commit/galaxy-central: 2 new changesets
2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c16fea918b33/ Changeset: c16fea918b33 Branch: next-stable User: jmchilton Date: 2014-11-26 01:52:30+00:00 Summary: Fixes for /dataset_collections API endpoint. Guess this is not as utilized as the variant under /histories. Affected #: 1 file diff -r 2d80e9cfb833b7cf50d5f60ae77368bc966ca29a -r c16fea918b33fd4e1ec52c3b5c38981d9c88cfa0 lib/galaxy/webapps/galaxy/api/dataset_collections.py --- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py +++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py @@ -56,7 +56,8 @@ @expose_api def show( self, trans, instance_type, id, **kwds ): - dataset_collection_instance = self.__service( trans ).get( + dataset_collection_instance = self.__service( trans ).get_dataset_collection_instance( + trans, id=id, instance_type=instance_type, ) @@ -67,7 +68,12 @@ else: trans.status = 501 return - return dictify_dataset_collection_instance( trans, dataset_collection_instance, parent ) + return dictify_dataset_collection_instance( + dataset_collection_instance, + security=trans.security, + parent=parent, + view='element' + ) def __service( self, trans ): service = trans.app.dataset_collections_service https://bitbucket.org/galaxy/galaxy-central/commits/bfa13d090966/ Changeset: bfa13d090966 User: jmchilton Date: 2014-11-26 01:53:50+00:00 Summary: Merge next-stable into default. Affected #: 12 files diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 client/galaxy/scripts/galaxy.masthead.js --- a/client/galaxy/scripts/galaxy.masthead.js +++ b/client/galaxy/scripts/galaxy.masthead.js @@ -251,28 +251,31 @@ }, // initialize - initialize: function (options){ + initialize: function ( options ){ // read in defaults - if (options) - this.options = _.defaults(options, this.options); - + if ( options ){ + this.options = _.defaults( options, this.options ); + } + // update url - if (this.options.content && this.options.content.indexOf('//') === -1) + if ( this.options.content !== undefined && this.options.content.indexOf( '//' ) === -1 ){ this.options.content = galaxy_config.root + this.options.content; + } // add template for tab - this.setElement($(this._template(this.options))); + this.setElement( $( this._template( this.options ) ) ); // disable menu items that are not available to anonymous user // also show title to explain why they are disabled - if (this.options.disabled){ - $(this.el).find('.root').addClass('disabled'); + if ( this.options.disabled ){ + $( this.el ).find( '.root' ).addClass( 'disabled' ); this._attachPopover(); } // visiblity - if (!this.options.visible) + if ( !this.options.visible ){ this.hide(); + } }, // show diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 client/galaxy/scripts/galaxy.menu.js --- a/client/galaxy/scripts/galaxy.menu.js +++ b/client/galaxy/scripts/galaxy.menu.js @@ -167,7 +167,7 @@ var tab_admin = new mod_masthead.GalaxyMastheadTab({ id : "admin", title : "Admin", - content : "admin/index", + content : "admin", extra_class : "admin-only", title_attribute : 'Administer this Galaxy' }); diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 lib/galaxy/webapps/galaxy/api/dataset_collections.py --- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py +++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py @@ -56,7 +56,8 @@ @expose_api def show( self, trans, instance_type, id, **kwds ): - dataset_collection_instance = self.__service( trans ).get( + dataset_collection_instance = self.__service( trans ).get_dataset_collection_instance( + trans, id=id, instance_type=instance_type, ) @@ -67,7 +68,12 @@ else: trans.status = 501 return - return dictify_dataset_collection_instance( trans, dataset_collection_instance, parent ) + return dictify_dataset_collection_instance( + dataset_collection_instance, + security=trans.security, + parent=parent, + view='element' + ) def __service( self, trans ): service = trans.app.dataset_collections_service diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -9,8 +9,7 @@ from galaxy.util.sanitize_html import sanitize_html from galaxy.util.json import loads from galaxy.web.base.controller import BaseUIController, ERROR, SUCCESS, url_for, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesExtendedMetadataMixin -from galaxy.web.framework.helpers import grids, iff, time_ago -from galaxy.web.framework.helpers import to_unicode +from galaxy.web.framework.helpers import grids, iff, time_ago, to_unicode, escape from galaxy.tools.errors import EmailErrorReporter eggs.require( "Paste" ) @@ -506,7 +505,7 @@ # Set referer message. referer = trans.request.referer if referer is not "": - referer_message = "<a href='%s'>return to the previous page</a>" % referer + referer_message = "<a href='%s'>return to the previous page</a>" % escape(referer) else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) # Error checking. diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -19,7 +19,7 @@ from galaxy.web.base.controller import ExportsHistoryMixin from galaxy.web.base.controller import ImportsHistoryMixin from galaxy.web.base.controller import ERROR, INFO, SUCCESS, WARNING -from galaxy.web.framework.helpers import grids, iff, time_ago +from galaxy.web.framework.helpers import grids, iff, time_ago, escape log = logging.getLogger( __name__ ) @@ -1291,7 +1291,7 @@ else: referer = trans.request.referer if referer is not "": - referer_message = "<a href='%s'>return to the previous page</a>" % referer + referer_message = "<a href='%s'>return to the previous page</a>" % escape(referer) else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -611,8 +611,8 @@ else: refresh_frames = [ 'masthead' ] trans.handle_user_logout( logout_all=logout_all ) - message = 'You have been logged out.<br>You can log in again, <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \ - ( trans.request.referer, url_for( '/' ) ) + message = 'You have been logged out.<br>To log in again <a target="_top" href="%s">go to the home page</a>.' % \ + ( url_for( '/' ) ) if biostar.biostar_logged_in( trans ): biostar_url = biostar.biostar_logout( trans ) if biostar_url: diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -9,7 +9,7 @@ from galaxy import model, web from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesVisualizationMixin -from galaxy.web.framework.helpers import time_ago, grids +from galaxy.web.framework.helpers import time_ago, grids, escape from galaxy import util from galaxy.datatypes.interval import Bed from galaxy.util.json import loads @@ -123,7 +123,7 @@ # or_( "metadata like '%%\"dbkey\": [\"?\"]%%'", "metadata like '%%\"dbkey\": \"?\"%%'" ) \ # ) # ) - + class HistoryColumn( grids.GridColumn ): """ Column for filtering by history id. """ @@ -360,7 +360,7 @@ @web.expose @web.require_login( "use Galaxy visualizations", use_panels=True ) def list( self, trans, *args, **kwargs ): - + # Handle operation if 'operation' in kwargs and 'id' in kwargs: session = trans.sa_session @@ -388,7 +388,7 @@ kwargs[ 'embedded' ] = True grid = self._user_list_grid( trans, *args, **kwargs ) return trans.fill_template( "visualization/list.mako", embedded_grid=grid, shared_by_others=shared_by_others ) - + # # -- Functions for operating on visualizations. -- # @@ -459,7 +459,7 @@ # Set referer message. referer = trans.request.referer if referer is not "": - referer_message = "<a href='%s'>return to the previous page</a>" % referer + referer_message = "<a href='%s'>return to the previous page</a>" % escape(referer) else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % web.url_for( '/' ) diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -22,8 +22,7 @@ from galaxy.web import error, url_for from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesStoredWorkflowMixin from galaxy.web.framework.formbuilder import form -from galaxy.web.framework.helpers import grids, time_ago -from galaxy.web.framework.helpers import to_unicode +from galaxy.web.framework.helpers import grids, time_ago, to_unicode, escape from galaxy.workflow.modules import WorkflowModuleInjector from galaxy.workflow.modules import MissingToolException from galaxy.workflow.modules import module_factory, is_tool_module_type @@ -389,7 +388,7 @@ # Set referer message. referer = trans.request.referer if referer is not "": - referer_message = "<a href='%s'>return to the previous page</a>" % referer + referer_message = "<a href='%s'>return to the previous page</a>" % escape(referer) else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 static/scripts/galaxy.masthead.js --- a/static/scripts/galaxy.masthead.js +++ b/static/scripts/galaxy.masthead.js @@ -251,28 +251,31 @@ }, // initialize - initialize: function (options){ + initialize: function ( options ){ // read in defaults - if (options) - this.options = _.defaults(options, this.options); - + if ( options ){ + this.options = _.defaults( options, this.options ); + } + // update url - if (this.options.content && this.options.content.indexOf('//') === -1) + if ( this.options.content !== undefined && this.options.content.indexOf( '//' ) === -1 ){ this.options.content = galaxy_config.root + this.options.content; + } // add template for tab - this.setElement($(this._template(this.options))); + this.setElement( $( this._template( this.options ) ) ); // disable menu items that are not available to anonymous user // also show title to explain why they are disabled - if (this.options.disabled){ - $(this.el).find('.root').addClass('disabled'); + if ( this.options.disabled ){ + $( this.el ).find( '.root' ).addClass( 'disabled' ); this._attachPopover(); } // visiblity - if (!this.options.visible) + if ( !this.options.visible ){ this.hide(); + } }, // show diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -167,7 +167,7 @@ var tab_admin = new mod_masthead.GalaxyMastheadTab({ id : "admin", title : "Admin", - content : "admin/index", + content : "admin", extra_class : "admin-only", title_attribute : 'Administer this Galaxy' }); diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 static/scripts/packed/galaxy.masthead.js --- a/static/scripts/packed/galaxy.masthead.js +++ b/static/scripts/packed/galaxy.masthead.js @@ -1,1 +1,1 @@ -define([],function(){var a=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(e){this.options=e;$("body").off();this.setElement($(this._template(e)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var d=this;$(window).on("beforeunload",function(){var g="";for(key in d.list){if(d.list[key].options.onunload){var f=d.list[key].options.onunload();if(f){g+=f+" "}}}if(g!=""){return g}})},events:{click:"_click",mousedown:function(d){d.preventDefault()}},append:function(d){return this._add(d,true)},prepend:function(d){return this._add(d,false)},highlight:function(e){var d=$(this.el).find("#"+e+"> li");if(d){d.addClass("active")}},_add:function(g,e){var d=$(this.el).find("#"+g.location);if(d){var f=$(g.el);f.addClass("masthead-item");if(e){d.append(f)}else{d.prepend(f)}this.list.push(g)}return null},_click:function(g){var f=$(this.el).find(".popup");if(f){f.hide()}var d=$(g.target).closest(".masthead-item").find(".popup");if($(g.target).hasClass("head")){d.show();this.$background.show()}else{this.$background.hide()}},_template:function(d){var e=d.brand?("/ "+d.brand):"";return'<div><div id="masthead" class="navbar navbar-fixed-top navbar-inverse"><div style="position: relative; right: -50%; float: left;"><div id="navbar" style="display: block; position: relative; right: 50%;"></div></div><div class="navbar-brand"><a href="'+d.logo_url+'"><img border="0" src="'+galaxy_config.root+'static/images/galaxyIcon_noText.png"><span id="brand"> Galaxy '+e+'</span></a></div><div class="quota-meter-container"></div><div id="iconbar" class="iconbar"></div></div><div id="masthead-background" style="display: none; position: absolute; top: 33px; width: 100%; height: 100%; z-index: 1010"></div></div>'}});var b=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:false,onclick:function(){alert("clicked")},onunload:null,visible:true},location:"iconbar",initialize:function(e){if(e){this.options=_.defaults(e,this.options)}this.setElement($(this._template(this.options)));var d=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",d.options.onclick);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(d){$(this.el).find(".icon").removeClass(this.options.icon).addClass(d);this.options.icon=d},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(d){$(this.el).find(".number").text(d)},_template:function(e){var d='<div id="'+e.id+'" class="symbol"><div class="icon fa fa-2x '+e.icon+'"></div>';if(e.with_number){d+='<div class="number"></div>'}d+="</div>";return d}});var c=Backbone.View.extend({options:{id:"",title:"",target:"_parent",content:"",type:"url",scratchbook:false,onunload:null,visible:true,disabled:false,title_attribute:""},location:"navbar",$menu:null,events:{"click .head":"_head"},initialize:function(d){if(d){this.options=_.defaults(d,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(this.options.disabled){$(this.el).find(".root").addClass("disabled");this._attachPopover()}if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},add:function(f){var g={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(f){g=_.defaults(f,g)}if(g.content&&g.content.indexOf("//")===-1){g.content=galaxy_config.root+g.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".popup")}var e=$(this._templateMenuItem(g));this.$menu.append(e);var d=this;e.on("click",function(h){h.preventDefault();if(d.options.target==="_blank"){return true}Galaxy.frame.add(f)});if(g.divider){this.$menu.append($(this._templateDivider()))}},_head:function(d){d.preventDefault();if(this.options.disabled){return}if(!this.$menu){Galaxy.frame.add(this.options)}},_attachPopover:function(){var d=$(this.el).find(".head");d.popover({html:true,content:'Please <a href="'+galaxy_config.root+'/user/login">log in</a> or <a href="'+galaxy_config.root+'/user/create">register</a> to use this feature.',placement:"bottom"}).on("shown.bs.popover",function(){setTimeout(function(){d.popover("hide")},5000)})},_templateMenuItem:function(d){return'<li><a href="'+d.content+'" target="'+d.target+'">'+d.title+"</a></li>"},_templateMenu:function(){return'<ul class="popup dropdown-menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var d='<ul id="'+e.id+'" class="nav navbar-nav" border="0" cellspacing="0"><li class="root dropdown" style=""><a class="head dropdown-toggle" data-toggle="dropdown" target="'+e.target+'" href="'+e.content+'" title="'+e.title_attribute+'">'+e.title+'<b class="symbol"></b></a></li></ul>';return d}});return{GalaxyMasthead:a,GalaxyMastheadTab:c,GalaxyMastheadIcon:b}}); \ No newline at end of file +define([],function(){var a=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(e){this.options=e;$("body").off();this.setElement($(this._template(e)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var d=this;$(window).on("beforeunload",function(){var g="";for(key in d.list){if(d.list[key].options.onunload){var f=d.list[key].options.onunload();if(f){g+=f+" "}}}if(g!=""){return g}})},events:{click:"_click",mousedown:function(d){d.preventDefault()}},append:function(d){return this._add(d,true)},prepend:function(d){return this._add(d,false)},highlight:function(e){var d=$(this.el).find("#"+e+"> li");if(d){d.addClass("active")}},_add:function(g,e){var d=$(this.el).find("#"+g.location);if(d){var f=$(g.el);f.addClass("masthead-item");if(e){d.append(f)}else{d.prepend(f)}this.list.push(g)}return null},_click:function(g){var f=$(this.el).find(".popup");if(f){f.hide()}var d=$(g.target).closest(".masthead-item").find(".popup");if($(g.target).hasClass("head")){d.show();this.$background.show()}else{this.$background.hide()}},_template:function(d){var e=d.brand?("/ "+d.brand):"";return'<div><div id="masthead" class="navbar navbar-fixed-top navbar-inverse"><div style="position: relative; right: -50%; float: left;"><div id="navbar" style="display: block; position: relative; right: 50%;"></div></div><div class="navbar-brand"><a href="'+d.logo_url+'"><img border="0" src="'+galaxy_config.root+'static/images/galaxyIcon_noText.png"><span id="brand"> Galaxy '+e+'</span></a></div><div class="quota-meter-container"></div><div id="iconbar" class="iconbar"></div></div><div id="masthead-background" style="display: none; position: absolute; top: 33px; width: 100%; height: 100%; z-index: 1010"></div></div>'}});var b=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:false,onclick:function(){alert("clicked")},onunload:null,visible:true},location:"iconbar",initialize:function(e){if(e){this.options=_.defaults(e,this.options)}this.setElement($(this._template(this.options)));var d=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",d.options.onclick);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(d){$(this.el).find(".icon").removeClass(this.options.icon).addClass(d);this.options.icon=d},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(d){$(this.el).find(".number").text(d)},_template:function(e){var d='<div id="'+e.id+'" class="symbol"><div class="icon fa fa-2x '+e.icon+'"></div>';if(e.with_number){d+='<div class="number"></div>'}d+="</div>";return d}});var c=Backbone.View.extend({options:{id:"",title:"",target:"_parent",content:"",type:"url",scratchbook:false,onunload:null,visible:true,disabled:false,title_attribute:""},location:"navbar",$menu:null,events:{"click .head":"_head"},initialize:function(d){if(d){this.options=_.defaults(d,this.options)}if(this.options.content!==undefined&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(this.options.disabled){$(this.el).find(".root").addClass("disabled");this._attachPopover()}if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},add:function(f){var g={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(f){g=_.defaults(f,g)}if(g.content&&g.content.indexOf("//")===-1){g.content=galaxy_config.root+g.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".popup")}var e=$(this._templateMenuItem(g));this.$menu.append(e);var d=this;e.on("click",function(h){h.preventDefault();if(d.options.target==="_blank"){return true}Galaxy.frame.add(f)});if(g.divider){this.$menu.append($(this._templateDivider()))}},_head:function(d){d.preventDefault();if(this.options.disabled){return}if(!this.$menu){Galaxy.frame.add(this.options)}},_attachPopover:function(){var d=$(this.el).find(".head");d.popover({html:true,content:'Please <a href="'+galaxy_config.root+'/user/login">log in</a> or <a href="'+galaxy_config.root+'/user/create">register</a> to use this feature.',placement:"bottom"}).on("shown.bs.popover",function(){setTimeout(function(){d.popover("hide")},5000)})},_templateMenuItem:function(d){return'<li><a href="'+d.content+'" target="'+d.target+'">'+d.title+"</a></li>"},_templateMenu:function(){return'<ul class="popup dropdown-menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var d='<ul id="'+e.id+'" class="nav navbar-nav" border="0" cellspacing="0"><li class="root dropdown" style=""><a class="head dropdown-toggle" data-toggle="dropdown" target="'+e.target+'" href="'+e.content+'" title="'+e.title_attribute+'">'+e.title+'<b class="symbol"></b></a></li></ul>';return d}});return{GalaxyMasthead:a,GalaxyMastheadTab:c,GalaxyMastheadIcon:b}}); \ No newline at end of file diff -r ce8a617dcdb199e97e7d4249f548e78a4530d18a -r bfa13d090966889c74512497bfcaafb732c08a41 static/scripts/packed/galaxy.menu.js --- a/static/scripts/packed/galaxy.menu.js +++ b/static/scripts/packed/galaxy.menu.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var e=new b.GalaxyMastheadTab({id:"analysis",title:"Analyze Data",content:"",title_attribute:"Analysis home view"});this.masthead.append(e);var g={id:"workflow",title:"Workflow",content:"workflow",title_attribute:"Chain tools into workflows"};if(!this.options.user.valid){g.disabled=true}var d=new b.GalaxyMastheadTab(g);this.masthead.append(d);var i=new b.GalaxyMastheadTab({id:"shared",title:"Shared Data",content:"library/index",title_attribute:"Access published resources"});i.add({title:"Data Libraries",content:"library/index"});i.add({title:"Data Libraries Beta",content:"library/list",divider:true});i.add({title:"Published Histories",content:"history/list_published"});i.add({title:"Published Workflows",content:"workflow/list_published"});i.add({title:"Published Visualizations",content:"visualization/list_published"});i.add({title:"Published Pages",content:"page/list_published"});this.masthead.append(i);if(this.options.user.requests){var j=new b.GalaxyMastheadTab({id:"lab",title:"Lab"});j.add({title:"Sequencing Requests",content:"requests/index"});j.add({title:"Find Samples",content:"requests/find_samples_index"});j.add({title:"Help",content:this.options.lims_doc_url});this.masthead.append(j)}var c={id:"visualization",title:"Visualization",content:"visualization/list",title_attribute:"Visualize datasets"};if(!this.options.user.valid){c.disabled=true}var m=new b.GalaxyMastheadTab(c);if(this.options.user.valid){m.add({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});m.add({title:"Saved Visualizations",content:"visualization/list",target:"_frame"})}this.masthead.append(m);if(this.options.enable_cloud_launch){var f=new b.GalaxyMastheadTab({id:"cloud",title:"Cloud",content:"cloudlaunch/index"});f.add({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(f)}if(this.options.is_admin_user){var h=new b.GalaxyMastheadTab({id:"admin",title:"Admin",content:"admin/index",extra_class:"admin-only",title_attribute:"Administer this Galaxy"});this.masthead.append(h)}var l=new b.GalaxyMastheadTab({id:"help",title:"Help",title_attribute:"Support, contact, and community hubs"});if(this.options.biostar_url){l.add({title:"Galaxy Biostar",content:this.options.biostar_url_redirect,target:"_blank"});l.add({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}l.add({title:"Support",content:this.options.support_url,target:"_blank"});l.add({title:"Search",content:this.options.search_url,target:"_blank"});l.add({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});l.add({title:"Videos",content:this.options.screencasts_url,target:"_blank"});l.add({title:"Wiki",content:this.options.wiki_url,target:"_blank"});l.add({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(this.options.terms_url){l.add({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(l);if(!this.options.user.valid){var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedout-only",title_attribute:"Account registration or login"});k.add({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){k.add({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(k)}else{var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedin-only",title_attribute:"Account preferences and saved data"});k.add({title:"Logged in as "+this.options.user.email});k.add({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});k.add({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});k.add({title:"Logout",content:"user/logout",target:"_top",divider:true});k.add({title:"Saved Histories",content:"history/list",target:"galaxy_main"});k.add({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});k.add({title:"Saved Pages",content:"page/list",target:"_top"});k.add({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){k.add({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(k)}if(this.options.active_view){this.masthead.highlight(this.options.active_view)}}});return{GalaxyMenu:a}}); \ No newline at end of file +define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var e=new b.GalaxyMastheadTab({id:"analysis",title:"Analyze Data",content:"",title_attribute:"Analysis home view"});this.masthead.append(e);var g={id:"workflow",title:"Workflow",content:"workflow",title_attribute:"Chain tools into workflows"};if(!this.options.user.valid){g.disabled=true}var d=new b.GalaxyMastheadTab(g);this.masthead.append(d);var i=new b.GalaxyMastheadTab({id:"shared",title:"Shared Data",content:"library/index",title_attribute:"Access published resources"});i.add({title:"Data Libraries",content:"library/index"});i.add({title:"Data Libraries Beta",content:"library/list",divider:true});i.add({title:"Published Histories",content:"history/list_published"});i.add({title:"Published Workflows",content:"workflow/list_published"});i.add({title:"Published Visualizations",content:"visualization/list_published"});i.add({title:"Published Pages",content:"page/list_published"});this.masthead.append(i);if(this.options.user.requests){var j=new b.GalaxyMastheadTab({id:"lab",title:"Lab"});j.add({title:"Sequencing Requests",content:"requests/index"});j.add({title:"Find Samples",content:"requests/find_samples_index"});j.add({title:"Help",content:this.options.lims_doc_url});this.masthead.append(j)}var c={id:"visualization",title:"Visualization",content:"visualization/list",title_attribute:"Visualize datasets"};if(!this.options.user.valid){c.disabled=true}var m=new b.GalaxyMastheadTab(c);if(this.options.user.valid){m.add({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});m.add({title:"Saved Visualizations",content:"visualization/list",target:"_frame"})}this.masthead.append(m);if(this.options.enable_cloud_launch){var f=new b.GalaxyMastheadTab({id:"cloud",title:"Cloud",content:"cloudlaunch/index"});f.add({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(f)}if(this.options.is_admin_user){var h=new b.GalaxyMastheadTab({id:"admin",title:"Admin",content:"admin",extra_class:"admin-only",title_attribute:"Administer this Galaxy"});this.masthead.append(h)}var l=new b.GalaxyMastheadTab({id:"help",title:"Help",title_attribute:"Support, contact, and community hubs"});if(this.options.biostar_url){l.add({title:"Galaxy Biostar",content:this.options.biostar_url_redirect,target:"_blank"});l.add({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}l.add({title:"Support",content:this.options.support_url,target:"_blank"});l.add({title:"Search",content:this.options.search_url,target:"_blank"});l.add({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});l.add({title:"Videos",content:this.options.screencasts_url,target:"_blank"});l.add({title:"Wiki",content:this.options.wiki_url,target:"_blank"});l.add({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(this.options.terms_url){l.add({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(l);if(!this.options.user.valid){var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedout-only",title_attribute:"Account registration or login"});k.add({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){k.add({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(k)}else{var k=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedin-only",title_attribute:"Account preferences and saved data"});k.add({title:"Logged in as "+this.options.user.email});k.add({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});k.add({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});k.add({title:"Logout",content:"user/logout",target:"_top",divider:true});k.add({title:"Saved Histories",content:"history/list",target:"galaxy_main"});k.add({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});k.add({title:"Saved Pages",content:"page/list",target:"_top"});k.add({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){k.add({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(k)}if(this.options.active_view){this.masthead.highlight(this.options.active_view)}}});return{GalaxyMenu:a}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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