing_tool_configs_dict.items(): msg += "%s\n" % missing_tool_config msg += "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n" diff -r 097abeb6969e93265135a8d6f3e566b5e913ca8f -r 185232cef732d9b79aad686ca0aa556bb7c63614 lib/tool_shed/galaxy_install/migrate/common.py --- a/lib/tool_shed/galaxy_install/migrate/common.py +++ b/lib/tool_shed/galaxy_install/migrate/common.py @@ -1,8 +1,10 @@ -import sys, os, ConfigParser +import ConfigParser +import os +import sys import galaxy.config import galaxy.datatypes.registry from galaxy import tools -from galaxy.tools.data import * +from galaxy.tools.data import ToolDataTableManager from galaxy.web import security import galaxy.model.mapping import galaxy.tools.search @@ -10,8 +12,10 @@ import tool_shed.tool_shed_registry from tool_shed.galaxy_install import install_manager + class MigrateToolsApplication( object ): """Encapsulates the state of a basic Galaxy Universe application in order to initiate the Install Manager""" + def __init__( self, tools_migration_config ): install_dependencies = 'install_dependencies' in sys.argv galaxy_config_file = 'universe_wsgi.ini' @@ -23,7 +27,7 @@ if not os.path.exists( galaxy_config_file ): print "Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): %s" % galaxy_config_file sys.exit( 1 ) - config_parser = ConfigParser.ConfigParser( { 'here':os.getcwd() } ) + config_parser = ConfigParser.ConfigParser( { 'here' : os.getcwd() } ) config_parser.read( galaxy_config_file ) galaxy_config_dict = {} for key, value in config_parser.items( "app:main" ): @@ -77,8 +81,10 @@ tools_migration_config ), migrated_tools_config=self.config.migrated_tools_config, install_dependencies=install_dependencies ) + @property def sa_session( self ): return self.model.context.current + def shutdown( self ): self.object_store.shutdown() diff -r 097abeb6969e93265135a8d6f3e566b5e913ca8f -r 185232cef732d9b79aad686ca0aa556bb7c63614 lib/tool_shed/util/common_util.py --- a/lib/tool_shed/util/common_util.py +++ b/lib/tool_shed/util/common_util.py @@ -76,7 +76,7 @@ return missing_tool_configs_dict def get_non_shed_tool_panel_configs( app ): - # Get the non-shed related tool panel configs - there can be more than one, and the default is tool_conf.xml. + """Get the non-shed related tool panel configs - there can be more than one, and the default is tool_conf.xml.""" config_filenames = [] for config_filename in app.config.tool_configs: # Any config file that includes a tool_path attribute in the root tag set like the following is shed-related. @@ -98,13 +98,13 @@ shed_url = shed_url.rstrip( '/' ) return shed_url return None - + def tool_shed_get( app, tool_shed_url, uri ): """Make contact with the tool shed via the uri provided.""" registry = app.tool_shed_registry urlopener = urllib2.build_opener() password_mgr = registry.password_manager_for_url( tool_shed_url ) - if ( password_mgr is not None ): + if password_mgr is not None: auth_handler = urllib2.HTTPBasicAuthHandler( password_mgr ) urlopener.add_handler( auth_handler ) response = urlopener.open( uri ) diff -r 097abeb6969e93265135a8d6f3e566b5e913ca8f -r 185232cef732d9b79aad686ca0aa556bb7c63614 scripts/migrate_tools/migrate_tools.py --- a/scripts/migrate_tools/migrate_tools.py +++ b/scripts/migrate_tools/migrate_tools.py @@ -1,4 +1,3 @@ - """ This script will start up its own web application which includes an InstallManager (~/lib/galaxy/tool_shed/install_manager.py). For each tool discovered missing, the tool shed repository that contains it will be installed on disk and a new entry will be @@ -8,11 +7,12 @@ layout of the local tool_conf.xml file. Entries will not be created in migrated_tools_conf.xml for tools included in the tool shed repository but not defined in tool_conf.xml. """ -import sys, os +import os +import sys new_path = [ os.path.join( os.getcwd(), "lib" ) ] # Remove scripts/ from the path. -new_path.extend( sys.path[1:] ) +new_path.extend( sys.path[ 1: ] ) sys.path = new_path from galaxy import eggs @@ -26,8 +26,8 @@ else: plural = 's' file_names = ', '.join( non_shed_tool_confs ) -msg = "\nThe installation process is finished. If any tools associated with this migration were defined in your file%s named\n" % plural -msg += "%s, then you should remove entries for them and start your Galaxy server.\n" % file_names +msg = "\nThe installation process is finished. All tools associated with this migration that were defined in your file%s named\n" % plural +msg += "%s, have been removed. You may now start your Galaxy server.\n" % file_names print msg app.shutdown() sys.exit( 0 ) 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: Workflow from_dict was creating duplicate PostJobActions -- this already happens in module.save_to_step
by commits-noreply＠bitbucket.org 22 Aug '13

22 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/097abeb6969e/ Changeset: 097abeb6969e User: dannon Date: 2013-08-22 16:05:09 Summary: Workflow from_dict was creating duplicate PostJobActions -- this already happens in module.save_to_step Affected #: 2 files diff -r 1859b9f04a6e665e90ed42441302e8486cbd6941 -r 097abeb6969e93265135a8d6f3e566b5e913ca8f lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1803,12 +1803,6 @@ if annotation: annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) - # Unpack and add post-job actions. - post_job_actions = step_dict.get( 'post_job_actions', {} ) - for name, pja_dict in post_job_actions.items(): - model.PostJobAction( pja_dict[ 'action_type' ], - step, pja_dict[ 'output_name' ], - pja_dict[ 'action_arguments' ] ) # Second pass to deal with connections between steps for step in steps: # Input connections diff -r 1859b9f04a6e665e90ed42441302e8486cbd6941 -r 097abeb6969e93265135a8d6f3e566b5e913ca8f lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -250,7 +250,6 @@ module.version_changes.append("%s: using version '%s' instead of version '%s' indicated in this workflow." % (tool_id, module.tool.version, step.tool_version)) module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) module.errors = step.tool_errors - # module.post_job_actions = step.post_job_actions module.workflow_outputs = step.workflow_outputs pjadict = {} for pja in step.post_job_actions: 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: Dave Bouvier: Update functional tests to check for the correct string on the 'Monitor installing tool shed repositories' page.
by commits-noreply＠bitbucket.org 22 Aug '13

22 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1859b9f04a6e/ Changeset: 1859b9f04a6e User: Dave Bouvier Date: 2013-08-22 15:49:25 Summary: Update functional tests to check for the correct string on the 'Monitor installing tool shed repositories' page. Affected #: 6 files diff -r e9ced769e4f3d348875d014a16c82b32ec748517 -r 1859b9f04a6e665e90ed42441302e8486cbd6941 test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py --- a/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py +++ b/test/tool_shed/functional/test_1100_install_repository_with_complex_dependencies.py @@ -232,7 +232,7 @@ category_name, install_tool_dependencies=True, preview_strings_displayed=preview_strings_displayed, - post_submit_strings_displayed=[ base_repository.name, tool_repository.name, 'new' ], + post_submit_strings_displayed=[ base_repository.name, tool_repository.name, 'New' ], includes_tools_for_display_in_tool_panel=True ) def test_0050_verify_installed_repositories( self ): diff -r e9ced769e4f3d348875d014a16c82b32ec748517 -r 1859b9f04a6e665e90ed42441302e8486cbd6941 test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py --- a/test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py +++ b/test/tool_shed/functional/test_1110_install_repository_with_invalid_repository_dependency.py @@ -176,7 +176,7 @@ install_tool_dependencies=False, install_repository_dependencies=True, preview_strings_displayed=preview_strings_displayed, - post_submit_strings_displayed=[ repository.name, repository.name, 'new' ], + post_submit_strings_displayed=[ repository.name, repository.name, 'New' ], includes_tools_for_display_in_tool_panel=True ) repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) self.display_installed_repository_manage_page( repository, strings_not_displayed=[ 'Repository dependencies' ] ) diff -r e9ced769e4f3d348875d014a16c82b32ec748517 -r 1859b9f04a6e665e90ed42441302e8486cbd6941 test/tool_shed/functional/test_1130_datatype_converters.py --- a/test/tool_shed/functional/test_1130_datatype_converters.py +++ b/test/tool_shed/functional/test_1130_datatype_converters.py @@ -79,7 +79,7 @@ preview_strings_displayed=preview_strings_displayed, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed, - post_submit_strings_displayed=[ repository.name, 'new' ], + post_submit_strings_displayed=[ repository.name, 'New' ], includes_tools_for_display_in_tool_panel=False ) def test_0015_uninstall_and_verify_tool_panel_section( self ): diff -r e9ced769e4f3d348875d014a16c82b32ec748517 -r 1859b9f04a6e665e90ed42441302e8486cbd6941 test/tool_shed/functional/test_1150_prior_installation_required.py --- a/test/tool_shed/functional/test_1150_prior_installation_required.py +++ b/test/tool_shed/functional/test_1150_prior_installation_required.py @@ -138,7 +138,7 @@ preview_strings_displayed=preview_strings_displayed, strings_displayed=strings_displayed, strings_not_displayed=[], - post_submit_strings_displayed=[ 'column_maker_0150', 'new' ], + post_submit_strings_displayed=[ 'column_maker_0150', 'New' ], includes_tools_for_display_in_tool_panel=True ) def test_0030_verify_installation_order( self ): diff -r e9ced769e4f3d348875d014a16c82b32ec748517 -r 1859b9f04a6e665e90ed42441302e8486cbd6941 test/tool_shed/functional/test_1160_circular_prior_installation_required.py --- a/test/tool_shed/functional/test_1160_circular_prior_installation_required.py +++ b/test/tool_shed/functional/test_1160_circular_prior_installation_required.py @@ -207,7 +207,7 @@ preview_strings_displayed=preview_strings_displayed, strings_displayed=strings_displayed, strings_not_displayed=[], - post_submit_strings_displayed=[ 'filtering_0160', 'new' ], + post_submit_strings_displayed=[ 'filtering_0160', 'New' ], includes_tools_for_display_in_tool_panel=True ) def test_0035_verify_installation_order( self ): diff -r e9ced769e4f3d348875d014a16c82b32ec748517 -r 1859b9f04a6e665e90ed42441302e8486cbd6941 test/tool_shed/functional/test_1170_complex_prior_installation_required.py --- a/test/tool_shed/functional/test_1170_complex_prior_installation_required.py +++ b/test/tool_shed/functional/test_1170_complex_prior_installation_required.py @@ -163,7 +163,7 @@ preview_strings_displayed=preview_strings_displayed, strings_displayed=[], strings_not_displayed=[], - post_submit_strings_displayed=[ 'package_matplotlib_1_2_0170', 'new' ], + post_submit_strings_displayed=[ 'package_matplotlib_1_2_0170', 'New' ], includes_tools_for_display_in_tool_panel=False ) def test_0030_verify_installation_order( self ): 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: Update hide action to reflect what output is being hidden.
by commits-noreply＠bitbucket.org 22 Aug '13

22 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e9ced769e4f3/ Changeset: e9ced769e4f3 User: dannon Date: 2013-08-22 15:05:41 Summary: Update hide action to reflect what output is being hidden. Affected #: 1 file diff -r 315ee3999082396e751e7478f0ac2a4247ba5e70 -r e9ced769e4f3d348875d014a16c82b32ec748517 lib/galaxy/jobs/actions/post.py --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -242,8 +242,8 @@ } """ @classmethod - def get_short_str(cls, trans): - return "Hide this dataset." + def get_short_str(cls, pja): + return "Hide output '%s'." % pja.output_name class DeleteDatasetAction(DefaultJobAction): # This is disabled for right now. Deleting a dataset in the middle of a workflow causes errors (obviously) for the subsequent steps using the data. 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: 5 new changesets
by commits-noreply＠bitbucket.org 22 Aug '13

22 Aug '13

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2f655d7df4de/ Changeset: 2f655d7df4de User: jmchilton Date: 2013-08-13 21:38:00 Summary: Add some overly simple baseline unit tests for visualizations plugin behavior. Affected #: 1 file diff -r 009088d5e76fb00794da78dc0ee3cdaa8524b7d8 -r 2f655d7df4de9731adf45ec1487a9e85c5671aaf test/unit/test_plugins.py --- /dev/null +++ b/test/unit/test_plugins.py @@ -0,0 +1,14 @@ +from os.path import join, dirname, basename +from galaxy.visualization.registry import VisualizationsRegistry + + +def test_visualization_loading(): + galaxy_root = join(dirname(__file__), '..', '..') + visualizations = join(galaxy_root, 'config', 'plugins', 'visualizations') + registry = VisualizationsRegistry(visualizations, 'foo') + assert "VisualizationsRegistry" in str(registry) + assert visualizations in str(registry) + assert registry.name == "visualizations" + assert 'scatterplot' in \ + [basename(path) for path in registry.get_plugin_directories()] + assert registry._get_template_paths() == [visualizations] https://bitbucket.org/galaxy/galaxy-central/commits/83139f9fed93/ Changeset: 83139f9fed93 User: jmchilton Date: 2013-08-13 21:38:00 Summary: Planning on refactoring out self.plugin_directory, is this simplified logic sufficient or was it the way it was for a good reason? Affected #: 1 file diff -r 2f655d7df4de9731adf45ec1487a9e85c5671aaf -r 83139f9fed93f4a3759ed1b5c2019c24fb8037c5 lib/galaxy/web/base/pluginframework.py --- a/lib/galaxy/web/base/pluginframework.py +++ b/lib/galaxy/web/base/pluginframework.py @@ -220,8 +220,7 @@ this version of `fill_template` allows `bler.mako` to call `import my_script`. """ try: - plugin_base_path = os.path.split( os.path.dirname( template_filename ) )[0] - plugin_path = os.path.join( self.plugin_directory, plugin_base_path ) + plugin_path = os.path.dirname( os.path.dirname( template_filename ) ) sys.path.append( plugin_path ) filled_template = self.fill_template( trans, template_filename, **kwargs ) https://bitbucket.org/galaxy/galaxy-central/commits/82b20714be81/ Changeset: 82b20714be81 User: jmchilton Date: 2013-08-13 21:38:00 Summary: Refactor plugin framework to allow multiple plugin directories (like tools framework allows multiple tool roots). Idea here is to allow some plugins to be managed by Galaxy team inside root and some plugins to be managed outside of Galaxy root by deployers, etc.... This will help keep merges unnecessary or as minimal as possible and should ease efforts like Debian packaging of Galaxy. The need to actually modify the Galaxy code base is an unfortunate aspect of the way dynamic job destinations and dynamic toolbox filters have been implemented. Bringing these under a generic plugin framework and allowing them to be tweaked outside of the Galaxy code base would be wins. Affected #: 2 files diff -r 83139f9fed93f4a3759ed1b5c2019c24fb8037c5 -r 82b20714be81946be9d6fa8ff0848fc6bd02b567 lib/galaxy/visualization/registry.py --- a/lib/galaxy/visualization/registry.py +++ b/lib/galaxy/visualization/registry.py @@ -61,9 +61,6 @@ #: directories under plugin_directory that aren't plugins non_plugin_directories = [] - def __str__( self ): - return 'VisualizationsRegistry(%s)' %( self.plugin_directory ) - def __init__( self, registry_filepath, template_cache_dir ): super( VisualizationsRegistry, self ).__init__( registry_filepath, 'visualizations', template_cache_dir ) @@ -84,7 +81,7 @@ self.listings = VisualizationsConfigParser.parse( self.get_plugin_directories() ) except Exception, exc: - log.exception( 'Error parsing visualizations plugins %s', self.plugin_directory ) + log.exception( 'Error parsing visualizations plugins %s', self.plugin_directories ) raise def get_visualization( self, trans, visualization_name, target_object ): diff -r 83139f9fed93f4a3759ed1b5c2019c24fb8037c5 -r 82b20714be81946be9d6fa8ff0848fc6bd02b567 lib/galaxy/web/base/pluginframework.py --- a/lib/galaxy/web/base/pluginframework.py +++ b/lib/galaxy/web/base/pluginframework.py @@ -14,6 +14,8 @@ pkg_resources.require( 'Mako' ) import mako +from galaxy.util import listify + import logging log = logging.getLogger( __name__ ) @@ -94,24 +96,29 @@ return None def __str__( self ): - return '%s(%s)' %( self.__class__.__name__, self.plugin_directory ) + return '%s(%s)' %( self.__class__.__name__, self.plugin_directories ) - def __init__( self, plugin_directory, name=None, template_cache_dir=None, debug=False ): + def __init__( self, plugin_directories, name=None, template_cache_dir=None, debug=False, assert_exists=True ): """ - :type plugin_directory: string - :param plugin_directory: the base directory where plugin code is kept - :type name: (optional) string (default: None) - :param name: the name of this plugin + :type plugin_directories: string or list + :param plugin_directories: the base directory where plugin code is kept + :type name: (optional) string (default: None) + :param name: the name of this plugin (that will appear in url pathing, etc.) - :type template_cache_dir: (optional) string (default: None) - :param template_cache_dir: the cache directory to store compiled mako + :type template_cache_dir: (optional) string (default: None) + :param template_cache_dir: the cache directory to store compiled mako + :type assert_exists: (optional) bool (default: False) + :param assert_exists: If True, each configured plugin directory must exist. """ - if not os.path.isdir( plugin_directory ): - raise PluginFrameworkException( 'Framework plugin directory not found: %s, %s' - %( self.__class__.__name__, plugin_directory ) ) - self.plugin_directory = plugin_directory + self.plugin_directories = listify( plugin_directories ) + if assert_exists: + for plugin_directory in self.plugin_directories: + if not os.path.isdir( plugin_directory ): + raise PluginFrameworkException( 'Framework plugin directory not found: %s, %s' + % ( self.__class__.__name__, plugin_directory ) ) + #TODO: or pass in from config - self.name = name or os.path.basename( self.plugin_directory ) + self.name = name or os.path.basename( self.plugin_directories[0] ) if self.has_config: self.load_configuration() @@ -127,14 +134,15 @@ themselves and whose ``basename`` is not in ``plugin_directory``. """ # could instead explicitly list on/off in master config file - for plugin_path in glob.glob( os.path.join( self.plugin_directory, '*' ) ): - if not os.path.isdir( plugin_path ): - continue + for plugin_directory in self.plugin_directories: + for plugin_path in glob.glob( os.path.join( plugin_directory, '*' ) ): + if not os.path.isdir( plugin_path ): + continue - if os.path.basename( plugin_path ) in self.non_plugin_directories: - continue + if os.path.basename( plugin_path ) in self.non_plugin_directories: + continue - yield plugin_path + yield plugin_path # ------------------------------------------------------------------------- config def load_configuration( self ): @@ -185,7 +193,7 @@ """ Get the paths that will be searched for templates. """ - return [ self.plugin_directory ] + return self.plugin_directories def _create_mako_template_lookup( self, cache_dir, paths, collection_size=500, output_encoding='utf-8' ): """ https://bitbucket.org/galaxy/galaxy-central/commits/b5f765e074f8/ Changeset: b5f765e074f8 User: jmchilton Date: 2013-08-13 21:38:00 Summary: Add some test cases for plugins configured from multiple directories. Affected #: 1 file diff -r 82b20714be81946be9d6fa8ff0848fc6bd02b567 -r b5f765e074f8ff5ba02dad1d841b92c15b3fb224 test/unit/test_plugins.py --- a/test/unit/test_plugins.py +++ b/test/unit/test_plugins.py @@ -1,14 +1,42 @@ +from os import makedirs from os.path import join, dirname, basename +from tempfile import mkdtemp +from shutil import rmtree + from galaxy.visualization.registry import VisualizationsRegistry def test_visualization_loading(): - galaxy_root = join(dirname(__file__), '..', '..') - visualizations = join(galaxy_root, 'config', 'plugins', 'visualizations') + visualizations = __default_viz_root() registry = VisualizationsRegistry(visualizations, 'foo') assert "VisualizationsRegistry" in str(registry) assert visualizations in str(registry) assert registry.name == "visualizations" + __assert_scatterplot_registered(registry) + assert registry._get_template_paths() == [visualizations] + + +def test_multiple_visualization_roots(): + temp_dir = mkdtemp() + try: + makedirs(join(temp_dir, "coolplugin5")) + visualization_dirs = "%s,%s" % (__default_viz_root(), temp_dir) + registry = VisualizationsRegistry(visualization_dirs, 'foo') + __assert_scatterplot_registered(registry) + assert "coolplugin5" in \ + [basename(path) for path in registry.get_plugin_directories()] + assert registry._get_template_paths() == \ + [__default_viz_root(), temp_dir] + finally: + rmtree(temp_dir) + + +def __assert_scatterplot_registered(registry): assert 'scatterplot' in \ [basename(path) for path in registry.get_plugin_directories()] - assert registry._get_template_paths() == [visualizations] + + +def __default_viz_root(): + galaxy_root = join(dirname(__file__), '..', '..') + visualizations = join(galaxy_root, 'config', 'plugins', 'visualizations') + return visualizations https://bitbucket.org/galaxy/galaxy-central/commits/315ee3999082/ Changeset: 315ee3999082 User: carlfeberhard Date: 2013-08-22 00:24:53 Summary: Merge John Chilton's pull request #204 Affected #: 3 files diff -r ee60297266b09d81a7906c32a7ec03199e50a0c7 -r 315ee3999082396e751e7478f0ac2a4247ba5e70 lib/galaxy/visualization/registry.py --- a/lib/galaxy/visualization/registry.py +++ b/lib/galaxy/visualization/registry.py @@ -61,9 +61,6 @@ #: directories under plugin_directory that aren't plugins non_plugin_directories = [] - def __str__( self ): - return 'VisualizationsRegistry(%s)' %( self.plugin_directory ) - def __init__( self, registry_filepath, template_cache_dir ): super( VisualizationsRegistry, self ).__init__( registry_filepath, 'visualizations', template_cache_dir ) @@ -84,7 +81,7 @@ self.listings = VisualizationsConfigParser.parse( self.get_plugin_directories() ) except Exception, exc: - log.exception( 'Error parsing visualizations plugins %s', self.plugin_directory ) + log.exception( 'Error parsing visualizations plugins %s', self.plugin_directories ) raise def get_visualization( self, trans, visualization_name, target_object ): diff -r ee60297266b09d81a7906c32a7ec03199e50a0c7 -r 315ee3999082396e751e7478f0ac2a4247ba5e70 lib/galaxy/web/base/pluginframework.py --- a/lib/galaxy/web/base/pluginframework.py +++ b/lib/galaxy/web/base/pluginframework.py @@ -14,6 +14,8 @@ pkg_resources.require( 'Mako' ) import mako +from galaxy.util import listify + import logging log = logging.getLogger( __name__ ) @@ -94,24 +96,29 @@ return None def __str__( self ): - return '%s(%s)' %( self.__class__.__name__, self.plugin_directory ) + return '%s(%s)' %( self.__class__.__name__, self.plugin_directories ) - def __init__( self, plugin_directory, name=None, template_cache_dir=None, debug=False ): + def __init__( self, plugin_directories, name=None, template_cache_dir=None, debug=False, assert_exists=True ): """ - :type plugin_directory: string - :param plugin_directory: the base directory where plugin code is kept - :type name: (optional) string (default: None) - :param name: the name of this plugin + :type plugin_directories: string or list + :param plugin_directories: the base directory where plugin code is kept + :type name: (optional) string (default: None) + :param name: the name of this plugin (that will appear in url pathing, etc.) - :type template_cache_dir: (optional) string (default: None) - :param template_cache_dir: the cache directory to store compiled mako + :type template_cache_dir: (optional) string (default: None) + :param template_cache_dir: the cache directory to store compiled mako + :type assert_exists: (optional) bool (default: False) + :param assert_exists: If True, each configured plugin directory must exist. """ - if not os.path.isdir( plugin_directory ): - raise PluginFrameworkException( 'Framework plugin directory not found: %s, %s' - %( self.__class__.__name__, plugin_directory ) ) - self.plugin_directory = plugin_directory + self.plugin_directories = listify( plugin_directories ) + if assert_exists: + for plugin_directory in self.plugin_directories: + if not os.path.isdir( plugin_directory ): + raise PluginFrameworkException( 'Framework plugin directory not found: %s, %s' + % ( self.__class__.__name__, plugin_directory ) ) + #TODO: or pass in from config - self.name = name or os.path.basename( self.plugin_directory ) + self.name = name or os.path.basename( self.plugin_directories[0] ) if self.has_config: self.load_configuration() @@ -127,14 +134,15 @@ themselves and whose ``basename`` is not in ``plugin_directory``. """ # could instead explicitly list on/off in master config file - for plugin_path in glob.glob( os.path.join( self.plugin_directory, '*' ) ): - if not os.path.isdir( plugin_path ): - continue + for plugin_directory in self.plugin_directories: + for plugin_path in glob.glob( os.path.join( plugin_directory, '*' ) ): + if not os.path.isdir( plugin_path ): + continue - if os.path.basename( plugin_path ) in self.non_plugin_directories: - continue + if os.path.basename( plugin_path ) in self.non_plugin_directories: + continue - yield plugin_path + yield plugin_path # ------------------------------------------------------------------------- config def load_configuration( self ): @@ -185,7 +193,7 @@ """ Get the paths that will be searched for templates. """ - return [ self.plugin_directory ] + return self.plugin_directories def _create_mako_template_lookup( self, cache_dir, paths, collection_size=500, output_encoding='utf-8' ): """ @@ -220,8 +228,7 @@ this version of `fill_template` allows `bler.mako` to call `import my_script`. """ try: - plugin_base_path = os.path.split( os.path.dirname( template_filename ) )[0] - plugin_path = os.path.join( self.plugin_directory, plugin_base_path ) + plugin_path = os.path.dirname( os.path.dirname( template_filename ) ) sys.path.append( plugin_path ) filled_template = self.fill_template( trans, template_filename, **kwargs ) diff -r ee60297266b09d81a7906c32a7ec03199e50a0c7 -r 315ee3999082396e751e7478f0ac2a4247ba5e70 test/unit/test_plugins.py --- /dev/null +++ b/test/unit/test_plugins.py @@ -0,0 +1,42 @@ +from os import makedirs +from os.path import join, dirname, basename +from tempfile import mkdtemp +from shutil import rmtree + +from galaxy.visualization.registry import VisualizationsRegistry + + +def test_visualization_loading(): + visualizations = __default_viz_root() + registry = VisualizationsRegistry(visualizations, 'foo') + assert "VisualizationsRegistry" in str(registry) + assert visualizations in str(registry) + assert registry.name == "visualizations" + __assert_scatterplot_registered(registry) + assert registry._get_template_paths() == [visualizations] + + +def test_multiple_visualization_roots(): + temp_dir = mkdtemp() + try: + makedirs(join(temp_dir, "coolplugin5")) + visualization_dirs = "%s,%s" % (__default_viz_root(), temp_dir) + registry = VisualizationsRegistry(visualization_dirs, 'foo') + __assert_scatterplot_registered(registry) + assert "coolplugin5" in \ + [basename(path) for path in registry.get_plugin_directories()] + assert registry._get_template_paths() == \ + [__default_viz_root(), temp_dir] + finally: + rmtree(temp_dir) + + +def __assert_scatterplot_registered(registry): + assert 'scatterplot' in \ + [basename(path) for path in registry.get_plugin_directories()] + + +def __default_viz_root(): + galaxy_root = join(dirname(__file__), '..', '..') + visualizations = join(galaxy_root, 'config', 'plugins', 'visualizations') + return visualizations Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Remove spurious type setting in Group object.
by commits-noreply＠bitbucket.org 22 Aug '13

22 Aug '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ee60297266b0/ Changeset: ee60297266b0 User: jgoecks Date: 2013-08-21 21:24:04 Summary: Remove spurious type setting in Group object. Affected #: 1 file diff -r 8ed926ee0b523bb16a90e218f1d8bd5ee082ffe8 -r ee60297266b09d81a7906c32a7ec03199e50a0c7 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -23,8 +23,7 @@ def __init__( self ): self.name = None - self.type = 'group' - + @property def visible( self ): return True 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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