galaxy-commits December 2012

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commit/galaxy-central: carlfeberhard: history panel and popupmenu: various fixes for IE
by Bitbucket 07 Dec '12

07 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/63fc9cbe381d/ changeset: 63fc9cbe381d user: carlfeberhard date: 2012-12-07 22:02:21 summary: history panel and popupmenu: various fixes for IE affected #: 3 files diff -r b516a3fb0fc102c1b0b527f072e86a4afc74679e -r 63fc9cbe381d2719134f87c019911565e3a934a1 templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -54,7 +54,7 @@ info : function(){}, warn : function(){}, error : function(){}, - assert : function(){}, + assert : function(){} }; // Set up needed paths. diff -r b516a3fb0fc102c1b0b527f072e86a4afc74679e -r 63fc9cbe381d2719134f87c019911565e3a934a1 templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -75,7 +75,7 @@ info : function(){}, warn : function(){}, error : function(){}, - assert : function(){}, + assert : function(){} }; // Set up needed paths. diff -r b516a3fb0fc102c1b0b527f072e86a4afc74679e -r 63fc9cbe381d2719134f87c019911565e3a934a1 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -287,7 +287,7 @@ top.Galaxy.currUser = top.Galaxy.currUser; top.Galaxy.currHistoryPanel = top.Galaxy.currHistoryPanel; - top.Galaxy.paths = galaxy_paths; + //top.Galaxy.paths = galaxy_paths; top.Galaxy.localization = GalaxyLocalization; window.Galaxy = top.Galaxy; @@ -297,12 +297,13 @@ GalaxyLocalization.setLocalizedString( ${ create_localization_json( get_page_localized_strings() ) } ); // add needed controller urls to GalaxyPaths +if( !galaxy_paths ){ galaxy_paths = top.galaxy_paths || new GalaxyPaths(); } galaxy_paths.set( 'hda', ${get_hda_url_templates()} ); galaxy_paths.set( 'history', ${get_history_url_templates()} ); $(function(){ galaxyPageSetUp(); - Galaxy.historyFrame = window; + //Galaxy.historyFrame = window; var debugging = ( new PersistantStorage( '__history_panel' ).get( 'debugging' ) || false ); @@ -387,6 +388,7 @@ } // lots of wtf here...due to infernalframes + //TODO: this is way tooo acrobatic var $historyButtonWindow = $( top.document ), HISTORY_MENU_BUTTON_ID = 'history-options-button', $historyMenuButton = $historyButtonWindow.find( '#' + HISTORY_MENU_BUTTON_ID ), @@ -410,44 +412,50 @@ // since the history frame reloads so often (compared to the main window), // we need to check whether these options are there already before we add them again - //NOTE: we use the global here because these remain bound in the main window even if panel refreshes + // In IE, however, NOT re-adding them creates a 'cant execute from freed script' error: + // so...we need to re-add the function in either case (just not the option itself) + //NOTE: we use the global Galaxy.currHistoryPanel here + // because these remain bound in the main window even if panel refreshes //TODO: too much boilerplate - if( popupMenu.findIndexByHtml( COLLAPSE_OPTION_TEXT ) === null ){ - popupMenu.addItem({ - html : COLLAPSE_OPTION_TEXT, - func : function() { - Galaxy.currHistoryPanel.collapseAllHdaBodies(); - } - }, START_INSERTING_AT_INDEX ) + //TODO: ugh...(in general) + var collapseOption = popupMenu.findItemByHtml( COLLAPSE_OPTION_TEXT ); + if( !collapseOption ){ + collapseOption = { + html : COLLAPSE_OPTION_TEXT + }; + popupMenu.addItem( collapseOption, START_INSERTING_AT_INDEX ) } + collapseOption.func = function() { + Galaxy.currHistoryPanel.collapseAllHdaBodies(); + }; - var deletedOptionIndex = popupMenu.findIndexByHtml( DELETED_OPTION_TEXT ); - if( deletedOptionIndex === null ){ - popupMenu.addItem({ - html : DELETED_OPTION_TEXT, - func : function( clickEvent, thisMenuOption ){ - var show_deleted = Galaxy.currHistoryPanel.toggleShowDeleted(); - thisMenuOption.checked = show_deleted; - } - }, START_INSERTING_AT_INDEX + 1 ) - deletedOptionIndex = START_INSERTING_AT_INDEX + 1; + var deletedOption = popupMenu.findItemByHtml( DELETED_OPTION_TEXT ); + if( !deletedOption ){ + deletedOption = { + html : DELETED_OPTION_TEXT + }; + popupMenu.addItem( deletedOption, START_INSERTING_AT_INDEX + 1 ) } + deletedOption.func = function( clickEvent, thisMenuOption ){ + var show_deleted = Galaxy.currHistoryPanel.toggleShowDeleted(); + thisMenuOption.checked = show_deleted; + }; // whether was there or added, update the checked option to reflect the panel's settings on the panel render - popupMenu.options[ deletedOptionIndex ].checked = Galaxy.currHistoryPanel.storage.get( 'show_deleted' ); + deletedOption.checked = Galaxy.currHistoryPanel.storage.get( 'show_deleted' ); - var hiddenOptionIndex = popupMenu.findIndexByHtml( HIDDEN_OPTION_TEXT ); - if( hiddenOptionIndex === null ){ - popupMenu.addItem({ - html : HIDDEN_OPTION_TEXT, - func : function( clickEvent, thisMenuOption ){ - var show_hidden = Galaxy.currHistoryPanel.toggleShowHidden(); - thisMenuOption.checked = show_hidden; - } - }, START_INSERTING_AT_INDEX + 2 ) - hiddenOptionIndex = START_INSERTING_AT_INDEX + 2; + var hiddenOption = popupMenu.findItemByHtml( HIDDEN_OPTION_TEXT ); + if( !hiddenOption ){ + hiddenOption = { + html : HIDDEN_OPTION_TEXT + }; + popupMenu.addItem( hiddenOption, START_INSERTING_AT_INDEX + 2 ) } + hiddenOption.func = function( clickEvent, thisMenuOption ){ + var show_hidden = Galaxy.currHistoryPanel.toggleShowHidden(); + thisMenuOption.checked = show_hidden; + }; // whether was there or added, update the checked option to reflect the panel's settings on the panel render - popupMenu.options[ hiddenOptionIndex ].checked = Galaxy.currHistoryPanel.storage.get( 'show_hidden' ); + hiddenOption.checked = Galaxy.currHistoryPanel.storage.get( 'show_hidden' ); })(); //TODO: both the quota meter and the options-menu stuff need to be moved out when iframes are removed Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: pack_scripts
by Bitbucket 07 Dec '12

07 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b516a3fb0fc1/ changeset: b516a3fb0fc1 user: carlfeberhard date: 2012-12-07 20:36:44 summary: pack_scripts affected #: 1 file diff -r 9c90d4c2f4ccfa6303b127a51c27bd2e57402594 -r b516a3fb0fc102c1b0b527f072e86a4afc74679e static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:null,enabled:true,visible:true}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=$(Handlebars.partials.iconButton(this.model.toJSON()));a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(this.model.attributes.on_click){this.model.attributes.on_click(a);return false}return true}});IconButtonView.templates={iconButton:Handlebars.partials.iconButton};var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b||$("<div/>");this.options=a||[];var c=this;this.$button.click(function(d){c._renderAndShow(d);return false});this.$button.data("PopupMenu",this);if(!this.templates.wrapper){this.templates.wrapper=Handlebars.templates["template-popupmenu-wrapper"]}},render:function(){var a=this;this.$el.addClass("popmenu-wrapper").css({position:"absolute",display:"none"});this.$el.html(PopupMenu.templates.menu({options:this.options,id:this.$button.attr("id")}));if(this.options.length){this.$el.find("li").each(function(c,b){var f=$(b),e=f.children("a.popupmenu-option"),d=a.options[c].func;if(e.length&&d){e.click(function(g){d(g,a.options[c])})}a.options[c].$li=f})}return this},_getShownPosition:function(b){var c=this.$el.width(),a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_renderAndShow:function(a){this.render();this.$el.appendTo("body");this.$el.css(this._getShownPosition(a));this._setUpCloseBehavior();this.$el.show()},_setUpCloseBehavior:function(){var b=this,a=function(c){c.bind("click.close_popup",function(){b.remove();c.unbind("click.close_popup")})};a($(window.document));a($(window.top.document));_.each(window.top.frames,function(c){a($(c.document))})},addItem:function(b,a){a=(a>=0)?(a):(this.options.length);this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if((_.has(this.options[a],"html"))&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.templates={menu:Handlebars.templates["template-popupmenu-menu"]};PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(j){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}var i;switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;case"demo":if(i===undefined||i.closed){i=window.open(j,k);i.creator=self}break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a}; \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:null,enabled:true,visible:true}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=$(Handlebars.partials.iconButton(this.model.toJSON()));a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(this.model.attributes.on_click){this.model.attributes.on_click(a);return false}return true}});IconButtonView.templates={iconButton:Handlebars.partials.iconButton};var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b||$("<div/>");this.options=a||[];var c=this;this.$button.click(function(d){c._renderAndShow(d);return false});this.$button.data("PopupMenu",this)},render:function(){var a=this;this.$el.addClass("popmenu-wrapper").css({position:"absolute",display:"none"});this.$el.html(PopupMenu.templates.menu({options:this.options,id:this.$button.attr("id")}));if(this.options.length){this.$el.find("li").each(function(c,b){var f=$(b),e=f.children("a.popupmenu-option"),d=a.options[c].func;if(e.length&&d){e.click(function(g){d(g,a.options[c])})}a.options[c].$li=f})}return this},_getShownPosition:function(b){var c=this.$el.width(),a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_renderAndShow:function(a){this.render();this.$el.appendTo("body");this.$el.css(this._getShownPosition(a));this._setUpCloseBehavior();this.$el.show()},_setUpCloseBehavior:function(){var b=this,a=function(c){c.bind("click.close_popup",function(){b.remove();c.unbind("click.close_popup")})};a($(window.document));a($(window.top.document));_.each(window.top.frames,function(c){a($(c.document))})},addItem:function(b,a){a=(a>=0)?(a):(this.options.length);this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if((_.has(this.options[a],"html"))&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.templates={menu:Handlebars.templates["template-popupmenu-menu"]};PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(j){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}var i;switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;case"demo":if(i===undefined||i.closed){i=window.open(j,k);i.creator=self}break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return 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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commit/galaxy-central: carlfeberhard: ui.js: fix to bad template reference
by Bitbucket 07 Dec '12

07 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9c90d4c2f4cc/ changeset: 9c90d4c2f4cc user: carlfeberhard date: 2012-12-07 20:13:25 summary: ui.js: fix to bad template reference affected #: 1 file diff -r cba8dbdb8312dcfa93e0be299fb560c067266064 -r 9c90d4c2f4ccfa6303b127a51c27bd2e57402594 static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -205,9 +205,6 @@ // template loading is problematic - ui is loaded in base.mako // and the template (prev.) needed to be loaded before ui - if( !this.templates.wrapper ){ - this.templates.wrapper = Handlebars.templates[ 'template-popupmenu-wrapper' ]; - } }, /** Render the menu. NOTE: doesn't attach itself to the DOM. 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 Bitbucket 07 Dec '12

07 Dec '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6d7e637883b7/ changeset: 6d7e637883b7 user: carlfeberhard date: 2012-12-07 19:56:53 summary: ui: adding PopupMenu view as alternate to make_popup_menu and allow changing option text, adding/removing options, and adding checkmarks for togglable options; index.mako: use PopupMenu for history-options-button; history panel: use alternate_history.mako to add 'collapse all', 'Include hidden datasets'(toggle), 'Include deleted datasets'(toggle) to history-options-button; alternate_history.mako: include better system for debugging js when changing source directly is problematic (main/test); pack_scripts; affected #: 19 files diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -98,7 +98,6 @@ return trans.fill_template_mako( "/my_data.mako" ) @web.expose - #def history( self, trans, as_xml=False, show_deleted=False, show_hidden=False, hda_id=None, **kwd ): def history( self, trans, as_xml=False, show_deleted=None, show_hidden=None, hda_id=None, **kwd ): """ Display the current history, creating a new history if necessary. diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -288,7 +288,7 @@ }, /** String representation. */ - toString : function(){ return 'PersistantStorage(' + data + ')'; } + toString : function(){ return 'PersistantStorage(' + storageKey + ')'; } }); return returnedStorage; diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -28,6 +28,7 @@ * @see Backbone.View#initialize */ initialize : function( attributes ){ + if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } this.log( this + '.initialize:', attributes ); /** list of rendering functions for the default, primary icon-buttons. */ @@ -334,6 +335,8 @@ //TODO: not a fan of this dispatch switch( this.model.get( 'state' ) ){ + case HistoryDatasetAssociation.STATES.NEW : + break; case HistoryDatasetAssociation.STATES.NOT_VIEWABLE : this._render_body_not_viewable( body ); break; diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -130,8 +130,7 @@ //TODO: to list inclusion test //TODO: class level readyStates list return ( - ( state === HistoryDatasetAssociation.STATES.NEW ) - || ( state === HistoryDatasetAssociation.STATES.OK ) + ( state === HistoryDatasetAssociation.STATES.OK ) || ( state === HistoryDatasetAssociation.STATES.EMPTY ) || ( state === HistoryDatasetAssociation.STATES.FAILED_METADATA ) || ( state === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -140,6 +140,8 @@ * @see Backbone.View#initialize */ initialize : function( attributes ){ + // set the logger if requested + if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } this.log( this + '.initialize:', attributes ); // set up url templates @@ -203,7 +205,7 @@ show_deleted : false, show_hidden : false }); - this.log( 'this.storage:', this.storage.get() ); + this.log( this + ' (prev) storage:', JSON.stringify( this.storage.get(), null, 2 ) ); // expanded Hdas is a map of hda.ids -> a boolean rep'ing whether this hda's body is expanded // store any pre-expanded ids passed in @@ -226,7 +228,7 @@ this.show_deleted = this.storage.get( 'show_deleted' ); this.show_hidden = this.storage.get( 'show_hidden' ); //this.log( 'this.show_deleted:', this.show_deleted, 'show_hidden', this.show_hidden ); - this.log( '(init\'d) this.storage:', this.storage.get() ); + this.log( this + ' (init\'d) storage:', this.storage.get() ); }, /** Add an hda to this history's collection @@ -351,7 +353,8 @@ historyView.hdaViews[ hdaId ] = new historyView.HDAView({ model : hda, expanded : expanded, - urlTemplates : historyView.hdaUrlTemplates + urlTemplates : historyView.hdaUrlTemplates, + logger : historyView.logger }); historyView._setUpHdaListeners( historyView.hdaViews[ hdaId ] ); @@ -432,19 +435,23 @@ /** Handle the user toggling the deleted visibility by: * (1) storing the new value in the persistant storage * (2) re-rendering the history + * @returns {Boolean} new show_deleted setting */ toggleShowDeleted : function(){ this.storage.set( 'show_deleted', !this.storage.get( 'show_deleted' ) ); this.render(); + return this.storage.get( 'show_deleted' ); }, /** Handle the user toggling the deleted visibility by: * (1) storing the new value in the persistant storage * (2) re-rendering the history + * @returns {Boolean} new show_hidden setting */ toggleShowHidden : function(){ this.storage.set( 'show_hidden', !this.storage.get( 'show_hidden' ) ); this.render(); + return this.storage.get( 'show_hidden' ); }, /** Collapse all hda bodies and clear expandedHdas in the storage diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -76,11 +76,11 @@ iconButton : Handlebars.partials.iconButton }; - var IconButtonCollection = Backbone.Collection.extend({ model: IconButton }); + //------------------------------------------------------------------------------ /** * Menu with multiple icon buttons. Views are not needed nor used for individual buttons. @@ -166,15 +166,319 @@ }); +// ============================================================================= +/** @class View for a popup menu + * @name PopupMenu + * + * @constructs + */ +var PopupMenu = Backbone.View.extend( +/** @lends PopupMenu.prototype */{ + /* TODO: + add submenus + add hrefs + test various html keys + add make_popupmenus style + get template inside this file somehow + */ + /** Cache the desired button element and options, set up the button click handler + * NOTE: attaches this view as HTML/jQ data on the button for later use. + */ + //TODO: include docs on special option keys (divider, checked, etc.) + initialize : function( $button, options ){ + // default settings + this.$button = $button || $( '<div/>' ); + this.options = options || []; + //console.debug( this + '.initialize, button:', $button, ', options:', options ); + // set up button click -> open menu behavior + var menu = this; + this.$button.click( function( event ){ + menu._renderAndShow( event ); + //event.stopPropagation(); + return false; + }); + // attach this view as a data object on the button - for later access + //TODO:?? memleak? + this.$button.data( 'PopupMenu', this ); + // template loading is problematic - ui is loaded in base.mako + // and the template (prev.) needed to be loaded before ui + if( !this.templates.wrapper ){ + this.templates.wrapper = Handlebars.templates[ 'template-popupmenu-wrapper' ]; + } + }, + /** Render the menu. NOTE: doesn't attach itself to the DOM. + * @see PopupMenu#_renderAndShow + */ + render : function(){ + var menu = this; + // render the menu body + this.$el.addClass( 'popmenu-wrapper' ) + .css({ + position: 'absolute', + display: 'none' + }); + //BUG: anchors within a.popupmenu-option render OUTSIDE the a.popupmenu-option!? + this.$el.html( PopupMenu.templates.menu({ + options : this.options, + // sets menu div id to '{{ id }}-menu' + id : this.$button.attr( 'id' ) + })); + //console.debug( this.$el, ':', this.$el.html() ); + // set up behavior on each link/anchor elem + if( this.options.length ){ + this.$el.find( 'li' ).each( function( i, li ){ + var $li = $( li ), + $anchor = $li.children( 'a.popupmenu-option' ), + menuFunc = menu.options[ i ].func; + //console.debug( 'setting up behavior:', i, menu.options[ i ], $li, $anchor ); + if( $anchor.length && menuFunc ){ + $anchor.click( function( event ){ + menuFunc( event, menu.options[ i ] ); + }); + } + // cache the anchor as a jq obj within the options obj + menu.options[ i ].$li = $li; + }); + } + return this; + }, + /** Get the absolute position/offset for the menu + */ + _getShownPosition : function( clickEvent ){ + var menuWidth = this.$el.width(), + // display menu horiz. centered on click... + x = clickEvent.pageX - menuWidth / 2 ; + // ...but adjust that to handle horiz. scroll and window dimensions (draw entirely on visible screen area) + x = Math.min( x, $( document ).scrollLeft() + $( window ).width() - menuWidth - 5 ); + x = Math.max( x, $( document ).scrollLeft() + 5 ); + + return { + top: clickEvent.pageY, + left: x + }; + }, + + /** Render the menu, append to the page body at the click position, and set up the 'click-away' handlers, show + */ + _renderAndShow : function( clickEvent ){ + this.render(); + this.$el.appendTo( 'body' ); + this.$el.css( this._getShownPosition( clickEvent ) ); + this._setUpCloseBehavior(); + this.$el.show(); + }, + + /** Bind an event handler to all available frames so that when anything is clicked + * * the menu is removed from the DOM + * * The event handler unbinds itself + */ + _setUpCloseBehavior : function(){ + var menu = this, + // function to close popup and unbind itself + closePopupWhenClicked = function( $elClicked ){ + $elClicked.bind( "click.close_popup", function(){ + menu.remove(); + $elClicked.unbind( "click.close_popup" ); + }); + }; + + // bind to current, parent, and sibling frames + //TODO: (Assuming for now that this is the best way to do this...) + closePopupWhenClicked( $( window.document ) ); + closePopupWhenClicked( $( window.top.document ) ); + _.each( window.top.frames, function( siblingFrame ){ + closePopupWhenClicked( $( siblingFrame.document ) ); + }); + }, + + /** Add a menu option/item at the given index + */ + addItem : function( item, index ){ + // append to end if no index + index = ( index >= 0 )?( index ):( this.options.length ); + this.options.splice( index, 0, item ); + return this; + }, + + /** Remove a menu option/item at the given index + */ + removeItem : function( index ){ + if( index >=0 ){ + this.options.splice( index, 1 ); + } + return this; + }, + + /** Search for a menu option by it's html + */ + findIndexByHtml : function( html ){ + for( var i=0; i<this.options.length; i++ ){ + if( ( _.has( this.options[i], 'html' ) ) + && ( this.options[i].html === html ) ){ + return i; + } + } + return null; + }, + + /** Search for a menu option by it's html + */ + findItemByHtml : function( html ){ + return this.options[( this.findIndexByHtml( html ) )]; + }, + + /** String representation. */ + toString : function(){ + return 'PopupMenu'; + } +}); +PopupMenu.templates = { + menu : Handlebars.templates[ 'template-popupmenu-menu' ] +}; + +// ----------------------------------------------------------------------------- +// the following class functions are bridges from the original make_popupmenu and make_popup_menus +// to the newer backbone.js PopupMenu + +/** Create a PopupMenu from simple map initial_options activated by clicking button_element. + * Converts initial_options to object array used by PopupMenu. + * @param {jQuery|DOMElement} button_element element which, when clicked, activates menu + * @param {Object} initial_options map of key -> values, where + * key is option text, value is fn to call when option is clicked + * @returns {PopupMenu} the PopupMenu created + */ +PopupMenu.make_popupmenu = function( button_element, initial_options ){ + var convertedOptions = []; + _.each( initial_options, function( optionVal, optionKey ){ + var newOption = { html: optionKey }; + + // keys with null values indicate: header + if( optionVal === null ){ // !optionVal? (null only?) + newOption.header = true; + + // keys with function values indicate: a menu option + } else if( jQuery.type( optionVal ) === 'function' ){ + newOption.func = optionVal; + } + //TODO:?? any other special optionVals? + // there was no divider option originally + convertedOptions.push( newOption ); + }); + return new PopupMenu( $( button_element ), convertedOptions ); +}; + +/** Find all anchors in $parent (using selector) and covert anchors into a PopupMenu options map. + * @param {jQuery} $parent the element that contains the links to convert to options + * @param {String} selector jq selector string to find links + * @returns {Object[]} the options array to initialize a PopupMenu + */ +//TODO: lose parent and selector, pass in array of links, use map to return options +PopupMenu.convertLinksToOptions = function( $parent, selector ){ + $parent = $( $parent ); + selector = selector || 'a'; + var options = []; + $parent.find( selector ).each( function( elem, i ){ + var option = {}, + $link = $( elem ); + + // convert link text to the option text (html) and the href into the option func + option.html = $link.text(); + if( linkHref ){ + var linkHref = $link.attr( 'href' ), + linkTarget = $link.attr( 'target' ), + confirmText = $link.attr( 'confirm' ); + + option.func = function(){ + // if there's a "confirm" attribute, throw up a confirmation dialog, and + // if the user cancels - do nothing + if( ( confirmText ) && ( !confirm( confirmText ) ) ){ return; } + + // if there's no confirm attribute, or the user accepted the confirm dialog: + var f; + switch( linkTarget ){ + // relocate the center panel + case '_parent': + window.parent.location = linkHref; + break; + + // relocate the entire window + case '_top': + window.top.location = linkHref; + break; + + // Http request target is a window named demolocal on the local box + //TODO: I still don't understand this option (where the hell does f get set? confirm?) + case 'demo': + if( f === undefined || f.closed ){ + f = window.open( linkHref, linkTarget ); + f.creator = self; + } + break; + + // relocate this panel + default: + window.location = linkHref; + } + }; + } + options.push( option ); + }); + return options; +}; + +/** Create a single popupmenu from existing DOM button and anchor elements + * @param {jQuery} $buttonElement the element that when clicked will open the menu + * @param {jQuery} $menuElement the element that contains the anchors to convert into a menu + * @param {String} menuElementLinkSelector jq selector string used to find anchors to be made into menu options + * @returns {PopupMenu} the PopupMenu (Backbone View) that can render, control the menu + */ +PopupMenu.fromExistingDom = function( $buttonElement, $menuElement, menuElementLinkSelector ){ + $buttonElement = $( $buttonElement ); + $menuElement = $( $menuElement ); + var options = PopupMenu.convertLinksToOptions( $menuElement, menuElementLinkSelector ); + // we're done with the menu (having converted it to an options map) + $menuElement.remove(); + return new PopupMenu( $buttonElement, options ); +}; + +/** Create all popupmenus within a document or a more specific element + * @param {DOMElement} parent the DOM element in which to search for popupmenus to build (defaults to document) + * @param {String} menuSelector jq selector string to find popupmenu menu elements (defaults to "div[popupmenu]") + * @param {Function} buttonSelectorBuildFn the function to build the jq button selector. + * Will be passed $menuElement, parent. + * (Defaults to return '#' + $menuElement.attr( 'popupmenu' ); ) + * @returns {PopupMenu[]} array of popupmenus created + */ +PopupMenu.make_popup_menus = function( parent, menuSelector, buttonSelectorBuildFn ){ + parent = parent || document; + // orig. Glx popupmenu menus have a (non-std) attribute 'popupmenu' + // which contains the id of the button that activates the menu + menuSelector = menuSelector || 'div[popupmenu]'; + // default to (orig. Glx) matching button to menu by using the popupmenu attr of the menu as the id of the button + buttonSelectorBuildFn = buttonSelectorBuildFn || function( $menuElement, parent ){ + return '#' + $menuElement.attr( 'popupmenu' ); + }; + + // aggregate and return all PopupMenus + var popupMenusCreated = []; + $( parent ).find( menuSelector ).each( function(){ + var $menuElement = $( this ), + $buttonElement = $( parent ).find( buttonSelectorBuildFn( $menuElement, parent ) ); + popupMenusCreated.push( PopupMenu.fromDom( $buttonElement, $menuElement ) ); + $buttonElement.addClass( 'popup' ); + }); + return popupMenusCreated; +} + diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 static/scripts/packed/mvc/base-mvc.js --- a/static/scripts/packed/mvc/base-mvc.js +++ b/static/scripts/packed/mvc/base-mvc.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){return this.logger.log.apply(this.logger,arguments)}return undefined}};var GalaxyLocalization=jQuery.extend({},{ALIAS_NAME:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(a){return this.localizedStrings[a]||a},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.ALIAS_NAME]=function(a){return GalaxyLocalization.localize(a)};var PersistantStorage=function(g,d){if(!g){throw ("PersistantStorage needs storageKey argument")}d=d||{};var b=jQuery.jStorage.get,c=jQuery.jStorage.set,a=jQuery.jStorage.deleteKey;function e(i,h){i=i||{};h=h||null;return{get:function(j){if(j===undefined){return i}else{if(i.hasOwnProperty(j)){return(jQuery.type(i[j])==="object")?(new e(i[j],this)):(i[j])}}return undefined},set:function(j,k){i[j]=k;this._save();return this},deleteKey:function(j){delete i[j];this._save();return this},_save:function(){return h._save()},toString:function(){return("StorageRecursionHelper("+i+")")}}}var f={};data=b(g);if(data===null){data=jQuery.extend(true,{},d);c(g,data)}f=new e(data);jQuery.extend(f,{_save:function(h){return c(g,f.get())},destroy:function(){return a(g)},toString:function(){return"PersistantStorage("+data+")"}});return f}; \ No newline at end of file +var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){return this.logger.log.apply(this.logger,arguments)}return undefined}};var GalaxyLocalization=jQuery.extend({},{ALIAS_NAME:"_l",localizedStrings:{},setLocalizedString:function(b,a){var c=this;var d=function(f,e){if(f!==e){c.localizedStrings[f]=e}};if(jQuery.type(b)==="string"){d(b,a)}else{if(jQuery.type(b)==="object"){jQuery.each(b,function(e,f){d(e,f)})}else{throw ("Localization.setLocalizedString needs either a string or object as the first argument, given: "+b)}}},localize:function(a){return this.localizedStrings[a]||a},toString:function(){return"GalaxyLocalization"}});window[GalaxyLocalization.ALIAS_NAME]=function(a){return GalaxyLocalization.localize(a)};var PersistantStorage=function(g,d){if(!g){throw ("PersistantStorage needs storageKey argument")}d=d||{};var b=jQuery.jStorage.get,c=jQuery.jStorage.set,a=jQuery.jStorage.deleteKey;function e(i,h){i=i||{};h=h||null;return{get:function(j){if(j===undefined){return i}else{if(i.hasOwnProperty(j)){return(jQuery.type(i[j])==="object")?(new e(i[j],this)):(i[j])}}return undefined},set:function(j,k){i[j]=k;this._save();return this},deleteKey:function(j){delete i[j];this._save();return this},_save:function(){return h._save()},toString:function(){return("StorageRecursionHelper("+i+")")}}}var f={};data=b(g);if(data===null){data=jQuery.extend(true,{},d);c(g,data)}f=new e(data);jQuery.extend(f,{_save:function(h){return c(g,f.get())},destroy:function(){return a(g)},toString:function(){return"PersistantStorage("+g+")"}});return f}; \ No newline at end of file diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -var HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"});this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.expanded){a.show()}else{a.hide()}return a},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+".</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to unpause")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred running this job")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this,d=this.$el.find(".historyItemBody");a=(a===undefined)?(!d.is(":visible")):(a);if(a){d.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{d.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(){},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file +var HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"});this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(a))}}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.expanded){a.show()}else{a.hide()}return a},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+".</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to unpause")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred running this job")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this,d=this.$el.find(".historyItemBody");a=(a===undefined)?(!d.is(":visible")):(a);if(a){d.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{d.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(){},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"ok",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:true},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",this.get("id"),a,this.previous("state"),b)}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.NEW)||(a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}}); \ No newline at end of file +var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"ok",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:true},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",this.get("id"),a,this.previous("state"),b)}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}}); \ No newline at end of file diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags"},initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:state",function(c,d,b){if((c.inReadyState())&&(!c.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHda(c)}},this);this.hdaViews={};this.urls={}},_setUpWebStorage:function(b,a,c){this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log("this.storage:",this.storage.get());if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log("(init'd) this.storage:",this.storage.get())},add:function(a){this.render()},addAll:function(){this.render()},removeHda:function(a,c){var b=this.hdaViews[a.get("id")];b.$el.fadeOut("fast",function(){b.$el.remove();if(c){c()}});this.model.hdas.remove(a)},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render()},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render()},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert(_l("Tagging failed"))},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:state",function(c,d,b){if((c.inReadyState())&&(!c.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHda(c)}},this);this.hdaViews={};this.urls={}},_setUpWebStorage:function(b,a,c){this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},add:function(a){this.render()},addAll:function(){this.render()},removeHda:function(a,c){var b=this.hdaViews[a.get("id")];b.$el.fadeOut("fast",function(){b.$el.remove();if(c){c()}});this.model.hdas.remove(a)},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert(_l("Tagging failed"))},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:null,enabled:true,visible:true}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=$(Handlebars.partials.iconButton(this.model.toJSON()));a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(this.model.attributes.on_click){this.model.attributes.on_click(a);return false}return true}});IconButtonView.templates={iconButton:Handlebars.partials.iconButton};var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}}); \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:null,enabled:true,visible:true}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=$(Handlebars.partials.iconButton(this.model.toJSON()));a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(this.model.attributes.on_click){this.model.attributes.on_click(a);return false}return true}});IconButtonView.templates={iconButton:Handlebars.partials.iconButton};var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var PopupMenu=Backbone.View.extend({templates:{wrapper:(function(){var a=['<ul id="<%= id %>-menu" class="dropdown-menu">',"<% if( options.length ){ %>","<% for( var i=0; i<options.length; i++ ){ var option = options[ i ]; %>","<% if( option.divider ){ %>",'<li class="divider"></li>',"<% } else { %>","<% if( option.header ){ %>",'<li class="head"><a href=""javascript:void(0);"><%- option.html %></a></li>',"<% } else { %>","<li><a ",'href="<% print( ( option.href )?( option.href ):( "javascript:void(0);" ) ) %>" ','<% if( option.target ){ %>target="<%= option.target %>" <% } %>','class="popupmenu-option">','<% if( option.checked ){ %><span class="ficon ok"></span><% } %>',"<%- option.html %>","</a></li>","<% } %>","<% } %>","<% } %>","<% } else { %>","<li>No Options.</li>","<% } %>","</ul>"];return _.template(a.join(""))}())},initialize:function(b,a){this.$button=b||$("<div/>");this.options=a||[];var c=this;this.$button.click(function(d){c._renderAndShow(d);return false});this.$button.data("PopupMenu",this);if(!this.templates.wrapper){this.templates.wrapper=Handlebars.templates["template-popupmenu-wrapper"]}},render:function(){var a=this;this.$el.addClass("popmenu-wrapper").css({position:"absolute",display:"none"});this.$el.html(PopupMenu.templates.menu({options:this.options,id:this.$button.attr("id")}));if(this.options.length){this.$el.find("li").each(function(c,b){var f=$(b),e=f.children("a.popupmenu-option"),d=a.options[c].func;if(e.length&&d){e.click(function(g){d(g,a.options[c])})}a.options[c].$li=f})}return this},_getShownPosition:function(b){var c=this.$el.width(),a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_renderAndShow:function(a){this.render();this.$el.appendTo("body");this.$el.css(this._getShownPosition(a));this._setUpCloseBehavior();this.$el.show()},_setUpCloseBehavior:function(){var b=this,a=function(c){c.bind("click.close_popup",function(){b.remove();c.unbind("click.close_popup")})};a($(window.document));a($(window.top.document));_.each(window.top.frames,function(c){a($(c.document))})},addItem:function(b,a){a=(a>=0)?(a):(this.options.length);this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if((_.has(this.options[a],"html"))&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.templates={menu:Handlebars.templates["template-popupmenu-menu"]};PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(j){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}var i;switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;case"demo":if(i===undefined||i.closed){i=window.open(j,k);i.creator=self}break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a}; \ No newline at end of file diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 static/scripts/packed/templates/compiled/template-popupmenu-menu.js --- /dev/null +++ b/static/scripts/packed/templates/compiled/template-popupmenu-menu.js @@ -0,0 +1,1 @@ +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-popupmenu-menu"]=b(function(f,s,q,l,x){q=q||f.helpers;var r="",i,h,d="function",c=this.escapeExpression,p=this;function o(B,A){var y="",z;y+="\n ";z=B.options;z=q.each.call(B,z,{hash:{},inverse:p.noop,fn:p.program(2,n,A)});if(z||z===0){y+=z}y+="\n";return y}function n(B,A){var y="",z;y+="\n ";z=B.divider;z=q["if"].call(B,z,{hash:{},inverse:p.program(5,k,A),fn:p.program(3,m,A)});if(z||z===0){y+=z}y+="\n ";return y}function m(z,y){return'\n <li class="divider"></li>\n '}function k(B,A){var y="",z;y+="\n ";z=B.header;z=q["if"].call(B,z,{hash:{},inverse:p.program(8,g,A),fn:p.program(6,j,A)});if(z||z===0){y+=z}y+="\n ";return y}function j(C,B){var z="",A,y;z+='\n <li class="head"><a href=""javascript:void(0);">';y=q.html;if(y){A=y.call(C,{hash:{}})}else{A=C.html;A=typeof A===d?A():A}if(A||A===0){z+=A}z+="</a></li>\n ";return z}function g(C,B){var z="",A,y;z+="\n ";z+='\n <li><a href="';A=C.href;A=q["if"].call(C,A,{hash:{},inverse:p.program(11,w,B),fn:p.program(9,e,B)});if(A||A===0){z+=A}z+='"\n ';A=C.href;A=q["if"].call(C,A,{hash:{},inverse:p.noop,fn:p.program(13,v,B)});if(A||A===0){z+=A}z+=' class="popupmenu-option">\n ';A=C.checked;A=q["if"].call(C,A,{hash:{},inverse:p.noop,fn:p.program(15,u,B)});if(A||A===0){z+=A}z+="\n ";y=q.html;if(y){A=y.call(C,{hash:{}})}else{A=C.html;A=typeof A===d?A():A}if(A||A===0){z+=A}z+="\n </a></li>\n ";return z}function e(B,A){var z,y;y=q.href;if(y){z=y.call(B,{hash:{}})}else{z=B.href;z=typeof z===d?z():z}return c(z)}function w(z,y){return"javascript:void(0);"}function v(C,B){var z="",A,y;z+='target="';y=q.target;if(y){A=y.call(C,{hash:{}})}else{A=C.target;A=typeof A===d?A():A}z+=c(A)+'"';return z}function u(z,y){return'<span class="ficon ok"></span>'}function t(z,y){return"\n <li>No Options.</li>\n"}r+='<ul id="';h=q.id;if(h){i=h.call(s,{hash:{}})}else{i=s.id;i=typeof i===d?i():i}r+=c(i)+'-menu" class="dropdown-menu">\n';i=s.options;i=i==null||i===false?i:i.length;i=q["if"].call(s,i,{hash:{},inverse:p.program(17,t,x),fn:p.program(1,o,x)});if(i||i===0){r+=i}r+="\n</ul>";return r})})(); \ No newline at end of file diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 static/scripts/templates/compiled/template-popupmenu-menu.js --- /dev/null +++ b/static/scripts/templates/compiled/template-popupmenu-menu.js @@ -0,0 +1,117 @@ +(function() { + var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; +templates['template-popupmenu-menu'] = template(function (Handlebars,depth0,helpers,partials,data) { + helpers = helpers || Handlebars.helpers; + var buffer = "", stack1, foundHelper, functionType="function", escapeExpression=this.escapeExpression, self=this; + +function program1(depth0,data) { + + var buffer = "", stack1; + buffer += "\n "; + stack1 = depth0.options; + stack1 = helpers.each.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(2, program2, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n"; + return buffer;} +function program2(depth0,data) { + + var buffer = "", stack1; + buffer += "\n "; + stack1 = depth0.divider; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(5, program5, data),fn:self.program(3, program3, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + return buffer;} +function program3(depth0,data) { + + + return "\n <li class=\"divider\"></li>\n ";} + +function program5(depth0,data) { + + var buffer = "", stack1; + buffer += "\n "; + stack1 = depth0.header; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(8, program8, data),fn:self.program(6, program6, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + return buffer;} +function program6(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n <li class=\"head\"><a href=\"\"javascript:void(0);\">"; + foundHelper = helpers.html; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.html; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "</a></li>\n "; + return buffer;} + +function program8(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "\n "; + buffer += "\n <li><a href=\""; + stack1 = depth0.href; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(11, program11, data),fn:self.program(9, program9, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\"\n "; + stack1 = depth0.href; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += " class=\"popupmenu-option\">\n "; + stack1 = depth0.checked; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(15, program15, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + foundHelper = helpers.html; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.html; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n </a></li>\n "; + return buffer;} +function program9(depth0,data) { + + var stack1, foundHelper; + foundHelper = helpers.href; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.href; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + return escapeExpression(stack1);} + +function program11(depth0,data) { + + + return "javascript:void(0);";} + +function program13(depth0,data) { + + var buffer = "", stack1, foundHelper; + buffer += "target=\""; + foundHelper = helpers.target; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.target; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "\""; + return buffer;} + +function program15(depth0,data) { + + + return "<span class=\"ficon ok\"></span>";} + +function program17(depth0,data) { + + + return "\n <li>No Options.</li>\n";} + + buffer += "<ul id=\""; + foundHelper = helpers.id; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } + else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + buffer += escapeExpression(stack1) + "-menu\" class=\"dropdown-menu\">\n"; + stack1 = depth0.options; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.length; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(17, program17, data),fn:self.program(1, program1, data)}); + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n</ul>"; + return buffer;}); +})(); \ No newline at end of file diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 static/scripts/templates/ui-templates.html --- a/static/scripts/templates/ui-templates.html +++ b/static/scripts/templates/ui-templates.html @@ -1,4 +1,4 @@ -<script type="text/template" class="template-history" id="template-user-quotaMeter-quota"> +<script type="text/template" class="template-user" id="template-user-quotaMeter-quota"><div id="quota-meter" class="quota-meter progress"><div id="quota-meter-bar" class="quota-meter-bar bar" style="width: {{quota_percent}}%"></div> {{! TODO: remove the hardcoded style }} @@ -8,7 +8,7 @@ </div></script> -<script type="text/template" class="template-history" id="template-user-quotaMeter-usage"> +<script type="text/template" class="template-user" id="template-user-quotaMeter-usage"> {{! TODO: remove the hardcoded styles }} <div id="quota-meter" class="quota-meter" style="background-color: transparent"><div id="quota-meter-text" class="quota-meter-text" style="top: 6px; color: white"> @@ -16,3 +16,28 @@ </div></div></script> + +<script type="text/template" class="template-ui" id="template-popupmenu-menu"> +<ul id="{{ id }}-menu" class="dropdown-menu"> +{{#if options.length }} + {{#each options }} + {{#if divider }} + <li class="divider"></li> + {{else}} + {{#if header }} + <li class="head"><a href=""javascript:void(0);">{{{ html }}}</a></li> + {{else}} + {{!NOTE: changed from # to void fn }} + <li><a href="{{#if href }}{{ href }}{{else}}javascript:void(0);{{/if}}" + {{#if href }}target="{{ target }}"{{/if}} class="popupmenu-option"> + {{#if checked }}<span class="ficon ok"></span>{{/if}} + {{{ html }}} + </a></li> + {{/if}} + {{/if}} + {{/each}} +{{else}} + <li>No Options.</li> +{{/if}} +</ul> +</script> diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 templates/base.mako --- a/templates/base.mako +++ b/templates/base.mako @@ -31,11 +31,18 @@ "libs/jquery/jquery", "libs/json2", "libs/bootstrap", - "galaxy.base", "libs/underscore", "libs/backbone/backbone", "libs/backbone/backbone-relational", "libs/handlebars.runtime", + "galaxy.base" + )} + + ${h.templates( + "template-popupmenu-menu" + )} + + ${h.js( "mvc/ui" )} diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -56,9 +56,17 @@ 'libs/backbone/backbone', 'libs/backbone/backbone-relational', 'libs/handlebars.runtime', - 'mvc/ui', 'galaxy.base' )} + + ${h.templates( + "template-popupmenu-menu" + )} + + ${h.js( + "mvc/ui" + )} + <script type="text/javascript"> // console protection window.console = window.console || { diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -223,10 +223,12 @@ ${h.js( "libs/jquery/jstorage", "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging", - "libs/json2", + ##"libs/json2", ##"libs/bootstrap", - "libs/backbone/backbone-relational", - "mvc/base-mvc", "mvc/ui" + ## I think we can remove some of these + ##"libs/backbone/backbone-relational", + "mvc/base-mvc", + ##"mvc/ui" )} ${h.templates( @@ -302,13 +304,9 @@ galaxyPageSetUp(); Galaxy.historyFrame = window; + var debugging = ( new PersistantStorage( '__history_panel' ).get( 'debugging' ) || false ); + // ostensibly, this is the App - //if( window.console && console.debug ){ - // //if( console.clear ){ console.clear(); } - // console.pretty = function( o ){ $( '<pre/>' ).text( JSON.stringify( o, null, ' ' ) ).appendTo( 'body' ); } - // top.storage = jQuery.jStorage - //} - // LOAD INITIAL DATA IN THIS PAGE - since we're already sending it... // ...use mako to 'bootstrap' the models var user = ${ get_current_user() }, @@ -325,7 +323,7 @@ var historyPanel = new HistoryPanel({ model : new History( history, hdas ), urlTemplates : galaxy_paths.attributes, - //logger : console, + logger : ( debugging )?( console ):( null ), // is page sending in show settings? if so override history's show_deleted : ${ 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) }, show_hidden : ${ 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) } @@ -336,13 +334,17 @@ //historyPanel = new HistoryPanel({ // model: new History(), // urlTemplates : galaxy_paths.attributes, - // logger : console, + // logger : ( debugging )?( console ):( null ), // // is page sending in show settings? if so override history's // show_deleted : ${ 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) }, // show_hidden : ${ 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) } //}); //historyPanel.model.loadFromApi( history.id ); + // set it up to be accessible across iframes + //TODO:?? mem leak + top.Galaxy.currHistoryPanel = historyPanel; + // QUOTA METER is a cross-frame ui element (meter in masthead, over quota message in history) // create it and join them here for now (via events) @@ -352,6 +354,7 @@ //window.currUser.logger = console; var quotaMeter = new UserQuotaMeter({ model : currUser, + //logger : ( debugging )?( console ):( null ), el : $( top.document ).find( '.quota-meter-container' ) }); //quotaMeter.logger = console; window.quotaMeter = quotaMeter @@ -373,9 +376,81 @@ quotaMeter.update() }, quotaMeter ); - // set it up to be accessible across iframes - //TODO:?? mem leak - top.Galaxy.currHistoryPanel = historyPanel; + + //ANOTHER cross-frame element is the history-options-button... + // in this case, we need to change the popupmenu options listed to include some functions for this history + // these include: current (1 & 2) 'show/hide' delete and hidden functions, and (3) the collapse all option + (function(){ + // don't try this if the history panel is in it's own window + if( top.document === window.document ){ + return; + } + + // lots of wtf here...due to infernalframes + var $historyButtonWindow = $( top.document ), + HISTORY_MENU_BUTTON_ID = 'history-options-button', + $historyMenuButton = $historyButtonWindow.find( '#' + HISTORY_MENU_BUTTON_ID ), + // jq data in another frame can only be accessed by the jQuery in that frame, + // get the jQuery from the top frame (that contains the history-options-button) + START_INSERTING_AT_INDEX = 11, + COLLAPSE_OPTION_TEXT = _l("Collapse Expanded Datasets"), + DELETED_OPTION_TEXT = _l("Include Deleted Datasets"), + HIDDEN_OPTION_TEXT = _l("Include Hidden Datasets"); + windowJQ = $( top )[0].jQuery, + popupMenu = ( windowJQ && $historyMenuButton[0] )?( windowJQ.data( $historyMenuButton[0], 'PopupMenu' ) ) + :( null ); + + //console.debug( + // '$historyButtonWindow:', $historyButtonWindow, + // '$historyMenuButton:', $historyMenuButton, + // 'windowJQ:', windowJQ, + // 'popupmenu:', popupMenu + //); + if( !popupMenu ){ return; } + + // since the history frame reloads so often (compared to the main window), + // we need to check whether these options are there already before we add them again + //NOTE: we use the global here because these remain bound in the main window even if panel refreshes + //TODO: too much boilerplate + if( popupMenu.findIndexByHtml( COLLAPSE_OPTION_TEXT ) === null ){ + popupMenu.addItem({ + html : COLLAPSE_OPTION_TEXT, + func : function() { + Galaxy.currHistoryPanel.collapseAllHdaBodies(); + } + }, START_INSERTING_AT_INDEX ) + } + + var deletedOptionIndex = popupMenu.findIndexByHtml( DELETED_OPTION_TEXT ); + if( deletedOptionIndex === null ){ + popupMenu.addItem({ + html : DELETED_OPTION_TEXT, + func : function( clickEvent, thisMenuOption ){ + var show_deleted = Galaxy.currHistoryPanel.toggleShowDeleted(); + thisMenuOption.checked = show_deleted; + } + }, START_INSERTING_AT_INDEX + 1 ) + deletedOptionIndex = START_INSERTING_AT_INDEX + 1; + } + // whether was there or added, update the checked option to reflect the panel's settings on the panel render + popupMenu.options[ deletedOptionIndex ].checked = Galaxy.currHistoryPanel.storage.get( 'show_deleted' ); + + var hiddenOptionIndex = popupMenu.findIndexByHtml( HIDDEN_OPTION_TEXT ); + if( hiddenOptionIndex === null ){ + popupMenu.addItem({ + html : HIDDEN_OPTION_TEXT, + func : function( clickEvent, thisMenuOption ){ + var show_hidden = Galaxy.currHistoryPanel.toggleShowHidden(); + thisMenuOption.checked = show_hidden; + } + }, START_INSERTING_AT_INDEX + 2 ) + hiddenOptionIndex = START_INSERTING_AT_INDEX + 2; + } + // whether was there or added, update the checked option to reflect the panel's settings on the panel render + popupMenu.options[ hiddenOptionIndex ].checked = Galaxy.currHistoryPanel.storage.get( 'show_hidden' ); + })(); + + //TODO: both the quota meter and the options-menu stuff need to be moved out when iframes are removed return; }); diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 templates/root/index.mako --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -10,7 +10,7 @@ $(function(){ // Init history options. $("#history-options-button").css( "position", "relative" ); - make_popupmenu( $("#history-options-button"), { + var popupmenu = PopupMenu.make_popupmenu( $("#history-options-button"), { "${_("History Lists")}": null, "${_("Saved Histories")}": function() { galaxy_main.location = "${h.url_for( controller='history', action='list')}"; @@ -40,18 +40,6 @@ "${_("Resume Paused Jobs")}": function() { galaxy_history.location = "${h.url_for( controller='history', action='resume_paused_jobs', current=True)}"; }, - "${_("Collapse Expanded Datasets")}": function() { - Galaxy.currHistoryPanel.collapseAllHdaBodies(); - //galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}"; - }, - "${_("Show/Hide Deleted Datasets")}": function() { - Galaxy.currHistoryPanel.toggleShowDeleted(); - //galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}"; - }, - "${_("Show/Hide Hidden Datasets")}": function() { - Galaxy.currHistoryPanel.toggleShowHidden(); - //galaxy_history.location = "${h.url_for( controller='root', action='history', show_hidden=True)}"; - }, "${_("Unhide Hidden Datasets")}": function() { if ( confirm( "Really unhide all hidden datasets?" ) ) { galaxy_main.location = "${h.url_for( controller='history', action='unhide_datasets', current=True )}"; @@ -83,7 +71,6 @@ galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}"; } }); - }); </script></%def> diff -r 330f05e523aee275c91f3e5de1177f8eb832d512 -r 6d7e637883b7e0e4c72c08a1269ca422da087661 test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py +++ b/test/functional/test_history_functions.py @@ -14,11 +14,12 @@ name = 'anonymous' self.new_history( name=name ) global anonymous_history - anonymous_history = sa_session.query( galaxy.model.History ) \ - .filter( and_( galaxy.model.History.table.c.deleted==False, - galaxy.model.History.table.c.name==name ) ) \ - .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ - .first() + anonymous_history = ( + sa_session.query( galaxy.model.History ) + .filter( and_( galaxy.model.History.table.c.deleted==False, galaxy.model.History.table.c.name==name ) ) + .order_by( desc( galaxy.model.History.table.c.create_time ) ) + .first() + ) assert anonymous_history is not None, "Problem retrieving anonymous_history from database" # Upload a dataset to anonymous_history so it will be set as the current history after login self.upload_file( '1.bed', dbkey='hg18' ) @@ -235,27 +236,35 @@ # Check list of histories to make sure shared history3 was cloned strings_displayed=[ "Clone of '%s' shared by '%s'" % ( history3.name, admin_user.email ) ] self.view_stored_active_histories( strings_displayed=strings_displayed ) + def test_035_clone_current_history( self ): """Testing cloning the current history""" # logged in as regular_user1 self.logout() self.login( email=admin_user.email ) + # Current history should be history3, add more datasets to history3, then delete them so we can # test cloning activatable datasets as well as only the active datasets self.upload_file( '2.bed', dbkey='hg18' ) - hda_2_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \ - .first() + hda_2_bed = ( + sa_session.query( galaxy.model.HistoryDatasetAssociation ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) + .first() + ) assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" self.delete_history_item( str( hda_2_bed.id ) ) + self.upload_file( '3.bed', dbkey='hg18' ) - hda_3_bed = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id, - galaxy.model.HistoryDatasetAssociation.table.c.name=='3.bed' ) ) \ - .first() + hda_3_bed = ( + sa_session.query( galaxy.model.HistoryDatasetAssociation ) + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history3.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='3.bed' ) ) + .first() + ) assert hda_3_bed is not None, "Problem retrieving hda_3_bed from database" self.delete_history_item( str( hda_3_bed.id ) ) + # Test cloning activatable datasets self.clone_history( self.security.encode_id( history3.id ), 'activatable', @@ -267,6 +276,7 @@ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() assert history3_clone2 is not None, "Problem retrieving history3_clone2 from database" + # Check list of histories to make sure shared history3 was cloned self.view_stored_active_histories( strings_displayed=[ "Clone of '%s'" % history3.name ] ) # Switch to the cloned history to make sure activatable datasets were cloned @@ -307,6 +317,7 @@ raise AssertionError, "Deleted datasets incorrectly included in cloned history history3_clone3" except: pass + def test_040_sharing_mulitple_histories_with_multiple_users( self ): """Testing sharing multiple histories containing only public datasets with multiple users""" # Logged in as admin_user https://bitbucket.org/galaxy/galaxy-central/changeset/cba8dbdb8312/ changeset: cba8dbdb8312 user: carlfeberhard date: 2012-12-07 20:00:51 summary: clean up; pack affected #: 3 files diff -r 6d7e637883b7e0e4c72c08a1269ca422da087661 -r cba8dbdb8312dcfa93e0be299fb560c067266064 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -66,7 +66,6 @@ //}); //this.bind( 'all', function( event ){ // //this.log( this + '', arguments ); - // console.info( this + '', arguments ); //}); }, diff -r 6d7e637883b7e0e4c72c08a1269ca422da087661 -r cba8dbdb8312dcfa93e0be299fb560c067266064 static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -190,7 +190,6 @@ // default settings this.$button = $button || $( '<div/>' ); this.options = options || []; - //console.debug( this + '.initialize, button:', $button, ', options:', options ); // set up button click -> open menu behavior var menu = this; @@ -230,7 +229,6 @@ // sets menu div id to '{{ id }}-menu' id : this.$button.attr( 'id' ) })); - //console.debug( this.$el, ':', this.$el.html() ); // set up behavior on each link/anchor elem if( this.options.length ){ @@ -239,7 +237,6 @@ $anchor = $li.children( 'a.popupmenu-option' ), menuFunc = menu.options[ i ].func; - //console.debug( 'setting up behavior:', i, menu.options[ i ], $li, $anchor ); if( $anchor.length && menuFunc ){ $anchor.click( function( event ){ menuFunc( event, menu.options[ i ] ); diff -r 6d7e637883b7e0e4c72c08a1269ca422da087661 -r cba8dbdb8312dcfa93e0be299fb560c067266064 static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:null,enabled:true,visible:true}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=$(Handlebars.partials.iconButton(this.model.toJSON()));a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(this.model.attributes.on_click){this.model.attributes.on_click(a);return false}return true}});IconButtonView.templates={iconButton:Handlebars.partials.iconButton};var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var PopupMenu=Backbone.View.extend({templates:{wrapper:(function(){var a=['<ul id="<%= id %>-menu" class="dropdown-menu">',"<% if( options.length ){ %>","<% for( var i=0; i<options.length; i++ ){ var option = options[ i ]; %>","<% if( option.divider ){ %>",'<li class="divider"></li>',"<% } else { %>","<% if( option.header ){ %>",'<li class="head"><a href=""javascript:void(0);"><%- option.html %></a></li>',"<% } else { %>","<li><a ",'href="<% print( ( option.href )?( option.href ):( "javascript:void(0);" ) ) %>" ','<% if( option.target ){ %>target="<%= option.target %>" <% } %>','class="popupmenu-option">','<% if( option.checked ){ %><span class="ficon ok"></span><% } %>',"<%- option.html %>","</a></li>","<% } %>","<% } %>","<% } %>","<% } else { %>","<li>No Options.</li>","<% } %>","</ul>"];return _.template(a.join(""))}())},initialize:function(b,a){this.$button=b||$("<div/>");this.options=a||[];var c=this;this.$button.click(function(d){c._renderAndShow(d);return false});this.$button.data("PopupMenu",this);if(!this.templates.wrapper){this.templates.wrapper=Handlebars.templates["template-popupmenu-wrapper"]}},render:function(){var a=this;this.$el.addClass("popmenu-wrapper").css({position:"absolute",display:"none"});this.$el.html(PopupMenu.templates.menu({options:this.options,id:this.$button.attr("id")}));if(this.options.length){this.$el.find("li").each(function(c,b){var f=$(b),e=f.children("a.popupmenu-option"),d=a.options[c].func;if(e.length&&d){e.click(function(g){d(g,a.options[c])})}a.options[c].$li=f})}return this},_getShownPosition:function(b){var c=this.$el.width(),a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_renderAndShow:function(a){this.render();this.$el.appendTo("body");this.$el.css(this._getShownPosition(a));this._setUpCloseBehavior();this.$el.show()},_setUpCloseBehavior:function(){var b=this,a=function(c){c.bind("click.close_popup",function(){b.remove();c.unbind("click.close_popup")})};a($(window.document));a($(window.top.document));_.each(window.top.frames,function(c){a($(c.document))})},addItem:function(b,a){a=(a>=0)?(a):(this.options.length);this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if((_.has(this.options[a],"html"))&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.templates={menu:Handlebars.templates["template-popupmenu-menu"]};PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(j){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}var i;switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;case"demo":if(i===undefined||i.closed){i=window.open(j,k);i.creator=self}break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a}; \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:null,enabled:true,visible:true}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=$(Handlebars.partials.iconButton(this.model.toJSON()));a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(this.model.attributes.on_click){this.model.attributes.on_click(a);return false}return true}});IconButtonView.templates={iconButton:Handlebars.partials.iconButton};var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var GalaxyPaths=Backbone.Model.extend({defaults:{root_path:"",image_path:""}});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b||$("<div/>");this.options=a||[];var c=this;this.$button.click(function(d){c._renderAndShow(d);return false});this.$button.data("PopupMenu",this);if(!this.templates.wrapper){this.templates.wrapper=Handlebars.templates["template-popupmenu-wrapper"]}},render:function(){var a=this;this.$el.addClass("popmenu-wrapper").css({position:"absolute",display:"none"});this.$el.html(PopupMenu.templates.menu({options:this.options,id:this.$button.attr("id")}));if(this.options.length){this.$el.find("li").each(function(c,b){var f=$(b),e=f.children("a.popupmenu-option"),d=a.options[c].func;if(e.length&&d){e.click(function(g){d(g,a.options[c])})}a.options[c].$li=f})}return this},_getShownPosition:function(b){var c=this.$el.width(),a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_renderAndShow:function(a){this.render();this.$el.appendTo("body");this.$el.css(this._getShownPosition(a));this._setUpCloseBehavior();this.$el.show()},_setUpCloseBehavior:function(){var b=this,a=function(c){c.bind("click.close_popup",function(){b.remove();c.unbind("click.close_popup")})};a($(window.document));a($(window.top.document));_.each(window.top.frames,function(c){a($(c.document))})},addItem:function(b,a){a=(a>=0)?(a):(this.options.length);this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if((_.has(this.options[a],"html"))&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.templates={menu:Handlebars.templates["template-popupmenu-menu"]};PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(j){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}var i;switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;case"demo":if(i===undefined||i.closed){i=window.open(j,k);i.creator=self}break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return 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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1 0

commit/galaxy-central: 2 new changesets
by Bitbucket 07 Dec '12

07 Dec '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d50bf81b0966/ changeset: d50bf81b0966 user: inithello date: 2012-12-07 18:04:42 summary: Generate new metadata when repository dependencies have been added or removed. affected #: 1 file diff -r 0b3db8ce29d68bf7fe8e2a37699f58c2d9fdbddb -r d50bf81b096669ae82b614b94a606be773943445 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -504,6 +504,35 @@ # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. reset_tool_data_tables( trans.app ) return repository, tool, message +def new_repository_dependency_metadata_required( trans, repository, metadata_dict ): + """ + Compare the last saved metadata for each repository dependency in the repository with the new + metadata in metadata_dict to determine if a new repository_metadata table record is required, + or if the last saved metadata record can be updated instead. + """ + if 'repository_dependencies' in metadata_dict: + repository_metadata = get_latest_repository_metadata( trans, repository.id ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata and 'repository_dependencies' in metadata: + saved_repository_dependencies = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] + new_repository_dependencies = metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] + # The saved metadata must be a subset of the new metadata. + for new_repository_dependency_metadata in new_repository_dependencies: + if new_repository_dependency_metadata not in saved_repository_dependencies: + return True + for saved_repository_dependency_metadata in saved_repository_dependencies: + if saved_repository_dependency_metadata not in new_repository_dependencies: + return True + else: + # We have repository metadata that does not include metadata for any repository dependencies in the + # repository, so we can update the existing repository metadata. + return False + else: + # There is no saved repository metadata, so we need to create a new repository_metadata table record. + return True + # The received metadata_dict includes no metadata for repository dependencies, so a new repository_metadata table record is not needed. + return False def new_tool_metadata_required( trans, repository, metadata_dict ): """ Compare the last saved metadata for each tool in the repository with the new metadata in metadata_dict to determine if a new repository_metadata @@ -579,7 +608,9 @@ if metadata_dict: downloadable = is_downloadable( metadata_dict ) repository_metadata = None - if new_tool_metadata_required( trans, repository, metadata_dict ) or new_workflow_metadata_required( trans, repository, metadata_dict ): + if new_repository_dependency_metadata_required( trans, repository, metadata_dict ) or \ + new_tool_metadata_required( trans, repository, metadata_dict ) or \ + new_workflow_metadata_required( trans, repository, metadata_dict ): # Create a new repository_metadata table row. repository_metadata = create_or_update_repository_metadata( trans, encoded_id, https://bitbucket.org/galaxy/galaxy-central/changeset/330f05e523ae/ changeset: 330f05e523ae user: inithello date: 2012-12-07 18:05:43 summary: Tool shed functional tests for repository dependency features. Cleaned up import *s. affected #: 9 files diff -r d50bf81b096669ae82b614b94a606be773943445 -r 330f05e523aee275c91f3e5de1177f8eb832d512 test/tool_shed/base/common.py --- a/test/tool_shed/base/common.py +++ b/test/tool_shed/base/common.py @@ -9,7 +9,7 @@ test_user_1_name = 'user1' new_repository_dependencies_xml = '''<?xml version="1.0"?> -<repositories> +<repositories${description}><repository toolshed="${toolshed_url}" name="${repository_name}" owner="${owner}" changeset_revision="${changeset_revision}" /></repositories> ''' diff -r d50bf81b096669ae82b614b94a606be773943445 -r 330f05e523aee275c91f3e5de1177f8eb832d512 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -1,8 +1,7 @@ -from base.twilltestcase import * -from galaxy.webapps.community.util.hgweb_config import * -from test_db_util import * -from common import * -import string +import galaxy.webapps.community.util.hgweb_config +import common, string, os +from base.twilltestcase import tc, from_json_string, TwillTestCase, security +from test_db_util import get_repository_metadata_by_repository_id_changeset_revision from galaxy import eggs eggs.require('mercurial') @@ -14,7 +13,7 @@ self.security = security.SecurityHelper( id_secret='changethisinproductiontoo' ) self.history_id = None self.hgweb_config_dir = os.environ.get( 'TEST_HG_WEB_CONFIG_DIR' ) - self.hgweb_config_manager = HgWebConfigManager() + self.hgweb_config_manager = galaxy.webapps.community.util.hgweb_config.HgWebConfigManager() self.hgweb_config_manager.hgweb_config_dir = self.hgweb_config_dir self.host = os.environ.get( 'TOOL_SHED_TEST_HOST' ) self.port = os.environ.get( 'TOOL_SHED_TEST_PORT' ) @@ -138,8 +137,12 @@ tc.fv( "1", "selected_files_to_delete", ','.join( files_to_delete ) ) tc.submit( 'select_files_to_delete_button' ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def display_manage_repository_page( self, repository, strings_displayed=[], strings_not_displayed=[] ): - url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) + def display_manage_repository_page( self, repository, changeset_revision=None, strings_displayed=[], strings_not_displayed=[] ): + base_url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) + if changeset_revision is not None: + url = '%s&changeset_revision=%s' % ( base_url, changeset_revision ) + else: + url = base_url self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) def display_repository_clone_page( self, owner_name, repository_name, strings_displayed=[], strings_not_displayed=[] ): @@ -209,14 +212,19 @@ else: string = string.replace( character, replacement ) return string - def generate_repository_dependency_xml( self, repository, xml_filename ): + def generate_repository_dependency_xml( self, repository, xml_filename, dependency_description='' ): changeset_revision = self.get_repository_tip( repository ) - template_parser = string.Template( new_repository_dependencies_xml ) + if dependency_description: + description = ' description="%s"' % dependency_description + else: + description = dependency_description + template_parser = string.Template( common.new_repository_dependencies_xml ) repository_dependency_xml = template_parser.safe_substitute( toolshed_url=self.url, owner=repository.user.username, repository_name=repository.name, - changeset_revision=changeset_revision ) - # Save the generated xml to test-data/emboss_5/repository_dependencies.xml. + changeset_revision=changeset_revision, + description=description ) + # Save the generated xml to the specified location. file( xml_filename, 'w' ).write( repository_dependency_xml ) def get_latest_repository_metadata_for_repository( self, repository ): # TODO: This will not work as expected. Fix it. @@ -293,6 +301,13 @@ ( self.security.encode_id( repository.id ), tool_xml_path, changeset_revision ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def repository_is_new( self, repository ): + repo = hg.repository( ui.ui(), self.get_repo_path( repository ) ) + tip_ctx = repo.changectx( repo.changelog.tip() ) + return tip_ctx.rev() < 0 + def reset_repository_metadata( self, repository ): + url = '/repository/reset_all_metadata?id=%s' % self.security.encode_id( repository.id ) + self.visit_url( url ) def revoke_write_access( self, repository, username ): url = '/repository/manage_repository?user_access_button=Remove&id=%s&remove_auth=%s' % \ ( self.security.encode_id( repository.id ), username ) diff -r d50bf81b096669ae82b614b94a606be773943445 -r 330f05e523aee275c91f3e5de1177f8eb832d512 test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -1,5 +1,5 @@ -from tool_shed.base.twilltestcase import * -from tool_shed.base.test_db_util import * +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +from tool_shed.base.test_db_util import get_repository_by_name_and_owner, get_user, get_private_role repository_name = 'filtering' repository_description = "Galaxy's filtering tool" @@ -9,14 +9,14 @@ def test_0000_initiate_users( self ): """Create necessary user accounts and login as an admin user.""" - self.login( email=test_user_1_email, username=test_user_1_name ) - test_user_1 = get_user( test_user_1_email ) + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = get_user( common.test_user_1_email ) assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email test_user_1_private_role = get_private_role( test_user_1 ) self.logout() - self.login( email=admin_email, username=admin_username ) - admin_user = get_user( admin_email ) - assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email admin_user_private_role = get_private_role( admin_user ) def test_0005_create_categories( self ): """Create categories""" @@ -33,27 +33,27 @@ strings_displayed=strings_displayed ) def test_0015_edit_repository( self ): """Edit the repository name, description, and long description""" - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) new_name = "renamed_filtering" new_description = "Edited filtering tool" new_long_description = "Edited long description" self.edit_repository_information( repository, repo_name=new_name, description=new_description, long_description=new_long_description ) def test_0020_change_repository_category( self ): """Change the categories associated with the filtering repository""" - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) self.edit_repository_categories( repository, categories_to_add=[ "Text Analysis" ], categories_to_remove=[ "Text Manipulation" ] ) def test_0025_grant_write_access( self ): '''Grant write access to another user''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) - self.grant_write_access( repository, usernames=[ test_user_1_name ] ) - self.revoke_write_access( repository, test_user_1_name ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) + self.grant_write_access( repository, usernames=[ common.test_user_1_name ] ) + self.revoke_write_access( repository, common.test_user_1_name ) def test_0030_upload_filtering_1_1_0( self ): """Upload filtering_1.1.0.tar to the repository""" - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" ) def test_0035_verify_repository( self ): '''Display basic repository pages''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) latest_changeset_revision = self.get_repository_tip( repository ) self.check_for_valid_tools( repository, strings_displayed=[ 'Filter1' ] ) self.check_count_of_metadata_revisions_associated_with_repository( repository, metadata_count=1 ) @@ -61,12 +61,12 @@ self.check_repository_tools_for_changeset_revision( repository, tip ) self.check_repository_metadata( repository, tip_only=False ) self.browse_repository( repository, strings_displayed=[ 'Browse %s revision' % repository.name, '(repository tip)' ] ) - self.display_repository_clone_page( admin_username, + self.display_repository_clone_page( common.admin_username, repository_name, strings_displayed=[ 'Uploaded filtering 1.1.0', latest_changeset_revision ] ) def test_0040_alter_repository_states( self ): '''Test toggling the malicious and deprecated repository flags.''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) self.set_repository_malicious( repository, set_malicious=True, strings_displayed=[ 'The repository tip has been defined as malicious.' ] ) self.set_repository_malicious( repository, set_malicious=False, @@ -82,7 +82,7 @@ set_deprecated=False ) def test_0045_display_repository_tip_file( self ): '''Display the contents of filtering.xml in the repository tip revision''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) self.display_repository_file_contents( repository=repository, filename='filtering.xml', filepath=None, @@ -90,7 +90,7 @@ strings_not_displayed=[] ) def test_0050_upload_filtering_txt_file( self ): '''Upload filtering.txt file associated with tool version 1.1.0.''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) self.upload_file( repository, 'filtering/filtering.txt', commit_message="Uploaded filtering.txt", @@ -99,7 +99,7 @@ self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) def test_0055_upload_filtering_test_data( self ): '''Upload filtering test data.''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) self.upload_file( repository, 'filtering/filtering_test_data.tar', commit_message="Uploaded filtering test data", remove_repo_files_not_in_tar='No' ) self.display_repository_file_contents( repository=repository, filename='1.bed', @@ -109,14 +109,14 @@ self.check_repository_metadata( repository, tip_only=True ) def test_0060_upload_filtering_2_2_0( self ): '''Upload filtering version 2.2.0''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) self.upload_file( repository, 'filtering/filtering_2.2.0.tar', commit_message="Uploaded filtering 2.2.0", remove_repo_files_not_in_tar='No' ) def test_0065_verify_filtering_repository( self ): '''Verify the new tool versions and repository metadata.''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) tip = self.get_repository_tip( repository ) self.check_for_valid_tools( repository ) strings_displayed = self.get_repository_metadata_revisions( repository ).append( 'Select a revision' ) @@ -126,7 +126,7 @@ self.check_repository_metadata( repository, tip_only=False ) def test_0070_upload_readme_txt_file( self ): '''Upload readme.txt file associated with tool version 2.2.0.''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) self.upload_file( repository, 'readme.txt', commit_message="Uploaded readme.txt" ) self.display_manage_repository_page( repository, strings_displayed=[ 'This is a readme file.' ] ) # Verify that there is a different readme file for each metadata revision. @@ -134,13 +134,13 @@ self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0', 'This is a readme file.' ] ) def test_0075_delete_readme_txt_file( self ): '''Delete the readme.txt file.''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) self.delete_files_from_repository( repository, filenames=[ 'readme.txt' ] ) self.check_count_of_metadata_revisions_associated_with_repository( repository, metadata_count=2 ) self.display_manage_repository_page( repository, strings_displayed=[ 'Readme file for filtering 1.1.0' ] ) def test_0080_search_for_valid_filter_tool( self ): '''Search for the filtering tool by tool ID, name, and version.''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) tip_changeset = self.get_repository_tip( repository ) search_fields = dict( tool_id='Filter1', tool_name='filter', tool_version='2.2.0' ) self.search_for_valid_tools( search_fields=search_fields, strings_displayed=[ tip_changeset ], strings_not_displayed=[] ) diff -r d50bf81b096669ae82b614b94a606be773943445 -r 330f05e523aee275c91f3e5de1177f8eb832d512 test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py @@ -1,5 +1,5 @@ -from tool_shed.base.twilltestcase import * -from tool_shed.base.test_db_util import * +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +from tool_shed.base.test_db_util import get_repository_by_name_and_owner, get_user, get_private_role repository_name = 'freebayes' repository_description = "Galaxy's freebayes tool" @@ -10,8 +10,8 @@ def test_0000_create_or_login_admin_user( self ): """Create necessary user accounts and login as an admin user.""" self.logout() - self.login( email=admin_email, username=admin_username ) - admin_user = get_user( admin_email ) + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = get_user( common.admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = get_private_role( admin_user ) def test_0005_create_category( self ): @@ -24,7 +24,7 @@ repository_long_description=repository_long_description, categories=[ 'SNP Analysis' ], strings_displayed=[] ) - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) self.upload_file( repository, 'freebayes/freebayes.xml', valid_tools_only=False, @@ -37,7 +37,7 @@ strings_displayed=[ 'requires an entry', 'tool_data_table_conf.xml' ] ) def test_0015_upload_missing_tool_data_table_conf_file( self ): '''Upload the missing tool_data_table_conf.xml.sample file to the repository.''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) self.upload_file( repository, 'freebayes/tool_data_table_conf.xml.sample', valid_tools_only=False, @@ -50,27 +50,27 @@ strings_displayed=[ 'refers to a file', 'sam_fa_indices.loc' ] ) def test_0020_upload_missing_sample_loc_file( self ): '''Upload the missing sam_fa_indices.loc.sample file to the repository.''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) self.upload_file( repository, 'freebayes/sam_fa_indices.loc.sample', strings_displayed=[], commit_message='Uploaded tool data table .loc file.' ) def test_0025_upload_invalid_tool_dependency_xml( self ): '''Upload tool_dependencies.xml defining version 0.9.5 of the freebayes package.''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) self.upload_file( repository, os.path.join( 'freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml' ), strings_displayed=[ 'Name, version and type from a tool requirement tag does not match' ], commit_message='Uploaded invalid tool dependency XML.' ) def test_0030_upload_valid_tool_dependency_xml( self ): '''Upload tool_dependencies.xml defining version 0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8 of the freebayes package.''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) self.upload_file( repository, os.path.join( 'freebayes', 'tool_dependencies.xml' ), commit_message='Uploaded valid tool dependency XML.' ) def test_0035_verify_tool_dependencies( self ): '''Verify that the uploaded tool_dependencies.xml specifies the correct package versions.''' - repository = get_repository_by_name_and_owner( repository_name, admin_username ) + repository = get_repository_by_name_and_owner( repository_name, common.admin_username ) self.display_manage_repository_page( repository, strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Valid tools' ], strings_not_displayed=[ 'Invalid tools' ] ) diff -r d50bf81b096669ae82b614b94a606be773943445 -r 330f05e523aee275c91f3e5de1177f8eb832d512 test/tool_shed/functional/test_0020_basic_repository_dependencies.py --- a/test/tool_shed/functional/test_0020_basic_repository_dependencies.py +++ b/test/tool_shed/functional/test_0020_basic_repository_dependencies.py @@ -1,11 +1,11 @@ -from tool_shed.base.twilltestcase import * -from tool_shed.base.test_db_util import * +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +from tool_shed.base.test_db_util import get_repository_by_name_and_owner, get_user, get_private_role datatypes_repository_name = 'emboss_datatypes' datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools." datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." -emboss_repository_name = 'emboss_5' +emboss_repository_name = 'emboss_0020' emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' @@ -14,56 +14,56 @@ def test_0000_initiate_users( self ): """Create necessary user accounts and login as an admin user.""" self.logout() - self.login( email=admin_email, username=admin_username ) - admin_user = get_user( admin_email ) - assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email admin_user_private_role = get_private_role( admin_user ) self.logout() - self.login( email=test_user_1_email, username=test_user_1_name ) - test_user_1 = get_user( test_user_1_email ) - assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % regular_email + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email test_user_1_private_role = get_private_role( test_user_1 ) def test_0005_create_category( self ): """Create Sequence Analysis category""" self.logout() - self.login( email=admin_email, username=admin_username ) + self.login( email=common.admin_email, username=common.admin_username ) self.create_category( 'Sequence Analysis', 'Tools for performing Protein and DNA/RNA analysis' ) def test_0010_create_emboss_datatypes_repository_and_upload_tarball( self ): '''Create and populate the emboss_datatypes repository.''' self.logout() - self.login( email=test_user_1_email, username=test_user_1_name ) + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) self.create_repository( datatypes_repository_name, datatypes_repository_description, repository_long_description=datatypes_repository_long_description, categories=[ 'Sequence Analysis' ], strings_displayed=[] ) - repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name ) + repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' ) def test_0015_verify_datatypes_in_datatypes_repository( self ): '''Verify that the emboss_datatypes repository contains datatype entries.''' - repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name ) + repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) self.display_manage_repository_page( repository, strings_displayed=[ 'Datatypes', 'equicktandem', 'hennig86', 'vectorstrip' ] ) def test_0020_create_emboss_5_repository_and_upload_files( self ): - '''Create and populate the emboss_5 repository.''' + '''Create and populate the emboss_5_0020 repository.''' self.create_repository( emboss_repository_name, emboss_repository_description, repository_long_description=emboss_repository_long_description, categories=[ 'Text Manipulation' ], strings_displayed=[] ) - repository = get_repository_by_name_and_owner( emboss_repository_name, test_user_1_name ) - self.upload_file( repository, 'emboss/5/emboss.tar', commit_message='Uploaded emboss_5.tar' ) + repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' ) def test_0025_generate_and_upload_repository_dependencies_xml( self ): '''Generate and upload the repository_dependencies.xml file''' - repository = get_repository_by_name_and_owner( emboss_repository_name, test_user_1_name ) - datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name ) + repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) self.generate_repository_dependency_xml( datatypes_repository, self.get_filename( 'emboss/5/repository_dependencies.xml' ) ) self.upload_file( repository, 'emboss/5/repository_dependencies.xml', commit_message='Uploaded repository_dependencies.xml' ) def test_0030_verify_emboss_5_repository_dependency_on_emboss_datatypes( self ): '''Verify that the emboss_5 repository now depends on the emboss_datatypes repository with correct name, owner, and changeset revision.''' - repository = get_repository_by_name_and_owner( emboss_repository_name, test_user_1_name ) - datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name ) + repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) changeset_revision = self.get_repository_tip( datatypes_repository ) - strings_displayed = [ datatypes_repository_name, test_user_1_name, changeset_revision, 'Repository dependencies' ] + strings_displayed = [ datatypes_repository_name, common.test_user_1_name, changeset_revision, 'Repository dependencies' ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) def test_0035_cleanup( self ): '''Clean up generated test data.''' diff -r d50bf81b096669ae82b614b94a606be773943445 -r 330f05e523aee275c91f3e5de1177f8eb832d512 test/tool_shed/functional/test_0030_repository_dependency_revisions.py --- /dev/null +++ b/test/tool_shed/functional/test_0030_repository_dependency_revisions.py @@ -0,0 +1,134 @@ +from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os +from tool_shed.base.test_db_util import get_repository_by_name_and_owner, get_user, get_private_role + +datatypes_repository_name = 'emboss_datatypes' +datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools." +datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." + +emboss_repository_name = 'emboss' +emboss_5_repository_name = 'emboss_5_0030' +emboss_6_repository_name = 'emboss_6_0030' +emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' +emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' + +class TestRepositoryDependencyRevisions( ShedTwillTestCase ): + '''Test dependencies on different revisions of a repository.''' + ''' + create repository emboss_5_0030 + create repository emboss_6_0030 + create repository emboss_datatypes if necessary + create repository emboss + emboss_5 has repository_dependency.xml file that defines emboss_datatypes + emboss_6 has repository_dependency.xml file that defines emboss_datatypes + get information to create repository dependency imformation for emboss + emboss depends on emboss_5 + then emboss depends on emboss_6 + verify per-changeset dependencies + ''' + def test_0000_initiate_users( self ): + """Create necessary user accounts.""" + self.logout() + self.login( email=common.admin_email, username=common.admin_username ) + admin_user = get_user( common.admin_email ) + assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email + admin_user_private_role = get_private_role( admin_user ) + self.logout() + self.login( email=common.test_user_1_email, username=common.test_user_1_name ) + test_user_1 = get_user( common.test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % regular_email + test_user_1_private_role = get_private_role( test_user_1 ) + def test_0005_create_repositories( self ): + '''Create the emboss_5_0030, emboss_6_0030, emboss_datatypes, and emboss repositories and populate the emboss_datatypes repository.''' + emboss_5_repository = get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) + if emboss_5_repository is None: + self.create_repository( emboss_5_repository_name, + emboss_repository_description, + repository_long_description=emboss_repository_long_description, + categories=[ 'Sequence Analysis' ], + strings_displayed=[] ) + emboss_5_repository = get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) + self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' ) + emboss_6_repository = get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) + if emboss_6_repository is None: + self.create_repository( emboss_6_repository_name, + emboss_repository_description, + repository_long_description=emboss_repository_long_description, + categories=[ 'Sequence Analysis' ], + strings_displayed=[] ) + emboss_6_repository = get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) + self.upload_file( emboss_6_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball..' ) + datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + if datatypes_repository is None: + self.create_repository( datatypes_repository_name, + datatypes_repository_description, + repository_long_description=datatypes_repository_long_description, + categories=[ 'Sequence Analysis' ], + strings_displayed=[] ) + datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + if self.repository_is_new( datatypes_repository ): + self.upload_file( datatypes_repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' ) + emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + if emboss_repository is None: + self.create_repository( emboss_repository_name, + emboss_repository_description, + repository_long_description=emboss_repository_long_description, + categories=[ 'Sequence Analysis' ], + strings_displayed=[] ) + emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' ) + def test_0010_generate_repository_dependencies_for_emboss_5( self ): + '''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_5 repository.''' + datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + self.generate_repository_dependency_xml( datatypes_repository, self.get_filename( 'emboss/repository_dependencies.xml' ) ) + emboss_5_repository = get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) + self.upload_file( emboss_5_repository, 'emboss/repository_dependencies.xml', commit_message='Uploaded repository_depepndencies.xml.' ) + def test_0015_generate_repository_dependencies_for_emboss_6( self ): + '''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_6 repository.''' + emboss_6_repository = get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) + self.upload_file( emboss_6_repository, 'emboss/repository_dependencies.xml', commit_message='Uploaded repository_depepndencies.xml.' ) + def test_0020_generate_repository_dependency_on_emboss_5( self ): + '''Create and upload repository_dependencies.xml for the emboss_5_0030 repository.''' + emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + emboss_5_repository = get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) + self.generate_repository_dependency_xml( emboss_5_repository, + self.get_filename( 'emboss/5/repository_dependencies.xml' ), + dependency_description='Emboss requires the Emboss 5 repository.' ) + self.upload_file( emboss_repository, + 'emboss/5/repository_dependencies.xml', + commit_message='Uploaded dependency configuration specifying emboss_5' ) + def test_0025_generate_repository_dependency_on_emboss_6( self ): + '''Create and upload repository_dependencies.xml for the emboss_6_0030 repository.''' + emboss_repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + emboss_6_repository = get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) + self.generate_repository_dependency_xml( emboss_6_repository, + self.get_filename( 'emboss/6/repository_dependencies.xml' ), + dependency_description='Emboss requires the Emboss 6 repository.' ) + self.upload_file( emboss_repository, + 'emboss/6/repository_dependencies.xml', + commit_message='Uploaded dependency configuration specifying emboss_6' ) + def test_0030_verify_repository_dependency_revisions( self ): + '''Verify that different metadata revisions of the emboss repository have different repository dependencies.''' + repository = get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) + # Reset emboss metadata to pick up the repository dependency changes. +# self.reset_repository_metadata( repository ) + repository_metadata = [ ( metadata.metadata, metadata.changeset_revision ) for metadata in self.get_repository_metadata( repository ) ] + datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) + datatypes_tip = self.get_repository_tip( datatypes_repository ) + # Iterate through all metadata revisions and check for repository dependencies. + for metadata, changeset_revision in repository_metadata: + repository_dependency_metadata = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ][ 0 ] + # Remove the tool shed URL, because that's not displayed on the page (yet?) + repository_dependency_metadata.pop( repository_dependency_metadata.index( self.url ) ) + # Add the dependency description and datatypes repository details to the strings to check. + repository_dependency_metadata.extend( [ metadata[ 'repository_dependencies' ][ 'description' ], + datatypes_repository_name, + datatypes_repository.user.username, + datatypes_tip ] ) + self.display_manage_repository_page( repository, + changeset_revision=changeset_revision, + strings_displayed=[ str( metadata ) for metadata in repository_dependency_metadata ] ) + def test_0035_cleanup( self ): + '''Clean up generated repository dependency XML files.''' + for filename in [ 'emboss/5/repository_dependencies.xml', 'emboss/6/repository_dependencies.xml', 'emboss/repository_dependencies.xml' ]: + if os.path.exists( self.get_filename( filename ) ): + os.remove( self.get_filename( filename ) ) diff -r d50bf81b096669ae82b614b94a606be773943445 -r 330f05e523aee275c91f3e5de1177f8eb832d512 test/tool_shed/test_data/emboss/5/emboss.tar Binary file test/tool_shed/test_data/emboss/5/emboss.tar has changed diff -r d50bf81b096669ae82b614b94a606be773943445 -r 330f05e523aee275c91f3e5de1177f8eb832d512 test/tool_shed/test_data/emboss/6/emboss.tar Binary file test/tool_shed/test_data/emboss/6/emboss.tar has changed diff -r d50bf81b096669ae82b614b94a606be773943445 -r 330f05e523aee275c91f3e5de1177f8eb832d512 test/tool_shed/test_data/emboss/emboss.tar Binary file test/tool_shed/test_data/emboss/emboss.tar has changed Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Visualization framework enhancements: (a) refactor orphan vars and functions into mixins; (b) remove overly-qualified model references; (c) add support for multiple data types, gracefully falling back if a converter is not available; and (d) add bigwig as an index datatype for BAM.
by Bitbucket 07 Dec '12

07 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0b3db8ce29d6/ changeset: 0b3db8ce29d6 user: jgoecks date: 2012-12-07 17:46:03 summary: Visualization framework enhancements: (a) refactor orphan vars and functions into mixins; (b) remove overly-qualified model references; (c) add support for multiple data types, gracefully falling back if a converter is not available; and (d) add bigwig as an index datatype for BAM. affected #: 6 files diff -r 6591b6ebfb4ea56118941deef03855412c2c00fd -r 0b3db8ce29d68bf7fe8e2a37699f58c2d9fdbddb lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -239,7 +239,7 @@ except: return "Binary bam alignments file (%s)" % ( data.nice_size( dataset.get_size() ) ) def get_track_type( self ): - return "ReadTrack", {"data": "bai", "index": "summary_tree"} + return "ReadTrack", { "data": "bai", "index": [ "bigwig", "summary_tree" ] } Binary.register_sniffable_binary_format("bam", "bam", Bam) diff -r 6591b6ebfb4ea56118941deef03855412c2c00fd -r 0b3db8ce29d68bf7fe8e2a37699f58c2d9fdbddb lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -872,6 +872,16 @@ PAUSED = 'paused', SETTING_METADATA = 'setting_metadata', FAILED_METADATA = 'failed_metadata' ) + + conversion_messages = Bunch( PENDING = "pending", + NO_DATA = "no data", + NO_CHROMOSOME = "no chromosome", + NO_CONVERTER = "no converter", + NO_TOOL = "no tool", + DATA = "data", + ERROR = "error", + OK = "ok" ) + permitted_actions = get_permitted_actions( filter='DATASET' ) file_path = "/tmp/" object_store = None # This get initialized in mapping.py (method init) by app.py @@ -996,6 +1006,7 @@ class DatasetInstance( object ): """A base class for all 'dataset instances', HDAs, LDAs, etc""" states = Dataset.states + conversion_messages = Dataset.conversion_messages permitted_actions = Dataset.permitted_actions def __init__( self, id=None, hid=None, name=None, info=None, blurb=None, peek=None, tool_version=None, extension=None, dbkey=None, metadata=None, history=None, dataset=None, deleted=False, designation=None, @@ -1170,9 +1181,9 @@ if dep_dataset is None: # None means converter is running first time return None - elif dep_dataset.state == trans.app.model.Job.states.ERROR: + elif dep_dataset.state == Job.states.ERROR: raise ConverterDependencyException("A dependency (%s) was in an error state." % dependency) - elif dep_dataset.state != trans.app.model.Job.states.OK: + elif dep_dataset.state != Job.states.OK: # Pending return None deps[dependency] = dep_dataset @@ -1196,12 +1207,11 @@ for name, value in self.metadata.items(): # HACK: MetadataFile objects do not have a type/ext, so need to use metadata name # to determine type. - if dataset_ext == 'bai' and name == 'bam_index' and isinstance( value, trans.app.model.MetadataFile ): + if dataset_ext == 'bai' and name == 'bam_index' and isinstance( value, MetadataFile ): # HACK: MetadataFile objects cannot be used by tools, so return # a fake HDA that points to metadata file. - fake_dataset = trans.app.model.Dataset( state=trans.app.model.Dataset.states.OK, - external_filename=value.file_name ) - fake_hda = trans.app.model.HistoryDatasetAssociation( dataset=fake_dataset ) + fake_dataset = Dataset( state=Dataset.states.OK, external_filename=value.file_name ) + fake_hda = HistoryDatasetAssociation( dataset=fake_dataset ) return fake_hda def clear_associated_files( self, metadata_safe = False, purge = False ): raise 'Unimplemented' @@ -1311,16 +1321,26 @@ track_type, data_sources = self.datatype.get_track_type() data_sources_dict = {} msg = None - for source_type, data_source in data_sources.iteritems(): + for source_type, source_list in data_sources.iteritems(): + data_source = None if source_type == "data_standalone": # Nothing to do. msg = None + data_source = source_list else: # Convert. - msg = self.convert_dataset( trans, data_source ) + if isinstance( source_list, str ): + source_list = [ source_list ] + + # Loop through sources until viable one is found. + for source in source_list: + msg = self.convert_dataset( trans, source ) + if msg == self.conversion_messages.PENDING: + data_source = source + break # Store msg. - data_sources_dict[ source_type ] = { "name" : data_source, "message": msg } + data_sources_dict[ source_type ] = { "name": data_source, "message": msg } return data_sources_dict @@ -1331,35 +1351,23 @@ was converted successfully. """ - # FIXME: copied from controller.py - messages = Bunch( - PENDING = "pending", - NO_DATA = "no data", - NO_CHROMOSOME = "no chromosome", - NO_CONVERTER = "no converter", - NO_TOOL = "no tool", - DATA = "data", - ERROR = "error", - OK = "ok" - ) - # Get converted dataset; this will start the conversion if necessary. try: converted_dataset = self.get_converted_dataset( trans, target_type ) except NoConverterException: - return messages.NO_CONVERTER + return self.conversion_messages.NO_CONVERTER except ConverterDependencyException, dep_error: - return { 'kind': messages.ERROR, 'message': dep_error.value } + return { 'kind': self.conversion_messages.ERROR, 'message': dep_error.value } # Check dataset state and return any messages. msg = None - if converted_dataset and converted_dataset.state == trans.app.model.Dataset.states.ERROR: - job_id = trans.sa_session.query( trans.app.model.JobToOutputDatasetAssociation ) \ + if converted_dataset and converted_dataset.state == Dataset.states.ERROR: + job_id = trans.sa_session.query( JobToOutputDatasetAssociation ) \ .filter_by( dataset_id=converted_dataset.id ).first().job_id - job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) - msg = { 'kind': messages.ERROR, 'message': job.stderr } - elif not converted_dataset or converted_dataset.state != trans.app.model.Dataset.states.OK: - msg = messages.PENDING + job = trans.sa_session.query( Job ).get( job_id ) + msg = { 'kind': self.conversion_messages.ERROR, 'message': job.stderr } + elif not converted_dataset or converted_dataset.state != Dataset.states.OK: + msg = self.conversion_messages.PENDING return msg @@ -2414,7 +2422,7 @@ elif not trans.app.config.smtp_server: comments = "Email notification failed as SMTP server not set in config file" if comments: - event = trans.app.model.RequestEvent( self, self.state, comments ) + event = RequestEvent( self, self.state, comments ) trans.sa_session.add( event ) trans.sa_session.flush() return comments diff -r 6591b6ebfb4ea56118941deef03855412c2c00fd -r 0b3db8ce29d68bf7fe8e2a37699f58c2d9fdbddb lib/galaxy/visualization/data_providers/registry.py --- a/lib/galaxy/visualization/data_providers/registry.py +++ b/lib/galaxy/visualization/data_providers/registry.py @@ -1,6 +1,9 @@ from galaxy.visualization.data_providers.basic import ColumnDataProvider -from galaxy.visualization.data_providers.genome import * +from galaxy.visualization.data_providers import genome +from galaxy.model import NoConverterException from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider +from galaxy.datatypes.tabular import Tabular, Vcf +from galaxy.datatypes.interval import Interval, ENCODEPeak, ChromatinInteractions, Gtf, Gff, Bed from galaxy.datatypes.xml import Phyloxml from galaxy.datatypes.data import Newick, Nexus @@ -15,20 +18,20 @@ # is original dataset type. self.dataset_type_name_to_data_provider = { "tabix": { - Vcf: VcfTabixDataProvider, - Bed: BedTabixDataProvider, - Gtf: GtfTabixDataProvider, - ENCODEPeak: ENCODEPeakTabixDataProvider, - Interval: IntervalTabixDataProvider, - ChromatinInteractions: ChromatinInteractionsTabixDataProvider, - "default" : TabixDataProvider + Vcf: genome.VcfTabixDataProvider, + Bed: genome.BedTabixDataProvider, + Gtf: genome.GtfTabixDataProvider, + ENCODEPeak: genome.ENCODEPeakTabixDataProvider, + Interval: genome.IntervalTabixDataProvider, + ChromatinInteractions: genome.ChromatinInteractionsTabixDataProvider, + "default" : genome.TabixDataProvider }, - "interval_index": IntervalIndexDataProvider, - "bai": BamDataProvider, - "bam": SamDataProvider, - "summary_tree": SummaryTreeDataProvider, - "bigwig": BigWigDataProvider, - "bigbed": BigBedDataProvider + "interval_index": genome.IntervalIndexDataProvider, + "bai": genome.BamDataProvider, + "bam": genome.SamDataProvider, + "summary_tree": genome.SummaryTreeDataProvider, + "bigwig": genome.BigWigDataProvider, + "bigbed": genome.BigBedDataProvider } def get_data_provider( self, trans, name=None, source='data', raw=False, original_dataset=None ): @@ -41,15 +44,15 @@ if raw: # Working with raw data. if isinstance( original_dataset.datatype, Gff ): - data_provider_class = RawGFFDataProvider + data_provider_class = genome.RawGFFDataProvider elif isinstance( original_dataset.datatype, Bed ): - data_provider_class = RawBedDataProvider + data_provider_class = genome.RawBedDataProvider elif isinstance( original_dataset.datatype, Vcf ): - data_provider_class = RawVcfDataProvider + data_provider_class = genome.RawVcfDataProvider elif isinstance( original_dataset.datatype, Tabular ): - data_provider_class = ColumnDataProvider + data_provider_class = genome.ColumnDataProvider elif isinstance( original_dataset.datatype, ( Nexus, Newick, Phyloxml ) ): - data_provider_class = PhylovizDataProvider + data_provider_class = genome.PhylovizDataProvider data_provider = data_provider_class( original_dataset=original_dataset ) @@ -87,10 +90,20 @@ # Get data provider mapping and data provider. _ , data_provider_mapping = original_dataset.datatype.get_track_type() if 'data_standalone' in data_provider_mapping: - data_provider_name = data_provider_mapping[ 'data_standalone' ] + data_provider = self.get_data_provider( trans, + name=data_provider_mapping[ 'data_standalone' ], + original_dataset=original_dataset ) else: - data_provider_name = data_provider_mapping[ source ] - - data_provider = self.get_data_provider( trans, name=data_provider_name, original_dataset=original_dataset ) + source_list = data_provider_mapping[ source ] + if isinstance( source_list, str ): + source_list = [ source_list ] + + # Find a valid data provider in the source list. + for source in source_list: + try: + data_provider = self.get_data_provider( trans, name=source, original_dataset=original_dataset ) + break + except NoConverterException: + pass return data_provider \ No newline at end of file diff -r 6591b6ebfb4ea56118941deef03855412c2c00fd -r 0b3db8ce29d68bf7fe8e2a37699f58c2d9fdbddb lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -190,37 +190,6 @@ # -- Mixins for working with Galaxy objects. -- # -# Message strings returned to browser -messages = Bunch( - PENDING = "pending", - NO_DATA = "no data", - NO_CHROMOSOME = "no chromosome", - NO_CONVERTER = "no converter", - NO_TOOL = "no tool", - DATA = "data", - ERROR = "error", - OK = "ok" -) - -def get_highest_priority_msg( message_list ): - """ - Returns highest priority message from a list of messages. - """ - return_message = None - - # For now, priority is: job error (dict), no converter, pending. - for message in message_list: - if message is not None: - if isinstance(message, dict): - return_message = message - break - elif message == messages.NO_CONVERTER: - return_message = message - elif return_message == None and message == messages.PENDING: - return_message = message - return return_message - - class SharableItemSecurityMixin: """ Mixin for handling security for sharable items. """ def security_check( self, trans, item, check_ownership=False, check_accessible=False ): @@ -313,11 +282,11 @@ Returns a message if dataset is not ready to be used in visualization. """ if not dataset: - return messages.NO_DATA + return dataset.conversion_messages.NO_DATA if dataset.state == trans.app.model.Job.states.ERROR: - return messages.ERROR + return dataset.conversion_messages.ERROR if dataset.state != trans.app.model.Job.states.OK: - return messages.PENDING + return dataset.conversion_messages.PENDING return None @@ -624,7 +593,7 @@ # If there are no messages (messages indicate data is not ready/available), get data. messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] - message = get_highest_priority_msg( messages_list ) + message = self._get_highest_priority_msg( messages_list ) if message: rval = message else: @@ -646,6 +615,27 @@ return rval + # FIXME: this method probably belongs down in the model.Dataset class. + def _get_highest_priority_msg( self, message_list ): + """ + Returns highest priority message from a list of messages. + """ + return_message = None + + # For now, priority is: job error (dict), no converter, pending. + for message in message_list: + if message is not None: + if isinstance(message, dict): + return_message = message + break + elif message == "no converter": + return_message = message + elif return_message == None and message == "pending": + return_message = message + return return_message + + + class UsesStoredWorkflowMixin( SharableItemSecurityMixin ): """ Mixin for controllers that use StoredWorkflow objects. """ def get_stored_workflow( self, trans, id, check_ownership=True, check_accessible=False ): diff -r 6591b6ebfb4ea56118941deef03855412c2c00fd -r 0b3db8ce29d68bf7fe8e2a37699f58c2d9fdbddb lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -4,7 +4,7 @@ import logging, os, string, shutil, urllib, re, socket from galaxy import util, datatypes, jobs, web, util from galaxy.visualization.data_providers.genome import FeatureLocationIndexDataProvider -from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin, get_highest_priority_msg, messages +from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin from galaxy.web.framework.helpers import is_true log = logging.getLogger( __name__ ) @@ -64,7 +64,7 @@ msg = self.check_dataset_state( trans, dataset ) if not msg: - msg = messages.DATA + msg = dataset.conversion_messages.DATA return msg @@ -80,7 +80,7 @@ # Get datasources and check for messages (which indicate errors). Retry if flag is set. data_sources = dataset.get_datasources( trans ) messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] - msg = get_highest_priority_msg( messages_list ) + msg = self._get_highest_priority_msg( messages_list ) if msg: if retry: # Clear datasources and then try again. @@ -92,12 +92,12 @@ # If there is a chrom, check for data on the chrom. if chrom: data_provider_registry = trans.app.data_provider_registry - data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset= dataset, source='index' ) + data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset=dataset, source='index' ) if not data_provider.has_data( chrom ): - return messages.NO_DATA + return dataset.conversion_messages.NO_DATA # Have data if we get here - return { "status": messages.DATA, "valid_chroms": None } + return { "status": dataset.conversion_messages.DATA, "valid_chroms": None } def _search_features( self, trans, dataset, query ): """ @@ -121,17 +121,17 @@ # Parameter check. if not chrom: - return messages.NO_DATA + return dataset.conversion_messages.NO_DATA # Dataset check. msg = self.check_dataset_state( trans, dataset ) if msg: return msg - # Get datasources and check for messages. + # Get datasources and check for essages. data_sources = dataset.get_datasources( trans ) messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] - return_message = get_highest_priority_msg( messages_list ) + return_message = self._get_highest_priority_msg( messages_list ) if return_message: return return_message diff -r 6591b6ebfb4ea56118941deef03855412c2c00fd -r 0b3db8ce29d68bf7fe8e2a37699f58c2d9fdbddb lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -1,5 +1,5 @@ from galaxy import web, util -from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin, messages, get_highest_priority_msg +from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin from galaxy.visualization.genome.visual_analytics import get_dataset_job from galaxy.visualization.genomes import GenomeRegion from galaxy.util.json import to_json_string, from_json_string @@ -57,7 +57,7 @@ tool_id = payload[ 'tool_id' ] tool = trans.app.toolbox.get_tool( tool_id ) if not tool: - return { "message": { "type": "error", "text" : messages.NO_TOOL } } + return { "message": { "type": "error", "text" : trans.app.model.Dataset.conversion_messages.NO_TOOL } } # Set running history from payload parameters. # History not set correctly as part of this API call for @@ -123,7 +123,7 @@ # tool = trans.app.toolbox.get_tool( tool_id ) if not tool: - return messages.NO_TOOL + return trans.app.model.Dataset.conversion_messages.NO_TOOL # HACK: add run button so that tool.handle_input will run tool. kwargs['runtool_btn'] = 'Execute' @@ -199,7 +199,7 @@ original_job = get_dataset_job( original_dataset ) tool = trans.app.toolbox.get_tool( original_job.tool_id ) if not tool: - return messages.NO_TOOL + return trans.app.model.Dataset.conversion_messages.NO_TOOL tool_params = dict( [ ( p.name, p.value ) for p in original_job.parameters ] ) # TODO: rather than set new inputs using dict of json'ed value, unpack parameters and set using set_param_value below. @@ -226,7 +226,7 @@ messages_list.append( msg ) # Return any messages generated during conversions. - return_message = get_highest_priority_msg( messages_list ) + return_message = self._get_highest_priority_msg( messages_list ) if return_message: return to_json_string( return_message ) @@ -290,7 +290,7 @@ break if not success: - return messages.ERROR + return trans.app.model.Dataset.conversion_messages.ERROR # # Set input datasets for tool. If running on regions, extract and use subset 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: Converter enhancements: (a) add bam to bigwig converter; (b) update datatypes.conf.sample to include new converter (disabled by default and documented with requirements) and remove unneeded dependency for bam to summary tree converter; and (c) remove deprecated page tags from bedgraph to bigwig converter.
by Bitbucket 07 Dec '12

07 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6591b6ebfb4e/ changeset: 6591b6ebfb4e user: jgoecks date: 2012-12-07 16:33:39 summary: Converter enhancements: (a) add bam to bigwig converter; (b) update datatypes.conf.sample to include new converter (disabled by default and documented with requirements) and remove unneeded dependency for bam to summary tree converter; and (c) remove deprecated page tags from bedgraph to bigwig converter. affected #: 3 files diff -r 8305907fa2312da14cf4d500fba1675a169b5517 -r 6591b6ebfb4ea56118941deef03855412c2c00fd datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -7,7 +7,12 @@ <datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/><datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true"><converter file="bam_to_bai.xml" target_datatype="bai"/> - <converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree" depends_on="bai"/> + <converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <display file="ucsc/bam.xml" /><display file="ensembl/ensembl_bam.xml" /><display file="igv/bam.xml" /> diff -r 8305907fa2312da14cf4d500fba1675a169b5517 -r 6591b6ebfb4ea56118941deef03855412c2c00fd lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml @@ -0,0 +1,14 @@ +<tool id="CONVERTER_bam_to_bigwig_0" name="Convert BAM to BigWig" version="1.0.0" hidden="true"> +  + <command> + bedtools genomecov -bg -split -ibam $input -g $chromInfo | wigToBigWig stdin $chromInfo $output + </command> + <inputs> + <param format="bam" name="input" type="data" label="Choose BAM file"/> + </inputs> + <outputs> + <data format="bigwig" name="output"/> + </outputs> + <help> + </help> +</tool> diff -r 8305907fa2312da14cf4d500fba1675a169b5517 -r 6591b6ebfb4ea56118941deef03855412c2c00fd lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml @@ -2,9 +2,7 @@ <command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command><inputs> - <page><param format="bedgraph" name="input" type="data" label="Choose wiggle"/> - </page></inputs><outputs><data format="bigwig" name="output"/> 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 Bitbucket 07 Dec '12

07 Dec '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/be37937a0b5b/ changeset: be37937a0b5b user: jgoecks date: 2012-12-07 16:15:48 summary: Add needed import. affected #: 1 file diff -r ad6d34f4decb896e65d988cdd71a09f3fad62722 -r be37937a0b5b05c6047720758bf330087c099e6c lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -3,6 +3,7 @@ """ import logging, os, string, shutil, urllib, re, socket from galaxy import util, datatypes, jobs, web, util +from galaxy.visualization.data_providers.genome import FeatureLocationIndexDataProvider from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin, get_highest_priority_msg, messages from galaxy.web.framework.helpers import is_true https://bitbucket.org/galaxy/galaxy-central/changeset/8305907fa231/ changeset: 8305907fa231 user: jgoecks date: 2012-12-07 16:18:50 summary: Fixes for bam_to_summary_tree converter: (a) remove deprecated page tags and (b) use bai from metadata rather than from dependency injection. affected #: 1 file diff -r be37937a0b5b05c6047720758bf330087c099e6c -r 8305907fa2312da14cf4d500fba1675a169b5517 lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml --- a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml +++ b/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.xml @@ -1,11 +1,10 @@ <tool id="CONVERTER_bam_to_summary_tree_0" name="Convert BAM to Summary Tree" version="1.0.0" hidden="true"> - - <command interpreter="python">sam_or_bam_to_summary_tree_converter.py --bam $input1 $bai $output1</command> +  + <command interpreter="python"> + sam_or_bam_to_summary_tree_converter.py --bam $input1 $input1.metadata.bam_index $output1 + </command><inputs> - <page> - <param format="bam" name="input1" type="data" label="Choose BAM file"/> - <param format="bai" name="bai" type="data" label="BAI index file"/> - </page> + <param format="bam" name="input1" type="data" label="Choose BAM file"/></inputs><outputs><data format="summary_tree" name="output1"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: history panel: fix to trackster links when dbkey is empty; pack_scripts
by Bitbucket 06 Dec '12

06 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ad6d34f4decb/ changeset: ad6d34f4decb user: carlfeberhard date: 2012-12-06 23:34:18 summary: history panel: fix to trackster links when dbkey is empty; pack_scripts affected #: 2 files diff -r 75e427a748d0b3e89ccdf246f22499c2f44d9e2a -r ad6d34f4decb896e65d988cdd71a09f3fad62722 static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -189,6 +189,8 @@ dataset_id: this.model.get( 'id' ), hda_ldda: 'hda' }; + // Add dbkey to params if it exists. + if( dbkey ){ params.dbkey = dbkey; } if( !( this.model.hasData() ) || !( visualizations && visualizations.length ) @@ -209,8 +211,6 @@ //TODO: make this more concise // map a function to each visualization in the icon's attributes // create a popupmenu from that map - // Add dbkey to params if it exists. - if( dbkey ){ params.dbkey = dbkey; } /** @inner */ function create_viz_action( visualization ) { @@ -513,10 +513,13 @@ //TODO: should be imported from trackster.js function create_trackster_action_fn(vis_url, dataset_params, dbkey) { return function() { - var params = {}; - if (dbkey) { params.dbkey = dbkey; } + var listTracksParams = {}; + if (dbkey){ + // list_tracks seems to use 'f-dbkey' (??) + listTracksParams[ 'f-dbkey' ] = dbkey; + } $.ajax({ - url: vis_url + '/list_tracks?f-' + $.param(params), + url: vis_url + '/list_tracks?' + $.param( listTracksParams ), dataType: "html", error: function() { alert( _l( "Could not add this dataset to browser" ) + '.' ); }, success: function(table_html) { diff -r 75e427a748d0b3e89ccdf246f22499c2f44d9e2a -r ad6d34f4decb896e65d988cdd71a09f3fad62722 static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a={title:_l("Delete"),href:this.urls["delete"],id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if(this.model.get("deleted")||this.model.get("purged")){a={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(!(this.model.hasData())||!(a&&a.length)||!(f)){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");if(c){g.dbkey=c}function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert(_l("Tagging failed"))},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotations failed"))},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d.dbkey=b}$.ajax({url:a+"/list_tracks?f-"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file +var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a={title:_l("Delete"),href:this.urls["delete"],id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if(this.model.get("deleted")||this.model.get("purged")){a={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}if(!(this.model.hasData())||!(a&&a.length)||!(f)){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert(_l("Tagging failed"))},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotations failed"))},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ 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: greg: Fixes for handling repository dependencies in the tool shed.
by Bitbucket 06 Dec '12

06 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/75e427a748d0/ changeset: 75e427a748d0 user: greg date: 2012-12-06 23:00:54 summary: Fixes for handling repository dependencies in the tool shed. affected #: 2 files diff -r 7b791a48be76604324f23445293d55948f789dde -r 75e427a748d0b3e89ccdf246f22499c2f44d9e2a lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1200,7 +1200,6 @@ if 'description' not in all_repository_dependencies: description = repository_dependencies_dict.get( 'description', None ) all_repository_dependencies[ 'description' ] = description - # The next key of interest in repository_dependencies_dict is 'repository_dependencies', which is a list of tuples. repository_dependencies_tups = repository_dependencies_dict[ 'repository_dependencies' ] for repository_dependency in repository_dependencies_tups: @@ -1231,6 +1230,7 @@ else: # Insert this repository_dependency. all_repository_dependencies[ repository_dependencies_root_key ] = [ repository_dependency ] + handled.append( repository_dependency ) if tool_shed_is_this_tool_shed( tool_shed ): # The repository is in the current tool shed. required_repository = get_repository_by_name_and_owner( trans, name, owner ) diff -r 7b791a48be76604324f23445293d55948f789dde -r 75e427a748d0b3e89ccdf246f22499c2f44d9e2a lib/galaxy/webapps/community/util/container_util.py --- a/lib/galaxy/webapps/community/util/container_util.py +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -36,7 +36,14 @@ listified_repository_dependency = repository_dependency.listify for contained_repository_dependency in self.repository_dependencies: if contained_repository_dependency.listify == listified_repository_dependency: - self.repository_dependencies.remove( contained_repository_dependency ) + self.repository_dependencies.remove( contained_repository_dependency ) + def to_repository_dependency( self, repository_dependency_id ): + toolshed, name, owner, changeset_revision = self.key.split( STRSEP ) + return RepositoryDependency( id=repository_dependency_id, + toolshed=toolshed, + repository_name=name, + repository_owner=owner, + changeset_revision=changeset_revision ) class Datatype( object ): """Datatype object""" @@ -199,36 +206,45 @@ # Create the Repository dependencies folder and add it to the root folder. repository_dependencies_folder_key = repository_dependencies[ 'root_key' ] repository_dependencies_folder = Folder( id=folder_id, key=repository_dependencies_folder_key, label=label, parent=repository_dependencies_root_folder ) - # The received repository_dependencies is a dictionary with a single 'description' key, and one or more repository_dependency keys. + del repository_dependencies[ 'root_key' ] + # The received repository_dependencies is a dictionary with keys: 'root_key', 'description', and one or more repository_dependency keys. # We want the description value associated with the repository_dependencies_folder. repository_dependencies_folder.description = repository_dependencies.get( 'description', None ) repository_dependencies_root_folder.folders.append( repository_dependencies_folder ) + del repository_dependencies[ 'description' ] + # The remaining keys in repository_dependencies should all be folders. + folder_keys = repository_dependencies.keys() + # If repository_dependencies_folder_key is an entry in repository_dependencies, process it first. + if repository_dependencies_folder_key in repository_dependencies: + val = repository_dependencies[ repository_dependencies_folder_key ] + repository_dependencies_folder, folder_id, repository_dependency_id = handle_repository_dependencies_entry( repository_dependencies_root_folder, + repository_dependencies_folder, + repository_dependencies_folder_key, + folder_keys, + folder_id, + repository_dependency_id, + repository_name, + repository_owner, + changeset_revision, + repository_dependencies_folder_key, + val ) + del repository_dependencies[ repository_dependencies_folder_key ] for key, val in repository_dependencies.items(): - if key in [ 'root_key', 'description' ]: - continue - # Only create a new folder object if necessary. - folder = get_folder( repository_dependencies_root_folder, key ) - if not folder: - # Create a new folder. - folder_id += 1 - label = generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, key ) - folder = Folder( id=folder_id, key=key, label=label, parent=repository_dependencies_folder ) - for repository_dependency_tup in val: - toolshed, name, owner, changeset_revision = repository_dependency_tup - # Create a new repository_dependency. - repository_dependency_id += 1 - repository_dependency = RepositoryDependency( id=repository_dependency_id, - toolshed=toolshed, - repository_name=name, - repository_owner=owner, - changeset_revision=changeset_revision ) - # Insert the repository_dependency into the folder. - folder.repository_dependencies.append( repository_dependency ) - if not get_folder( repository_dependencies_folder, key ): - # Insert the folder into the list. - repository_dependencies_folder.folders.append( folder ) + repository_dependencies_folder, folder_id, repository_dependency_id = handle_repository_dependencies_entry( repository_dependencies_root_folder, + repository_dependencies_folder, + repository_dependencies_folder_key, + folder_keys, + folder_id, + repository_dependency_id, + repository_name, + repository_owner, + changeset_revision, + key, + val ) + # Cast empty folders to be repository dependencies. + repository_dependencies_folder, repository_dependency_id = cast_empty_repository_dependency_folders( repository_dependencies_folder, + repository_dependency_id ) # Remove repository_dependencies that are also folders, and coerce empty folders into repository dependencies. - prune_repository_dependencies( repository_dependencies_folder, repository_dependencies_folder ) else: repository_dependencies_root_folder = None return folder_id, repository_dependencies_root_folder @@ -360,13 +376,23 @@ else: workflows_root_folder = None return folder_id, workflows_root_folder +def cast_empty_repository_dependency_folders( folder, repository_dependency_id ): + if not folder.folders and not folder.repository_dependencies: + repository_dependency_id += 1 + repository_dependency = folder.to_repository_dependency( repository_dependency_id ) + if not folder.parent.contains_repository_dependency( repository_dependency ): + folder.parent.repository_dependencies.append( repository_dependency ) + folder.parent.folders.remove( folder ) + for sub_folder in folder.folders: + return cast_empty_repository_dependency_folders( sub_folder, repository_dependency_id ) + return folder, repository_dependency_id def generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, key ): """Return a repository dependency label based on the repository dependency key.""" if key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, key ): label = 'Repository dependencies' else: - toolshed_base_url, name, owner, revision = get_components_from_key( key ) - label = "Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>" % ( name, revision, owner ) + #toolshed_base_url, name, owner, revision = get_components_from_key( key ) + label = "Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>" % ( repository_name, changeset_revision, repository_owner ) return label def generate_repository_dependencies_key_for_repository( toolshed_base_url, repository_name, repository_owner, changeset_revision ): # FIXME: assumes tool shed is current tool shed since repository dependencies across tool sheds is not yet supported. @@ -391,25 +417,61 @@ repository_owner = items[ 2 ] changeset_revision = items[ 3 ] return toolshed_base_url, repository_name, repository_owner, changeset_revision -def is_folder( folder_keys, toolshed_base_url, repository_name, repository_owner, changeset_revision ): - key = '%s%s%s%s%s%s%s' % ( toolshed_base_url, STRSEP, repository_name, STRSEP, repository_owner, STRSEP, changeset_revision ) +def handle_repository_dependencies_entry( repository_dependencies_root_folder, repository_dependencies_folder, repository_dependencies_folder_key, + folder_keys, folder_id, repository_dependency_id, repository_name, repository_owner, changeset_revision, + key, val ): + # Only create a new folder object if necessary. + folder = get_folder( repository_dependencies_root_folder, key ) + if not folder: + folder_id += 1 + label = generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, key ) + folder = Folder( id=folder_id, key=key, label=label, parent=repository_dependencies_folder ) + for repository_dependency_tup in val: + toolshed, name, owner, changeset_revision = repository_dependency_tup + if is_root_repository( repository_dependencies_folder_key, toolshed, name, owner ): + # Do not include repository dependencies that point to a revision within the same repository. + continue + if is_or_should_be_folder( folder_keys, toolshed, name, owner, changeset_revision ): + check_folder_key = generate_repository_dependencies_key_for_repository( toolshed, name, owner, changeset_revision ) + if get_folder( repository_dependencies_root_folder, check_folder_key ): + continue + else: + # Create a new folder, which may be populated later. + folder_id += 1 + label = generate_repository_dependencies_folder_label_from_key( name, owner, changeset_revision, key ) + sub_folder = Folder( id=folder_id, key=check_folder_key, label=label, parent=repository_dependencies_folder ) + folder.folders.append( sub_folder ) + else: + repository_dependency_id += 1 + repository_dependency = RepositoryDependency( id=repository_dependency_id, + toolshed=toolshed, + repository_name=name, + repository_owner=owner, + changeset_revision=changeset_revision ) + # Insert the repository_dependency into the folder. + folder.repository_dependencies.append( repository_dependency ) + if not get_folder( repository_dependencies_folder, folder.key ): + if folder.folders: + # Insert the folder into the list. + repository_dependencies_folder.folders.append( folder ) + return repository_dependencies_folder, folder_id, repository_dependency_id +def is_or_should_be_folder( folder_keys, toolshed, repository_name, repository_owner, changeset_revision ): + key = '%s%s%s%s%s%s%s' % ( toolshed, STRSEP, repository_name, STRSEP, repository_owner, STRSEP, changeset_revision ) return key in folder_keys +def is_root_repository( repository_dependencies_folder_key, toolshed, repository_name, repository_owner ): + # Return True if a repository dependency points to a revision within it's own repository. + repository_dependencies_folder_tup = repository_dependencies_folder_key.split( STRSEP ) + rdf_toolshed, rdf_repository_name, rdf_repository_owner, rdf_changeset_revision = repository_dependencies_folder_tup + return rdf_toolshed == toolshed and rdf_repository_name == repository_name and rdf_repository_owner == repository_owner def key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, key ): toolshed_base_url, key_name, key_owner, key_changeset_revision = get_components_from_key( key ) return repository_name == key_name and repository_owner == key_owner and changeset_revision == key_changeset_revision -def prune_folder( folder, repository_dependency, key ): - if get_folder( folder, key ): - folder.remove_repository_dependency( repository_dependency ) +def print_folders( pad, folder ): + # For debugging... + pad_str = '' + for i in range( 1, pad ): + pad_str += ' ' + print '%s%s' % ( pad_str, folder.key ) for sub_folder in folder.folders: - prune_folder( sub_folder, repository_dependency, key ) -def prune_repository_dependencies( folder, root_folder ): - """Remove repository_dependencies that are also folders, and coerce empty folders into repository dependencies.""" - remove_repository_dependencies( folder, root_folder ) - for sub_folder in folder.folders: - prune_repository_dependencies( sub_folder, root_folder ) -def remove_repository_dependencies( folder, root_folder ): - for repository_dependency in folder.repository_dependencies: - toolshed, name, owner, changeset_revision = repository_dependency.listify - key = generate_repository_dependencies_key_for_repository( toolshed, name, owner, changeset_revision ) - prune_folder( root_folder, repository_dependency, key ) + print_folders( pad+5, sub_folder ) \ 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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galaxy-commits December 2012