mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge branch 'release_16.10' into dev
Conflicts: static/maps/mvc/form/form-section.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map static/scripts/bundled/login.bundled.js.map static/scripts/mvc/form/form-section.js
This commit is contained in:
Nicola Soranzo
@@ -139,7 +139,7 @@ function( Utils, Ui, Portlet, Repeat, InputElement, Parameters ) {
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_addRow: function( input_def ) {
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var self = this;
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var id = input_def.id;
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input_def.onchange = function() { self.app.trigger( 'change', id ) };
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input_def.onchange = input_def.onchange || function() { self.app.trigger( 'change', id ) };
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var field = this.parameters.create( input_def );
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this.app.field_list[ id ] = field;
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var input_element = new InputElement( this.app, {
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@@ -24,7 +24,7 @@ var menu = [
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},
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{
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html : _l( 'History Actions' ),
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html : _l( 'Current History' ),
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header : true,
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anon : true
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},
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@@ -40,7 +40,7 @@ define( [ 'utils/utils', 'mvc/tool/tool-form-base' ],
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// state stored on the client with. User needs to save
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// for this to take effect.
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self.node.update_field_data( data );
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self.form.errors( data && data.tool_model )
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self.form.errors( data && data.tool_model );
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}
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}));
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this.$el.append( this.form.$el );
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@@ -638,11 +638,9 @@ class AdminToolshed( AdminGalaxy ):
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checked=install_tool_dependencies_check_box_checked )
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view = views.DependencyResolversView(self.app)
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if view.installable_resolvers:
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install_resolver_dependencies_check_box_checked = True
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install_resolver_dependencies_check_box = CheckboxField( 'install_resolver_dependencies', checked=True )
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else:
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install_resolver_dependencies_check_box_checked = False
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install_resolver_dependencies_check_box = CheckboxField( 'install_resolver_dependencies',
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checked=install_resolver_dependencies_check_box_checked )
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install_resolver_dependencies_check_box = None
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return trans.fill_template( '/admin/tool_shed_repository/install_tool_dependencies_with_update.mako',
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repository=repository,
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updating_repository_id=updating_repository_id,
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@@ -1206,11 +1204,9 @@ class AdminToolshed( AdminGalaxy ):
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install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True )
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view = views.DependencyResolversView(self.app)
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if view.installable_resolvers:
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install_resolver_dependencies_check_box_checked = True
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install_resolver_dependencies_check_box = CheckboxField( 'install_resolver_dependencies', checked=True )
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else:
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install_resolver_dependencies_check_box_checked = False
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install_resolver_dependencies_check_box = CheckboxField( 'install_resolver_dependencies',
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checked=install_resolver_dependencies_check_box_checked )
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install_resolver_dependencies_check_box = None
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encoded_repo_info_dicts = encoding_util.encoding_sep.join( encoded_repo_info_dicts )
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tool_shed_url = kwd[ 'tool_shed_url' ]
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if includes_tools_for_display_in_tool_panel:
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@@ -1674,11 +1670,9 @@ class AdminToolshed( AdminGalaxy ):
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install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked )
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view = views.DependencyResolversView(self.app)
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if view.installable_resolvers:
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install_resolver_dependencies_check_box_checked = True
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install_resolver_dependencies_check_box = CheckboxField( 'install_resolver_dependencies', checked=True )
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else:
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install_resolver_dependencies_check_box_checked = False
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install_resolver_dependencies_check_box = CheckboxField( 'install_resolver_dependencies',
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checked=install_resolver_dependencies_check_box_checked )
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install_resolver_dependencies_check_box = None
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return trans.fill_template( '/admin/tool_shed_repository/reselect_tool_panel_section.mako',
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repository=tool_shed_repository,
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no_changes_check_box=no_changes_check_box,
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@@ -1 +1 @@
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@@ -1 +1 @@
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define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f){var g=Backbone.View.extend({initialize:function(a,b){this.app=a,this.inputs=b.inputs,this.parameters=new f,this.setElement($("<div/>")),this.render()},render:function(){var a=this;this.$el.empty(),_.each(this.inputs,function(b){a.add(b)})},add:function(b){var c=jQuery.extend(!0,{},b);switch(c.id=b.id=a.uid(),this.app.input_list[c.id]=c,c.type){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id,this.app.options.sustain_conditionals&&(a.test_param.disabled=!0);var c=this._addRow(a.test_param);c.model&&c.model.set("onchange",function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=b.$("#"+a.id+"-section-"+e),h=!1;for(var i in f.inputs)if(!f.inputs[i].hidden){h=!0;break}e==d&&h?g.fadeIn("fast"):g.hide()}b.app.trigger("change")});for(var d in a.cases){var e=new g(this.app,{inputs:a.cases[d].inputs});this._append(e.$el.addClass("ui-form-section"),a.id+"-section-"+d)}c.trigger("change")},_addRepeat:function(a){function b(b){var d=a.id+"-section-"+f++,e=new g(c.app,{inputs:b});h.add({id:d,$el:e.$el,ondel:function(){h.del(d),c.app.trigger("change")}})}for(var c=this,f=0,h=new d.View({title:a.title||"Repeat",min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=_.size(a.cache),j=0;j<Math.max(Math.max(i,a.min||0),a.default||0);j++)b(i>j?a.cache[j]:a.inputs);this.app.options.sustain_repeats&&h.hideOptions();var k=new e(this.app,{label:a.title||a.name,help:a.help,field:h});this._append(k.$el,a.id)},_addSection:function(a){var b=new c.View({title:a.title||a.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!a.expanded});b.append(new g(this.app,{inputs:a.inputs}).$el),b.append($("<div/>").addClass("ui-form-info").html(a.help)),this.app.on("expand",function(a){b.$("#"+a).length>0&&b.expand()}),this._append(b.$el,a.id)},_addRow:function(a){var b=this,c=a.id;a.onchange=function(){b.app.trigger("change",c)};var d=this.parameters.create(a);this.app.field_list[c]=d;var f=new e(this.app,{name:a.name,label:a.label||a.name,value:a.value,text_value:a.text_value,collapsible_value:a.collapsible_value,collapsible_preview:a.collapsible_preview,help:a.help,argument:a.argument,disabled:a.disabled,color:a.color,style:a.style,backdrop:a.backdrop,hidden:a.hidden,field:d});return this.app.element_list[c]=f,this._append(f.$el,a.id),d},_append:function(a,b){this.$el.append(a.addClass("section-row").attr("id",b))}});return{View:g}});
|
||||
define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/form/form-repeat","mvc/form/form-input","mvc/form/form-parameters"],function(a,b,c,d,e,f){var g=Backbone.View.extend({initialize:function(a,b){this.app=a,this.inputs=b.inputs,this.parameters=new f,this.setElement($("<div/>")),this.render()},render:function(){var a=this;this.$el.empty(),_.each(this.inputs,function(b){a.add(b)})},add:function(b){var c=jQuery.extend(!0,{},b);switch(c.id=b.id=a.uid(),this.app.input_list[c.id]=c,c.type){case"conditional":this._addConditional(c);break;case"repeat":this._addRepeat(c);break;case"section":this._addSection(c);break;default:this._addRow(c)}},_addConditional:function(a){var b=this;a.test_param.id=a.id,this.app.options.sustain_conditionals&&(a.test_param.disabled=!0);var c=this._addRow(a.test_param);c.model&&c.model.set("onchange",function(c){var d=b.app.data.matchCase(a,c);for(var e in a.cases){var f=a.cases[e],g=b.$("#"+a.id+"-section-"+e),h=!1;for(var i in f.inputs)if(!f.inputs[i].hidden){h=!0;break}e==d&&h?g.fadeIn("fast"):g.hide()}b.app.trigger("change")});for(var d in a.cases){var e=new g(this.app,{inputs:a.cases[d].inputs});this._append(e.$el.addClass("ui-form-section"),a.id+"-section-"+d)}c.trigger("change")},_addRepeat:function(a){function b(b){var d=a.id+"-section-"+f++,e=new g(c.app,{inputs:b});h.add({id:d,$el:e.$el,ondel:function(){h.del(d),c.app.trigger("change")}})}for(var c=this,f=0,h=new d.View({title:a.title||"Repeat",min:a.min,max:a.max,onnew:function(){b(a.inputs),c.app.trigger("change")}}),i=_.size(a.cache),j=0;j<Math.max(Math.max(i,a.min||0),a.default||0);j++)b(i>j?a.cache[j]:a.inputs);this.app.options.sustain_repeats&&h.hideOptions();var k=new e(this.app,{label:a.title||a.name,help:a.help,field:h});this._append(k.$el,a.id)},_addSection:function(a){var b=new c.View({title:a.title||a.name,cls:"ui-portlet-section",collapsible:!0,collapsible_button:!0,collapsed:!a.expanded});b.append(new g(this.app,{inputs:a.inputs}).$el),b.append($("<div/>").addClass("ui-form-info").html(a.help)),this.app.on("expand",function(a){b.$("#"+a).length>0&&b.expand()}),this._append(b.$el,a.id)},_addRow:function(a){var b=this,c=a.id;a.onchange=a.onchange||function(){b.app.trigger("change",c)};var d=this.parameters.create(a);this.app.field_list[c]=d;var f=new e(this.app,{name:a.name,label:a.label||a.name,value:a.value,text_value:a.text_value,collapsible_value:a.collapsible_value,collapsible_preview:a.collapsible_preview,help:a.help,argument:a.argument,disabled:a.disabled,color:a.color,style:a.style,backdrop:a.backdrop,hidden:a.hidden,field:d});return this.app.element_list[c]=f,this._append(f.$el,a.id),d},_append:function(a,b){this.$el.append(a.addClass("section-row").attr("id",b))}});return{View:g}});
|
||||
//# sourceMappingURL=../../../maps/mvc/form/form-section.js.map
|
||||
@@ -1,2 +1,2 @@
|
||||
define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{initial_errors:!1,cls:"ui-portlet-limited",icon:null,always_refresh:!0}),this.setElement("<div/>"),this.render()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[c];if(d&&d.options&&!_.isEqual(d.options,a.options)){d.options=a.options;var e=b.field_list[c];if(e.update){var f=[];if(["data","data_collection","drill_down"].indexOf(d.type)!=-1)f=d.options;else for(var g in a.options){var h=a.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+c)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&c[a?"wait":"unwait"]()}},highlight:function(a,b,c){var d=this.element_list[a];if(d&&(d.error(b||"Please verify this parameter."),this.portlet.expand(),this.trigger("expand",a),!c)){var e=this.$el.parents().filter(function(){return["auto","scroll"].indexOf($(this).css("overflow"))!=-1}).first();e.animate({scrollTop:e.scrollTop()+d.$el.offset().top-120},500)}},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){this.element_list[c];b[c]&&this.highlight(c,b[c],!0)}}},render:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e.Manager(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();return this.on("change",function(c){var d=a.input_list[c];if(!d||d.refresh_on_change||a.options.always_refresh){var e=a.data.checksum();e!=b&&(b=e,a.options.onchange&&a.options.onchange())}}),this.on("reset",function(){_.each(a.element_list,function(a){a.reset()})}),this},_renderForm:function(){$(".tooltip").remove(),this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.portlet=new b.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$el),this.portlet.append(this.section.$el),this.$el.empty(),this.options.inputs&&this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})});
|
||||
define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/form/form-section","mvc/form/form-data"],function(a,b,c,d,e){return Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{initial_errors:!1,cls:"ui-portlet-limited",icon:null,always_refresh:!0}),this.setElement("<div/>"),this.render()},update:function(a){var b=this;this.data.matchModel(a,function(a,c){var d=b.input_list[c];if(d&&d.options&&!_.isEqual(d.options,a.options)){d.options=a.options;var e=b.field_list[c];if(e.update){var f=[];if(-1!=["data","data_collection","drill_down"].indexOf(d.type))f=d.options;else for(var g in a.options){var h=a.options[g];h.length>2&&f.push({label:h[0],value:h[1]})}e.update(f),e.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+c)}}})},wait:function(a){for(var b in this.input_list){var c=this.field_list[b],d=this.input_list[b];d.is_dynamic&&c.wait&&c.unwait&&c[a?"wait":"unwait"]()}},highlight:function(a,b,c){var d=this.element_list[a];if(d&&(d.error(b||"Please verify this parameter."),this.portlet.expand(),this.trigger("expand",a),!c)){var e=this.$el.parents().filter(function(){return-1!=["auto","scroll"].indexOf($(this).css("overflow"))}).first();e.animate({scrollTop:e.scrollTop()+d.$el.offset().top-120},500)}},errors:function(a){if(this.trigger("reset"),a&&a.errors){var b=this.data.matchResponse(a.errors);for(var c in this.element_list){{this.element_list[c]}b[c]&&this.highlight(c,b[c],!0)}}},render:function(){var a=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new e.Manager(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var b=this.data.checksum();return this.on("change",function(c){var d=a.input_list[c];if(!d||d.refresh_on_change||a.options.always_refresh){var e=a.data.checksum();e!=b&&(b=e,a.options.onchange&&a.options.onchange())}}),this.on("reset",function(){_.each(a.element_list,function(a){a.reset()})}),this},_renderForm:function(){$(".tooltip").remove(),this.message=new c.Message,this.section=new d.View(this,{inputs:this.options.inputs}),this.portlet=new b.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$el),this.portlet.append(this.section.$el),this.$el.empty(),this.options.inputs&&this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})});
|
||||
//# sourceMappingURL=../../../maps/mvc/form/form-view.js.map
|
||||
@@ -1,2 +1,2 @@
|
||||
define(["mvc/ui/popup-menu","mvc/history/copy-dialog","mvc/base-mvc","utils/localization","mvc/webhooks"],function(a,b,c,d,e){"use strict";function f(a,b,c){return _.clone(g).filter(function(d){return a&&!d.anon?!1:!b&&d.purge?!1:(d.href&&(d.href=c+d.href,d.target="galaxy_main"),d.confirm&&(d.func=function(){confirm(d.confirm)&&(galaxy_main.location=d.href)}),!0)})}var g=[{html:d("History Lists"),header:!0},{html:d("Saved Histories"),href:"history/list"},{html:d("Histories Shared with Me"),href:"history/list_shared"},{html:d("History Actions"),header:!0,anon:!0},{html:d("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:d("Copy History"),func:function(){b(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:d("Share or Publish"),href:"history/sharing"},{html:d("Show Structure"),href:"history/display_structured",anon:!0},{html:d("Extract Workflow"),href:"workflow/build_from_current_history"},{html:d("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete the current history?"))&&(galaxy_main.window.location.href="history/delete?id="+Galaxy.currHistoryPanel.model.id)}},{html:d("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete the current history permanently? This cannot be undone."))&&(galaxy_main.window.location.href="history/delete?purge=True&id="+Galaxy.currHistoryPanel.model.id)}},{html:d("Dataset Actions"),header:!0,anon:!0},{html:d("Copy Datasets"),href:"dataset/copy_datasets"},{html:d("Dataset Security"),href:"root/history_set_default_permissions"},{html:d("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:d("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:d("Unhide Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really unhide all hidden datasets?"))){var a=Galaxy.currHistoryPanel.model.contents.hidden();a.ajaxQueue(Backbone.Model.prototype.save,{visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error unhiding the datasets"),console.error(arguments)})}}},{html:d("Delete Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete all hidden datasets?"))){var a=Galaxy.currHistoryPanel.model.contents.hidden();a.ajaxQueue(Backbone.Model.prototype.save,{deleted:!0,visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error deleting the datasets"),console.error(arguments)})}}},{html:d("Purge Deleted Datasets"),confirm:d("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:d("Downloads"),header:!0},{html:d("Export Tool Citations"),href:"history/citations",anon:!0},{html:d("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:d("Other Actions"),header:!0},{html:d("Import from File"),href:"history/import_archive"}];e.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(a){var b=[];$.each(a.models,function(a,c){var e=c.toJSON();e.activate&&b.push({html:d(e.config.title),anon:!0})}),b.length>0&&(b.unshift({html:d("Webhooks"),header:!0}),$.merge(g,b))}});var h=function(b,c){c=c||{};var d=void 0===c.anonymous?!0:c.anonymous,e=c.purgeAllowed||!1,g=f(d,e,Galaxy.root);return new a(b,g)};return h});
|
||||
define(["mvc/ui/popup-menu","mvc/history/copy-dialog","mvc/base-mvc","utils/localization","mvc/webhooks"],function(a,b,c,d,e){"use strict";function f(a,b,c){return _.clone(g).filter(function(d){return a&&!d.anon?!1:!b&&d.purge?!1:(d.href&&(d.href=c+d.href,d.target="galaxy_main"),d.confirm&&(d.func=function(){confirm(d.confirm)&&(galaxy_main.location=d.href)}),!0)})}var g=[{html:d("History Lists"),header:!0},{html:d("Saved Histories"),href:"history/list"},{html:d("Histories Shared with Me"),href:"history/list_shared"},{html:d("Current History"),header:!0,anon:!0},{html:d("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:d("Copy History"),func:function(){b(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:d("Share or Publish"),href:"history/sharing"},{html:d("Show Structure"),href:"history/display_structured",anon:!0},{html:d("Extract Workflow"),href:"workflow/build_from_current_history"},{html:d("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete the current history?"))&&(galaxy_main.window.location.href="history/delete?id="+Galaxy.currHistoryPanel.model.id)}},{html:d("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete the current history permanently? This cannot be undone."))&&(galaxy_main.window.location.href="history/delete?purge=True&id="+Galaxy.currHistoryPanel.model.id)}},{html:d("Dataset Actions"),header:!0,anon:!0},{html:d("Copy Datasets"),href:"dataset/copy_datasets"},{html:d("Dataset Security"),href:"root/history_set_default_permissions"},{html:d("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:d("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:d("Unhide Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really unhide all hidden datasets?"))){var a=Galaxy.currHistoryPanel.model.contents.hidden();a.ajaxQueue(Backbone.Model.prototype.save,{visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error unhiding the datasets"),console.error(arguments)})}}},{html:d("Delete Hidden Datasets"),anon:!0,func:function(){if(Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete all hidden datasets?"))){var a=Galaxy.currHistoryPanel.model.contents.hidden();a.ajaxQueue(Backbone.Model.prototype.save,{deleted:!0,visible:!0}).done(function(){Galaxy.currHistoryPanel.renderItems()}).fail(function(){alert("There was an error deleting the datasets"),console.error(arguments)})}}},{html:d("Purge Deleted Datasets"),confirm:d("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:d("Downloads"),header:!0},{html:d("Export Tool Citations"),href:"history/citations",anon:!0},{html:d("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:d("Other Actions"),header:!0},{html:d("Import from File"),href:"history/import_archive"}];e.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(a){var b=[];$.each(a.models,function(a,c){var e=c.toJSON();e.activate&&b.push({html:d(e.config.title),anon:!0})}),b.length>0&&(b.unshift({html:d("Webhooks"),header:!0}),$.merge(g,b))}});var h=function(b,c){c=c||{};var d=void 0===c.anonymous?!0:c.anonymous,e=c.purgeAllowed||!1,g=f(d,e,Galaxy.root);return new a(b,g)};return h});
|
||||
//# sourceMappingURL=../../../maps/mvc/history/options-menu.js.map
|
||||
@@ -1,2 +1,2 @@
|
||||
define(["mvc/form/form-view","mvc/ui/ui-misc"],function(a,b){var c=Backbone.View.extend({initialize:function(){this.defs={information:{title:"Manage information",description:"Edit your email, addresses and custom parameters or change your username.",url:"api/users/"+Galaxy.user.id+"/information/inputs",icon:"fa-user"},password:{title:"Change password",description:"Allows you to change your login credentials.",icon:"fa-unlock-alt",url:"api/users/"+Galaxy.user.id+"/password/inputs",submit_title:"Save password"},communication:{title:"Change communication settings",description:"Enable or disable the communication feature to chat with other users.",url:"api/users/"+Galaxy.user.id+"/communication/inputs",icon:"fa-comments-o"},permissions:{title:"Set dataset permissions for new histories",description:"Grant others default access to newly created histories. Changes made here will only affect histories created after these settings have been stored.",url:"api/users/"+Galaxy.user.id+"/permissions/inputs",icon:"fa-users",submit_title:"Save permissions"},api_key:{title:"Manage API key",description:"Access your current API key or create a new one.",url:"api/users/"+Galaxy.user.id+"/api_key/inputs",icon:"fa-key",submit_title:"Create a new key",submit_icon:"fa-check"},toolbox_filters:{title:"Manage Toolbox filters",description:"Customize your Toolbox by displaying or omitting sets of Tools.",url:"api/users/"+Galaxy.user.id+"/toolbox_filters/inputs",icon:"fa-filter",submit_title:"Save filters"},openids:{title:"Manage OpenIDs",description:"Associate OpenIDs with your account.",icon:"fa-openid",onclick:function(){window.location.href=Galaxy.root+"user/openid_manage?cntrller=user&use_panels=True"}},logout:{title:"Sign out",description:"Click here to sign out of all sessions.",icon:"fa-sign-out",onclick:function(){Galaxy.modal.show({title:"Sign out",body:"Do you want to continue and sign out of all active sessions?",buttons:{Cancel:function(){Galaxy.modal.hide()},"Sign out":function(){window.location.href=Galaxy.root+"user/logout"}}})}}},this.message=new b.Message,this.setElement("<div/>"),this.render()},render:function(){var a=this,b=Galaxy.config;$.getJSON(Galaxy.root+"api/users/"+Galaxy.user.id,function(c){a.$preferences=$("<div/>").addClass("ui-panel").append(a.message.$el).append($("<h2/>").append("User preferences")).append($("<p/>").append("You are logged in as <strong>"+_.escape(c.email)+"</strong>.")).append(a.$table=$("<table/>").addClass("ui-panel-table")),b.use_remote_user||(a._link(a.defs.information),a._link(a.defs.password)),b.enable_communication_server&&a._link(a.defs.communication),a._link(a.defs.permissions),a._link(a.defs.api_key),b.has_user_tool_filters&&a._link(a.defs.toolbox_filters),b.enable_openid&&!b.use_remote_user&&a._link(a.defs.openids),a._link(a.defs.logout),a.$preferences.append(a._templateFooter(c)),a.$el.empty().append(a.$preferences)})},_link:function(c){var d=this,e=$(this._templateRow(c));this.$table.append(e),e.find("a").on("click",function(){c.url?$.ajax({url:Galaxy.root+c.url,type:"GET"}).done(function(e){var f=$.extend({},c,e),g=new a({title:f.title,icon:f.icon,inputs:f.inputs,operations:{submit:new b.ButtonIcon({tooltip:f.submit_tooltip,title:f.submit_title||"Save settings",icon:f.submit_icon||"fa-save",onclick:function(){d._submit(g,f)}}),back:new b.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to user preferences",title:"Preferences",onclick:function(){g.remove(),d.$preferences.show()}})}});d.$preferences.hide(),d.$el.append(g.$el)}).fail(function(a){d.message.update({message:"Failed to load resource "+c.url+".",status:"danger"})}):c.onclick()})},_submit:function(a,b){var c=this;$.ajax({url:b.url,data:JSON.stringify(a.data.create()),type:"PUT",contentType:"application/json"}).done(function(b){var d=!1;a.data.matchModel(b,function(b,c){a.field_list[c].value(b.value),d=!0}),d?a.message.update({message:b.message,status:"success"}):(a.remove(),c.$preferences.show(),c.message.update({message:b.message,status:"success"}))}).fail(function(b){a.message.update({message:b.responseJSON.err_msg,status:"danger"})})},_templateRow:function(a){return'<tr><td><div class="ui-panel-icon fa '+a.icon+'"></td><td><a class="ui-panel-anchor" href="javascript:void(0)">'+a.title+'</a><div class="ui-form-info">'+a.description+"</div></td></tr>"},_templateFooter:function(a){return'<p class="ui-panel-footer">You are using <strong>'+a.nice_total_disk_usage+"</strong> of disk space in this Galaxy instance. "+(Galaxy.config.enable_quotas?"Your disk quota is: <strong>"+a.quota+"</strong>. ":"")+'Is your usage more than expected? See the <a href="https://wiki.galaxyproject.org/Learn/ManagingDatasets" target="_blank">documentation</a> for tips on how to find all of the data in your account.</p>'}});return{View:c}});
|
||||
define(["mvc/form/form-view","mvc/ui/ui-misc"],function(a,b){var c=Backbone.View.extend({initialize:function(){this.defs={information:{title:"Manage information",description:"Edit your email, addresses and custom parameters or change your username.",url:"api/users/"+Galaxy.user.id+"/information/inputs",icon:"fa-user"},password:{title:"Change password",description:"Allows you to change your login credentials.",icon:"fa-unlock-alt",url:"api/users/"+Galaxy.user.id+"/password/inputs",submit_title:"Save password"},communication:{title:"Change communication settings",description:"Enable or disable the communication feature to chat with other users.",url:"api/users/"+Galaxy.user.id+"/communication/inputs",icon:"fa-comments-o"},permissions:{title:"Set dataset permissions for new histories",description:"Grant others default access to newly created histories. Changes made here will only affect histories created after these settings have been stored.",url:"api/users/"+Galaxy.user.id+"/permissions/inputs",icon:"fa-users",submit_title:"Save permissions"},api_key:{title:"Manage API key",description:"Access your current API key or create a new one.",url:"api/users/"+Galaxy.user.id+"/api_key/inputs",icon:"fa-key",submit_title:"Create a new key",submit_icon:"fa-check"},toolbox_filters:{title:"Manage Toolbox filters",description:"Customize your Toolbox by displaying or omitting sets of Tools.",url:"api/users/"+Galaxy.user.id+"/toolbox_filters/inputs",icon:"fa-filter",submit_title:"Save filters"},openids:{title:"Manage OpenIDs",description:"Associate OpenIDs with your account.",icon:"fa-openid",onclick:function(){window.location.href=Galaxy.root+"user/openid_manage?cntrller=user&use_panels=True"}},logout:{title:"Sign out",description:"Click here to sign out of all sessions.",icon:"fa-sign-out",onclick:function(){Galaxy.modal.show({title:"Sign out",body:"Do you want to continue and sign out of all active sessions?",buttons:{Cancel:function(){Galaxy.modal.hide()},"Sign out":function(){window.location.href=Galaxy.root+"user/logout"}}})}}},this.message=new b.Message,this.setElement("<div/>"),this.render()},render:function(){var a=this,b=Galaxy.config;$.getJSON(Galaxy.root+"api/users/"+Galaxy.user.id,function(c){a.$preferences=$("<div/>").addClass("ui-panel").append(a.message.$el).append($("<h2/>").append("User preferences")).append($("<p/>").append("You are logged in as <strong>"+_.escape(c.email)+"</strong>.")).append(a.$table=$("<table/>").addClass("ui-panel-table")),b.use_remote_user||(a._link(a.defs.information),a._link(a.defs.password)),b.enable_communication_server&&a._link(a.defs.communication),a._link(a.defs.permissions),a._link(a.defs.api_key),b.has_user_tool_filters&&a._link(a.defs.toolbox_filters),b.enable_openid&&!b.use_remote_user&&a._link(a.defs.openids),a._link(a.defs.logout),a.$preferences.append(a._templateFooter(c)),a.$el.empty().append(a.$preferences)})},_link:function(c){var d=this,e=$(this._templateRow(c));this.$table.append(e),e.find("a").on("click",function(){c.url?$.ajax({url:Galaxy.root+c.url,type:"GET"}).done(function(e){var f=$.extend({},c,e),g=new a({title:f.title,icon:f.icon,inputs:f.inputs,operations:{submit:new b.ButtonIcon({tooltip:f.submit_tooltip,title:f.submit_title||"Save settings",icon:f.submit_icon||"fa-save",onclick:function(){d._submit(g,f)}}),back:new b.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to user preferences",title:"Preferences",onclick:function(){g.remove(),d.$preferences.show()}})}});d.$preferences.hide(),d.$el.append(g.$el)}).fail(function(){d.message.update({message:"Failed to load resource "+c.url+".",status:"danger"})}):c.onclick()})},_submit:function(a,b){var c=this;$.ajax({url:b.url,data:JSON.stringify(a.data.create()),type:"PUT",contentType:"application/json"}).done(function(b){var d=!1;a.data.matchModel(b,function(b,c){a.field_list[c].value(b.value),d=!0}),d?a.message.update({message:b.message,status:"success"}):(a.remove(),c.$preferences.show(),c.message.update({message:b.message,status:"success"}))}).fail(function(b){a.message.update({message:b.responseJSON.err_msg,status:"danger"})})},_templateRow:function(a){return'<tr><td><div class="ui-panel-icon fa '+a.icon+'"></td><td><a class="ui-panel-anchor" href="javascript:void(0)">'+a.title+'</a><div class="ui-form-info">'+a.description+"</div></td></tr>"},_templateFooter:function(a){return'<p class="ui-panel-footer">You are using <strong>'+a.nice_total_disk_usage+"</strong> of disk space in this Galaxy instance. "+(Galaxy.config.enable_quotas?"Your disk quota is: <strong>"+a.quota+"</strong>. ":"")+'Is your usage more than expected? See the <a href="https://wiki.galaxyproject.org/Learn/ManagingDatasets" target="_blank">documentation</a> for tips on how to find all of the data in your account.</p>'}});return{View:c}});
|
||||
//# sourceMappingURL=../../../maps/mvc/user/user-preferences.js.map
|
||||
File diff suppressed because one or more lines are too long
@@ -13,7 +13,7 @@
|
||||
onPostInit: function(isReloading, isError) {
|
||||
// Re-fire onActivate, so the text is updated
|
||||
this.reactivate();
|
||||
},
|
||||
},
|
||||
fx: { height: "toggle", duration: 200 },
|
||||
// initAjax is hard to fake, so we pass the children as object array:
|
||||
initAjax: {url: "${h.url_for( controller='admin_toolshed', action='open_folder' )}",
|
||||
@@ -71,11 +71,27 @@
|
||||
width:100%;
|
||||
overflow-wrap:normal;
|
||||
overflow:hidden;
|
||||
border:0px;
|
||||
border:0px;
|
||||
word-break:keep-all;
|
||||
word-wrap:break-word;
|
||||
line-break:strict; }
|
||||
</style>
|
||||
<script type="text/javascript">
|
||||
$(function(){
|
||||
$(".detail-section").hide();
|
||||
var hidden = true;
|
||||
$(".toggle-detail-section").click(function(e){
|
||||
e.preventDefault();
|
||||
hidden = !hidden;
|
||||
if (hidden === true){
|
||||
$(".toggle-detail-section").text('Display Details');
|
||||
} else{
|
||||
$(".toggle-detail-section").text('Hide Details');
|
||||
}
|
||||
$(".detail-section").toggle();
|
||||
})
|
||||
});
|
||||
</script>
|
||||
<%
|
||||
from markupsafe import escape
|
||||
class RowCounter( object ):
|
||||
@@ -97,20 +113,31 @@
|
||||
else:
|
||||
revision_label_str = ' '
|
||||
%>
|
||||
<div class="form-row">
|
||||
<p>
|
||||
By default Galaxy will install all needed dependencies for${revision_label_str}the repository. See the
|
||||
<a target="_blank" href="https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html">
|
||||
dependency resolver documentation
|
||||
</a>.
|
||||
</p>
|
||||
<p>
|
||||
You can control how dependencies are installed (this is an advanced option, if in doubt, use the default)
|
||||
<button class="toggle-detail-section">
|
||||
Display Details
|
||||
</button>
|
||||
</p>
|
||||
</div>
|
||||
%if export:
|
||||
<div class="form-row">
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
<p>
|
||||
%if export:
|
||||
The following additional repositories are required by${revision_label_str}the <b>${repository.name|h}</b> repository
|
||||
and they can be exported as well.
|
||||
%else:
|
||||
These dependencies can be automatically handled with${revision_label_str}the installed repository, providing significant
|
||||
benefits, and Galaxy includes various features to manage them.
|
||||
%endif
|
||||
The following additional repositories are required by${revision_label_str}the <b>${repository.name|h}</b> repository and they can be exported as well.
|
||||
</p>
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
<div style="clear: both"></div>
|
||||
<div class="detail-section">
|
||||
%if repository_dependencies_root_folder or missing_repository_dependencies_root_folder:
|
||||
%if repository_dependencies_check_box:
|
||||
<div class="form-row">
|
||||
@@ -124,7 +151,7 @@
|
||||
%if export:
|
||||
Select to export the following additional repositories that are required by this repository.
|
||||
%else:
|
||||
Select to automatically install these additional repositories required by this repository.
|
||||
Select to automatically install these additional Tool Shed repositories required by this repository.
|
||||
%endif
|
||||
</div>
|
||||
</div>
|
||||
@@ -154,14 +181,14 @@
|
||||
%if tool_dependencies_root_folder or missing_tool_dependencies_root_folder:
|
||||
%if install_tool_dependencies_check_box is not None:
|
||||
<div class="form-row">
|
||||
<label>When available, install tool shed managed dependencies?</label>
|
||||
<label>When available, install Tool Shed managed tool dependencies?</label>
|
||||
<% disabled = trans.app.config.tool_dependency_dir is None %>
|
||||
${install_tool_dependencies_check_box.get_html( disabled=disabled )}
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
%if disabled:
|
||||
Set the tool_dependency_dir configuration value in your Galaxy config to automatically handle tool dependencies.
|
||||
%else:
|
||||
Select to automatically handle tool dependencies.
|
||||
Select to automatically handle tool dependencies via Tool Shed.
|
||||
%endif
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
@@ -191,13 +218,14 @@
|
||||
<div style="clear: both"></div>
|
||||
%if install_resolver_dependencies_check_box:
|
||||
<div class="form-row">
|
||||
<label>When available, install externally managed dependencies (e.g. conda)? <i>Beta</i></label>
|
||||
<label>When available, install <a href="https://docs.galaxyproject.org/en/master/admin/conda_faq.html" target="_blank">Conda</a> managed tool dependencies?</label>
|
||||
${install_resolver_dependencies_check_box.get_html()}
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Select to automatically install tool dependencies.
|
||||
Select to automatically install tool dependencies via Conda.
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
</div>
|
||||
</%def>
|
||||
|
||||
<%def name="render_readme_section( containers_dict )">
|
||||
@@ -225,8 +253,8 @@
|
||||
|
||||
<%def name="dependency_status_updater()">
|
||||
<script type="text/javascript">
|
||||
// Tool dependency status updater - used to update the installation status on the Tool Dependencies Grid.
|
||||
// Looks for changes in tool dependency installation status using an async request. Keeps calling itself
|
||||
// Tool dependency status updater - used to update the installation status on the Tool Dependencies Grid.
|
||||
// Looks for changes in tool dependency installation status using an async request. Keeps calling itself
|
||||
// (via setTimeout) until dependency installation status is neither 'Installing' nor 'Building'.
|
||||
var tool_dependency_status_updater = function( dependency_status_list ) {
|
||||
// See if there are any items left to track
|
||||
@@ -264,7 +292,7 @@
|
||||
cell1.html( val[ 'html_status' ] );
|
||||
dependency_status_list[ index ] = val;
|
||||
});
|
||||
tool_dependency_status_updater( dependency_status_list );
|
||||
tool_dependency_status_updater( dependency_status_list );
|
||||
},
|
||||
});
|
||||
};
|
||||
@@ -273,7 +301,7 @@
|
||||
|
||||
<%def name="repository_installation_status_updater()">
|
||||
<script type="text/javascript">
|
||||
// Tool shed repository status updater - used to update the installation status on the Repository Installation Grid.
|
||||
// Tool shed repository status updater - used to update the installation status on the Repository Installation Grid.
|
||||
// Looks for changes in repository installation status using an async request. Keeps calling itself (via setTimeout) until
|
||||
// repository installation status is not one of: 'New', 'Cloning', 'Setting tool versions', 'Installing tool dependencies',
|
||||
// 'Loading proprietary datatypes'.
|
||||
@@ -319,7 +347,7 @@
|
||||
cell1.html( val[ 'html_status' ] );
|
||||
repository_status_list[ index ] = val;
|
||||
});
|
||||
tool_shed_repository_status_updater( repository_status_list );
|
||||
tool_shed_repository_status_updater( repository_status_list );
|
||||
},
|
||||
});
|
||||
};
|
||||
@@ -327,7 +355,7 @@
|
||||
</%def>
|
||||
|
||||
<%def name="tool_dependency_installation_updater()">
|
||||
<%
|
||||
<%
|
||||
can_update = False
|
||||
if query.count():
|
||||
# Get the first tool dependency to get to the tool shed repository.
|
||||
|
||||
@@ -55,7 +55,7 @@
|
||||
sending all necessary information, and appropriate action will be taken.
|
||||
</p>
|
||||
<p>
|
||||
<a href="https://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Contact_repository_owner" target="_blank">Contact the repository owner</a> for
|
||||
<a href="https://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Contact_repository_owner" target="_blank">Contact the repository owner</a> for
|
||||
general questions or concerns.
|
||||
</p>
|
||||
</div>
|
||||
@@ -100,6 +100,7 @@
|
||||
<th bgcolor="#EBD9B2">Choose the tool panel section to contain the installed tools (optional)</th>
|
||||
</table>
|
||||
</div>
|
||||
<div class="detail-section">
|
||||
<%
|
||||
if len( shed_tool_conf_select_field.options ) == 1:
|
||||
select_help = "Your Galaxy instance is configured with 1 shed-related tool configuration file, so repositories will be "
|
||||
@@ -116,6 +117,7 @@
|
||||
</div>
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
%else:
|
||||
<input type="hidden" name="shed_tool_conf" value="${shed_tool_conf|h}"/>
|
||||
%endif
|
||||
@@ -130,7 +132,7 @@
|
||||
<label>Select existing tool panel section:</label>
|
||||
${tool_panel_section_select_field.get_html()}
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Choose an existing section in your tool panel to contain the installed tools (optional).
|
||||
Choose an existing section in your tool panel to contain the installed tools (optional).
|
||||
</div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
|
||||
+1
-1
@@ -103,7 +103,7 @@ class ToolWithToolDependencies( ShedTwillTestCase ):
|
||||
|
||||
def test_0015_install_freebayes_repository( self ):
|
||||
'''Install the freebayes repository without installing tool dependencies.'''
|
||||
strings_displayed = [ 'Never installed', 'dependencies can be automatically handled', 'install tool shed managed', 'tool dependencies' ]
|
||||
strings_displayed = [ 'Never installed', 'install all needed dependencies', 'install Tool Shed managed', 'tool dependencies' ]
|
||||
strings_displayed.extend( [ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18' ] )
|
||||
self.install_repository( repository_name,
|
||||
common.test_user_1_name,
|
||||
|
||||
+1
-1
@@ -89,7 +89,7 @@ class UninstallingAndReinstallingRepositories( ShedTwillTestCase ):
|
||||
def test_0010_install_freebayes_repository( self ):
|
||||
'''Install the freebayes repository into the Galaxy instance.'''
|
||||
self.galaxy_login( email=common.admin_email, username=common.admin_username )
|
||||
strings_displayed = [ 'install tool shed managed', 'tool dependencies', 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18' ]
|
||||
strings_displayed = [ 'install Tool Shed managed', 'tool dependencies', 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18' ]
|
||||
self.install_repository( 'freebayes_0010',
|
||||
common.test_user_1_name,
|
||||
'Test 0010 Repository With Tool Dependencies',
|
||||
|
||||
Reference in New Issue
Block a user