From 062387374c47a8e124ce4d8bee8b60954156b27c Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Thu, 11 Apr 2013 13:00:38 -0400 Subject: [PATCH] base_panels: move quota meter js into base_panels, provide bootstrapped user JSON, create Galaxy js namespace; history panel: don't use backbone-relational in dataset, user, or history; misc jsHint cleanup; expose_api: defend against no key provided; pack scripts --- lib/galaxy/web/framework/__init__.py | 2 + lib/galaxy/webapps/galaxy/controllers/root.py | 2 + static/scripts/galaxy.base.js | 107 +++++++++--------- static/scripts/mvc/base-mvc.js | 13 +-- static/scripts/mvc/dataset/hda-base.js | 6 +- static/scripts/mvc/dataset/hda-edit.js | 14 ++- static/scripts/mvc/dataset/hda-model.js | 4 +- static/scripts/mvc/history/history-model.js | 4 +- static/scripts/mvc/history/history-panel.js | 12 +- static/scripts/mvc/user/user-model.js | 6 +- static/scripts/mvc/user/user-quotameter.js | 8 +- static/scripts/packed/galaxy.base.js | 2 +- static/scripts/packed/mvc/base-mvc.js | 2 +- static/scripts/packed/mvc/data.js | 2 +- static/scripts/packed/mvc/dataset/hda-base.js | 2 +- static/scripts/packed/mvc/dataset/hda-edit.js | 2 +- .../scripts/packed/mvc/dataset/hda-model.js | 2 +- .../packed/mvc/history/history-model.js | 2 +- .../packed/mvc/history/history-panel.js | 2 +- static/scripts/packed/mvc/user/user-model.js | 2 +- .../packed/mvc/user/user-quotameter.js | 2 +- .../template-user-quotaMeter-quota.js | 2 +- .../template-user-quotaMeter-usage.js | 2 +- .../template-user-quotaMeter-quota.js | 18 ++- .../template-user-quotaMeter-usage.js | 25 ++-- static/scripts/templates/ui-templates.html | 5 +- templates/base.mako | 1 + templates/base/base_panels.mako | 1 + templates/webapps/galaxy/base_panels.mako | 87 +++++++------- templates/webapps/galaxy/root/history.mako | 105 +++++++---------- templates/webapps/galaxy/root/index.mako | 5 +- 31 files changed, 240 insertions(+), 209 deletions(-) diff --git a/lib/galaxy/web/framework/__init__.py b/lib/galaxy/web/framework/__init__.py index 5c479bd9f86..2557746d21c 100644 --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -126,6 +126,8 @@ def expose_api( func, to_json=True, key_required=True ): #If no key supplied, we use the existing session which may be an anonymous user. if key_required and not trans.user: try: + if 'key' not in kwargs: + raise NoResultFound( 'No key provided' ) provided_key = trans.sa_session.query( trans.app.model.APIKeys ).filter( trans.app.model.APIKeys.table.c.key == kwargs['key'] ).one() except NoResultFound: error_message = 'Provided API key is not valid.' diff --git a/lib/galaxy/webapps/galaxy/controllers/root.py b/lib/galaxy/webapps/galaxy/controllers/root.py index 4c471484794..5ebce370f33 100644 --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -134,6 +134,8 @@ class RootController( BaseUIController, UsesHistoryMixin, UsesHistoryDatasetAsso show_hidden = util.string_as_bool_or_none( show_hidden ) params = util.Params( kwd ) message = params.get( 'message', '' ) + #TODO: ugh... + message = message if message != 'None' else '' status = params.get( 'status', 'done' ) if trans.app.config.require_login and not trans.user: diff --git a/static/scripts/galaxy.base.js b/static/scripts/galaxy.base.js index 838577b6587..aed5dd12253 100644 --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -12,7 +12,7 @@ window.requestAnimationFrame = function(callback, element) { var currTime = new Date().getTime(); var timeToCall = Math.max(0, 16 - (currTime - lastTime)); - var id = window.setTimeout(function() { callback(currTime + timeToCall); }, + var id = window.setTimeout(function() { callback(currTime + timeToCall); }, timeToCall); lastTime = currTime + timeToCall; return id; @@ -70,7 +70,7 @@ $.fn.makeAbsolute = function(rebase) { */ function make_popupmenu(button_element, initial_options) { /* Use the $.data feature to store options with the link element. - This allows options to be changed at a later time + This allows options to be changed at a later time */ var element_menu_exists = (button_element.data("menu_options")); button_element.data("menu_options", initial_options); @@ -82,7 +82,7 @@ function make_popupmenu(button_element, initial_options) { // Close existing visible menus $(".popmenu-wrapper").remove(); - // Need setTimeouts so clicks don't interfere with each other + // Need setTimeouts so clicks don't interfere with each other setTimeout( function() { // Dynamically generate the wrapper holding all the selectable options of the menu. var menu_element = $( "" ); @@ -171,15 +171,15 @@ function make_popup_menus( parent ) { if ( !confirmtext || confirm( confirmtext ) ) { var f; // relocate the center panel - if ( target == "_parent" ) { + if ( target === "_parent" ) { window.parent.location = href; // relocate the entire window - } else if ( target == "_top" ) { + } else if ( target === "_top" ) { window.top.location = href; //??...wot? - } else if ( target == "demo" ) { + } else if ( target === "demo" ) { // Http request target is a window named // demolocal on the local box if ( f === undefined || f.closed ) { @@ -242,7 +242,7 @@ function naturalSort(a, b) { $.fn.refresh_select2 = function() { var select_elt = $(this); var options = { width: "resolve", - closeOnSelect: !select_elt.is("[MULTIPLE]"), + closeOnSelect: !select_elt.is("[MULTIPLE]") }; return select_elt.select2( options ); } @@ -263,7 +263,7 @@ function replace_big_select_inputs(min_length, max_length, select_elts) { max_length = 3000; } - var select_elts = select_elts || $('select'); + select_elts = select_elts || $('select'); select_elts.each( function() { var select_elt = $(this); @@ -278,18 +278,18 @@ function replace_big_select_inputs(min_length, max_length, select_elts) { } /* Replaced jQuery.autocomplete with select2, notes: - * - multiple selects are supported + * - multiple selects are supported * - the original element is updated with the value, convert_to_values should not be needed * - events are fired when updating the original element, so refresh_on_change should just work * - * - should we still sort dbkey fields here? + * - should we still sort dbkey fields here? */ select_elt.refresh_select2(); }); } /** - * Make an element with text editable: (a) when user clicks on text, a textbox/area + * Make an element with text editable: (a) when user clicks on text, a textbox/area * is provided for editing; (b) when enter key pressed, element's text is set and on_finish * is called. */ @@ -336,12 +336,14 @@ $.fn.make_text_editable = function(config_dict) { input_elt, button_elt; if (use_textarea) { - input_elt = $("").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!==""){l.text(o)}else{l.html("None")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStorage.get("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStorage.deleteKey("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id,h=$(this).children("div.historyItemBody"),i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("").click(function(){var k;if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){k=$.jStorage.get("history_expand_state");if(k){delete k[j];$.jStorage.set("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){k=$.jStorage.get("history_expand_state");if(!k){k={}}k[j]=true;$.jStorage.set("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStorage.get("history_expand_state");if(!h){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStorage.set("history_expand_state",h)}).show()};b()}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tooltip){$(".tooltip").tooltip({placement:"top"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); 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\ No newline at end of file diff --git a/static/scripts/packed/mvc/base-mvc.js b/static/scripts/packed/mvc/base-mvc.js index 47012eec270..2d1b49c16e2 100644 --- a/static/scripts/packed/mvc/base-mvc.js +++ b/static/scripts/packed/mvc/base-mvc.js @@ -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){var a=this.logger.log;if(typeof this.logger.log=="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.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 +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){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.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 --git a/static/scripts/packed/mvc/data.js b/static/scripts/packed/mvc/data.js index a07655fca21..260c196ad4b 100644 --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1 +1 @@ -define(["libs/backbone/backbone-relational"],function(){var d=Backbone.RelationalModel.extend({});var e=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){var i=new d();_.each(_.keys(this.attributes),function(j){if(j.indexOf("metadata_")===0){var l=j.split("metadata_")[1];i.set(l,this.attributes[j]);delete this.attributes[j]}},this);this.set("metadata",i)},get_metadata:function(i){return this.attributes.metadata.get(i)},urlRoot:galaxy_paths.get("datasets_url")});var c=e.extend({defaults:_.extend({},e.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(i){e.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var i=this,j=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:i.attributes.chunk_index++}).success(function(k){var l;if(k.ck_data!==""){l=k}else{i.attributes.at_eof=true;l=null}j.resolve(l)});return j}});var g=Backbone.Collection.extend({model:e});var f=Backbone.View.extend({initialize:function(i){},render:function(){var m=$("").attr({id:"content_table",cellpadding:0});this.$el.append(m);var i=this.model.get_metadata("column_names");if(i){m.append("")}var k=this.model.get("first_data_chunk");if(k){this._renderChunk(k)}var j=this,n=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"}),l=false;if(!n){n=window}n=$(n);n.scroll(function(){if(!l&&(j.$el.height()-n.scrollTop()-n.height()<=0)){l=true;$.when(j.model.get_next_chunk()).then(function(o){if(o){j._renderChunk(o);l=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(k,i,l){var j=this.model.get_metadata("column_types");if(l!==undefined){return $(""),k=this.model.get_metadata("columns");if(j.length===k){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this)}else{if(j.length>k){_.each(j.slice(0,k-1),function(n,m){l.append(this._renderCell(n,m))},this);l.append(this._renderCell(j.slice(k-1).join("\t"),k-1))}else{if(k>5&&j.length===k-1){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this);l.append($("
    "+i.join("")+"
    ").attr("colspan",l).addClass("stringalign").text(k)}else{if(j[i]==="str"||j==="list"){return $("").addClass("stringalign").text(k)}else{return $("").text(k)}}},_renderRow:function(i){var j=i.split("\t"),l=$("
    "))}else{l.append(this._renderCell(i,0,k))}}}return l},_renderChunk:function(i){var j=this.$el.find("table");_.each(i.ck_data.split("\n"),function(k,l){j.append(this._renderRow(k))},this)}});var b=f.extend({col:{chrom:null,start:null,end:null,},url_viz:null,dataset_id:null,genome_build:null,get_type:function(i){return({}).toString.call(i).match(/\s([a-zA-Z]+)/)[1].toLowerCase()},initialize:function(i){var j=i.model.attributes.metadata.attributes;if(typeof j.chromCol==="undefined"||typeof j.startCol==="undefined"||typeof j.endCol==="undefined"){console.log("TabularDatasetChunkedViewWithButton : Metadata for column identification is missing.")}else{this.col.chrom=j.chromCol-1;this.col.start=j.startCol-1;this.col.end=j.endCol-1}if(this.col.chrom==null){return}if(typeof i.model.attributes.id==="undefined"){console.log("TabularDatasetChunkedViewWithButton : Dataset identification is missing.")}else{this.dataset_id=i.model.attributes.id}if(typeof i.model.attributes.url_viz==="undefined"){console.log("TabularDatasetChunkedViewWithButton : Url for visualization controller is missing.")}else{this.url_viz=i.model.attributes.url_viz}if(typeof i.model.attributes.genome_build!=="undefined"){this.genome_build=i.model.attributes.genome_build}},events:{"mouseover tr":"btn_viz_show",mouseleave:"btn_viz_hide"},btn_viz_show:function(l){if(this.col.chrom==null){return}var n=$(l.target).parent();var i={dataset_id:this.dataset_id,gene_region:n.children().eq(this.col.chrom).html()+":"+n.children().eq(this.col.start).html()+"-"+n.children().eq(this.col.end).html()};if(n.children().eq(this.col.chrom).html()!=""){var m=n.offset();var k=m.left-10;var j=m.top;$("#btn_viz").css({position:"fixed",top:j+"px",left:k+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,i,this.genome_build));$("#btn_viz").show()}},btn_viz_hide:function(i){$("#btn_viz").hide()},create_trackster_action_new:function(i,k,j){return function(){window.parent.location.href=i+"/trackster?"+$.param(k)}},create_trackster_action:function(i,k,j){return function(){var l={};if(j){l["f-dbkey"]=j}$.ajax({url:i+"/list_tracks?"+$.param(l),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(m){var n=window.parent;n.show_modal(("View Data in a New or Saved Visualization"),"",{Cancel:function(){n.hide_modal()},"View in saved visualization":function(){n.show_modal(("Add Data to Saved Visualization"),m,{Cancel:function(){n.hide_modal()},"Add to visualization":function(){$(n.document).find("input[name=id]:checked").each(function(){var o=$(this).val();k.id=o;n.location=i+"/trackster?"+$.param(k)})}})},"View in new visualization":function(){n.location=i+"/trackster?"+$.param(k)}})}});return false}},render:function(){var i=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.$el.append(i.render().$el);$("#btn_viz").hide();f.prototype.render.call(this)}});var a=function(l,j,m,i){var k=new j({model:new l(m)});k.render();if(i){i.append(k.$el)}return k};var h=function(k,i){var j=$("
    ").appendTo(i);return new b({el:j,model:new c(k)}).render()};return{Dataset:e,TabularDataset:c,DatasetCollection:g,TabularDatasetChunkedView:f,createTabularDatasetChunkedView:h}}); \ No newline at end of file +define(["libs/backbone/backbone-relational"],function(){var d=Backbone.RelationalModel.extend({});var e=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){var i=new d();_.each(_.keys(this.attributes),function(j){if(j.indexOf("metadata_")===0){var l=j.split("metadata_")[1];i.set(l,this.attributes[j]);delete this.attributes[j]}},this);this.set("metadata",i)},get_metadata:function(i){return this.attributes.metadata.get(i)},urlRoot:galaxy_paths.get("datasets_url")});var c=e.extend({defaults:_.extend({},e.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(i){e.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var i=this,j=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:i.attributes.chunk_index++}).success(function(k){var l;if(k.ck_data!==""){l=k}else{i.attributes.at_eof=true;l=null}j.resolve(l)});return j}});var g=Backbone.Collection.extend({model:e});var f=Backbone.View.extend({initialize:function(i){(new b(i)).render()},render:function(){var m=$("").attr({id:"content_table",cellpadding:0});this.$el.append(m);var i=this.model.get_metadata("column_names");if(i){m.append("")}var k=this.model.get("first_data_chunk");if(k){this._renderChunk(k)}var j=this,n=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"}),l=false;if(!n){n=window}n=$(n);n.scroll(function(){if(!l&&(j.$el.height()-n.scrollTop()-n.height()<=0)){l=true;$.when(j.model.get_next_chunk()).then(function(o){if(o){j._renderChunk(o);l=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(k,i,l){var j=this.model.get_metadata("column_types");if(l!==undefined){return $(""),k=this.model.get_metadata("columns");if(j.length===k){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this)}else{if(j.length>k){_.each(j.slice(0,k-1),function(n,m){l.append(this._renderCell(n,m))},this);l.append(this._renderCell(j.slice(k-1).join("\t"),k-1))}else{if(k>5&&j.length===k-1){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this);l.append($("
    "+i.join("")+"
    ").attr("colspan",l).addClass("stringalign").text(k)}else{if(j[i]==="str"||j==="list"){return $("").addClass("stringalign").text(k)}else{return $("").text(k)}}},_renderRow:function(i){var j=i.split("\t"),l=$("
    "))}else{l.append(this._renderCell(i,0,k))}}}return l},_renderChunk:function(i){var j=this.$el.find("table");_.each(i.ck_data.split("\n"),function(k,l){j.append(this._renderRow(k))},this)}});var b=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,initialize:function(i){var j=i.model.attributes.metadata.attributes;if(typeof j.chromCol==="undefined"||typeof j.startCol==="undefined"||typeof j.endCol==="undefined"){console.log("TabularButtonTrackster : Metadata for column identification is missing.")}else{this.col.chrom=j.chromCol-1;this.col.start=j.startCol-1;this.col.end=j.endCol-1}if(this.col.chrom===null){return}if(typeof i.model.attributes.id==="undefined"){console.log("TabularButtonTrackster : Dataset identification is missing.")}else{this.dataset_id=i.model.attributes.id}if(typeof i.model.attributes.url_viz==="undefined"){console.log("TabularButtonTrackster : Url for visualization controller is missing.")}else{this.url_viz=i.model.attributes.url_viz}if(typeof i.model.attributes.genome_build!=="undefined"){this.genome_build=i.model.attributes.genome_build}},events:{"mouseover tr":"btn_viz_show",mouseleave:"btn_viz_hide"},btn_viz_show:function(m){if(this.col.chrom===null){return}var q=$(m.target).parent();var n=q.children().eq(this.col.chrom).html();var i=q.children().eq(this.col.start).html();var k=q.children().eq(this.col.end).html();if(n!==""&&i!==""&&k!==""){var p={dataset_id:this.dataset_id,gene_region:n+":"+i+"-"+k};var l=q.offset();var j=l.left-10;var o=l.top;$("#btn_viz").css({position:"fixed",top:o+"px",left:j+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,p,this.genome_build));$("#btn_viz").show()}},btn_viz_hide:function(){$("#btn_viz").hide()},create_trackster_action:function(i,k,j){return function(){var l={};if(j){l["f-dbkey"]=j}$.ajax({url:i+"/list_tracks?"+$.param(l),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(m){var n=window.parent;n.show_modal(("View Data in a New or Saved Visualization"),"",{Cancel:function(){n.hide_modal()},"View in saved visualization":function(){n.show_modal(("Add Data to Saved Visualization"),m,{Cancel:function(){n.hide_modal()},"Add to visualization":function(){$(n.document).find("input[name=id]:checked").each(function(){var o=$(this).val();k.id=o;n.location=i+"/trackster?"+$.param(k)})}})},"View in new visualization":function(){n.location=i+"/trackster?"+$.param(k)}})}});return false}},render:function(){var i=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.$el.append(i.render().$el);$("#btn_viz").hide()}});var a=function(l,j,m,i){var k=new j({model:new l(m)});k.render();if(i){i.append(k.$el)}return k};var h=function(k,i){var j=$("
    ").appendTo(i);return new f({el:j,model:new c(k)}).render()};return{Dataset:e,TabularDataset:c,DatasetCollection:g,TabularDatasetChunkedView:f,createTabularDatasetChunkedView:h}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/dataset/hda-base.js b/static/scripts/packed/mvc/dataset/hda-base.js index 64abe59d8f5..b413196269c 100644 --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1 +1 @@ -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",function(c,d){var b=_.without(_.keys(d.changes),"display_apps","display_types");if(b.length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("
    ").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);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}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('
    ');a.append(this._render_titleButtons());a.append('');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('
    ');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("View data");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("
    ").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_displayAppArea:function(){return $("
    ").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("
    ").append($("
    ").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("
    ").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('
    Error: unknown dataset state "'+this.model.get("state")+'".
    '))}a.append('
    ');this._setUpBehaviors(a)},_render_body_new:function(b){var a="This is a new dataset and not all of its data are available yet";b.append($("
    "+_l(a)+"
    "))},_render_body_not_viewable:function(a){a.append($("
    "+_l("You do not have permission to view dataset")+"
    "))},_render_body_uploading:function(a){a.append($("
    "+_l("Dataset is uploading")+"
    "))},_render_body_queued:function(a){a.append($("
    "+_l("Job is waiting to run")+"
    "));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("
    "+_l("Job is paused.  Use the history menu to resume")+"
    "));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("
    "+_l("Job is currently running")+"
    ");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("
    "+this.model.get("misc_blurb")+"
    "))}a.append((_l("An error occurred with this dataset")+": "+$.trim(this.model.get("misc_info"))+""));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("
    "+_l("The job creating this dataset was cancelled before completion")+".
    ");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("
    "+_l("Metadata is being auto-detected")+".
    "))},_render_body_empty:function(a){a.append($("
    "+_l("No data")+": "+this.model.get("misc_blurb")+"
    "));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));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('
    ');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();if(b){b()}})},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=Backbone.View.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",function(c,d){var b=_.without(_.keys(d.changes),"display_apps","display_types");if(b.length){this.render()}else{if(this.expanded){this._render_displayApps()}}},this)},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("
    ").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this._setUpBehaviors(a);this.body=$(this._render_body());a.append(this.body);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}})},_setUpBehaviors:function(a){a=a||this.$el;make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"})},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('
    ');a.append(this._render_titleButtons());a.append('');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('
    ');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("View data");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("
    ").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_displayAppArea:function(){return $("
    ").addClass("display-apps")},_render_displayApps:function(c){c=c||this.$el;var d=c.find("div.display-apps"),a=this.model.get("display_types"),b=this.model.get("display_apps");if((!this.model.hasData())||(!c||!c.length)||(!d.length)){return}d.html(null);if(!_.isEmpty(a)){d.append(HDABaseView.templates.displayApps({displayApps:a}))}if(!_.isEmpty(b)){d.append(HDABaseView.templates.displayApps({displayApps:b}))}},_render_peek:function(){var a=this.model.get("peek");if(!a){return null}return $("
    ").append($("
    ").attr("id","peek"+this.model.get("id")).addClass("peek").append(a))},_render_body:function(){var a=$("
    ").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: none");if(this.expanded){this._render_body_html(a);a.css("display","block")}return a},_render_body_html:function(a){a.html("");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NEW:this._render_body_new(a);break;case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('
    Error: unknown dataset state "'+this.model.get("state")+'".
    '))}a.append('
    ');this._setUpBehaviors(a)},_render_body_new:function(b){var a="This is a new dataset and not all of its data are available yet";b.append($("
    "+_l(a)+"
    "))},_render_body_not_viewable:function(a){a.append($("
    "+_l("You do not have permission to view dataset")+"
    "))},_render_body_uploading:function(a){a.append($("
    "+_l("Dataset is uploading")+"
    "))},_render_body_queued:function(a){a.append($("
    "+_l("Job is waiting to run")+"
    "));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("
    "+_l("Job is paused.  Use the history menu to resume")+"
    "));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("
    "+_l("Job is currently running")+"
    ");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("
    "+this.model.get("misc_blurb")+"
    "))}a.append((_l("An error occurred with this dataset")+": "+$.trim(this.model.get("misc_info"))+""));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("
    "+_l("The job creating this dataset was cancelled before completion")+".
    ");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("
    "+_l("Metadata is being auto-detected")+".
    "))},_render_body_empty:function(a){a.append($("
    "+_l("No data")+": "+this.model.get("misc_blurb")+"
    "));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(_.extend(this.model.toJSON(),{urls:this.urls}))));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('
    ');a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this;this.expanded=(a===undefined)?(!this.body.is(":visible")):(a);if(this.expanded){b._render_body_html(b.body);this.body.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{this.body.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},remove:function(b){var a=this;this.$el.fadeOut("fast",function(){a.$el.remove();if(b){b()}})},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 --git a/static/scripts/packed/mvc/dataset/hda-edit.js b/static/scripts/packed/mvc/dataset/hda-edit.js
index bd17f6bdde6..c5d293893d7 100644
--- a/static/scripts/packed/mvc/dataset/hda-edit.js
+++ b/static/scripts/packed/mvc/dataset/hda-edit.js
@@ -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]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true)});f.error(function(h,g,i){alert("("+h.status+") "+_l("Unable to purge this dataset")+":\n"+h)})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('
    ');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.NEW)||(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().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$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=$("
    "),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$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 $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('
    ');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var a=this,d=this.$el.find(".tag-area"),b=d.find(".tag-elt");if(d.is(":hidden")){if(!jQuery.trim(b.html())){$.ajax({url:this.urls.tags.get,error:function(g,e,f){a.log("Tagging failed",g,e,f);a.trigger("error",_l("Tagging failed"),g,e,f)},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotations failed"))},success:function(e){if(e===""){e=""+_l("Describe or add notes to dataset")+""}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(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
+var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true);a.trigger("purged",a)});f.error(function(h,g,i){a.trigger("error",_l("Unable to purge this dataset"),h,g,i)})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('
    ');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.NEW)||(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().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$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=$("
    "),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$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 $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('
    ');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var a=this,d=this.$el.find(".tag-area"),b=d.find(".tag-elt");if(d.is(":hidden")){if(!jQuery.trim(b.html())){$.ajax({url:this.urls.tags.get,error:function(g,e,f){a.log("Tagging failed",g,e,f);a.trigger("error",_l("Tagging failed"),g,e,f)},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){view.log("Annotation failed",xhr,status,error);view.trigger("error",_l("Annotation failed"),xhr,status,error)},success:function(e){if(e===""){e=""+_l("Describe or add notes to dataset")+""}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(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
diff --git a/static/scripts/packed/mvc/dataset/hda-model.js b/static/scripts/packed/mvc/dataset/hda-model.js
index a2402459382..d82946365d0 100644
--- a/static/scripts/packed/mvc/dataset/hda-model.js
+++ b/static/scripts/packed/mvc/dataset/hda-model.js
@@ -1 +1 @@
-var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:true,accessible:true},urlRoot:"api/histories/",url:function(){return this.urlRoot+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",b,a,this.previous("state"))}})},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(this.isDeletedOrPurged()||(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("hid")+' :"'+this.get("name")+'",'+a}return"HDA("+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})},getByHid:function(a){return _.first(this.filter(function(b){return b.get("hid")===a}))},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(c0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a=this.get("hid")+' :"'+this.get("name")+'",'+a}return"HDA("+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})},getByHid:function(a){return _.first(this.filter(function(b){return b.get("hid")===a}))},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(c0){this.updateDisplayApplications()}}this.hdas.bind("state:ready",function(e,g,d){if(e.get("force_history_refresh")){var f=this;setTimeout(function(){f.stateUpdater()},History.UPDATE_DELAY)}},this);if(this.logger){this.bind("all",function(d){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{a.log("Error updating hdas from api history contents",b,h,c,d,f);var g=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",g,h,c,d)}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(e,d,f){c.hdas.set(e)},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"});
\ No newline at end of file
+var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();if(c&&_.isArray(c)){this.hdas.reset(c);this.checkForUpdates();if(this.hdas.length>0){this.updateDisplayApplications()}}this.hdas.bind("state:ready",function(e,g,d){if(e.get("force_history_refresh")){var f=this;setTimeout(function(){f.stateUpdater()},History.UPDATE_DELAY)}},this);if(this.logger){this.bind("all",function(d){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.fetchHdaUpdates(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(h,c,d){if((h.readyState===0)&&(h.status===0)){return}var f=JSON.parse(h.responseText);if(_.isArray(f)){var e=_.groupBy(f,function(i){if(_.has(i,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",e.errored);a.updateHdas(f)}else{a.log("Error updating hdas from api history contents",b,h,c,d,f);var g=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",g,h,c,d)}},success:function(d,c,e){a.log(a+".fetchHdaUpdates, success:",c,e);a.updateHdas(d)}})},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(e,d,f){c.hdas.set(e)},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"});
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/history/history-panel.js b/static/scripts/packed/mvc/history/history-panel.js
index a33130c919f..0a64fc66d33 100644
--- a/static/scripts/packed/mvc/history/history-panel.js
+++ b/static/scripts/packed/mvc/history/history-panel.js
@@ -1 +1 @@
-var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags","click #message-container":"removeMessage"},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._setUpEventHandlers();this.hdaViews={};this.urls={}},_setUpEventHandlers:function(){this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.bind("error",function(d,c,b,a){this.displayMessage("error",d);this.model.attributes.error=undefined},this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.bind("state:ready",function(b,c,a){if((!b.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(b.get("id"))}},this);this.bind("error",function(d,c,b,a){this.displayMessage("error",d)});if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},_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()},handleHdaDeletionChange:function(a){if(a.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(a.get("id"))}},removeHdaView:function(c,b){var a=this.hdaViews[c];if(!a){return}a.remove(b);delete this.hdaViews[c];if(_.isEmpty(this.hdaViews)){this.render()}},render:function(){var b=this,d=b.toString()+".set-up",c=$("
    "),a=this.model.toJSON(),e=(this.$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)});b.bind("error",function(f,e,c,d){a.displayMessage("error",f)})},_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.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(d){this.log(this+".loadAndDisplayTags",d);var b=this,e=this.$el.find("#history-tag-area"),c=e.find(".tag-elt");this.log("\t tagArea",e," tagElt",c);if(e.is(":hidden")){if(!jQuery.trim(c.html())){var a=this;$.ajax({url:a.urls.tag,error:function(h,g,f){b.log("Error loading tag area html",h,g,f);b.trigger("error",_l("Tagging failed"),h,g,f)},success:function(f){c.html(f);c.find(".tooltip").tooltip();e.slideDown("fast")}})}else{e.slideDown("fast")}}else{e.slideUp("fast")}return false},displayMessage:function(c,d){var b=this.$el.find("#message-container"),a=$("
    ").addClass(c+"message").text(d);b.html(a)},removeMessage:function(){var a=this.$el.find("#message-container");a.html(null)},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=Backbone.View.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags","click #message-container":"removeMessage"},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._setUpEventHandlers();this.hdaViews={};this.urls={}},_setUpEventHandlers:function(){this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.bind("error",function(d,c,b,a){this.displayMessage("error",d);this.model.attributes.error=undefined},this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.bind("change:purged",function(a){this.model.fetch()},this);this.model.hdas.bind("state:ready",function(b,c,a){if((!b.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(b.get("id"))}},this);this.bind("error",function(d,c,b,a){this.displayMessage("error",d)});if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},_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()},handleHdaDeletionChange:function(a){if(a.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(a.get("id"))}},removeHdaView:function(c,b){var a=this.hdaViews[c];if(!a){return}a.remove(b);delete this.hdaViews[c];if(_.isEmpty(this.hdaViews)){this.render()}},render:function(){var b=this,d=b.toString()+".set-up",c=$("
    "),a=this.model.toJSON(),e=(this.$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)});b.bind("error",function(f,e,c,d){a.displayMessage("error",f)})},_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.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(d){this.log(this+".loadAndDisplayTags",d);var b=this,e=this.$el.find("#history-tag-area"),c=e.find(".tag-elt");this.log("\t tagArea",e," tagElt",c);if(e.is(":hidden")){if(!jQuery.trim(c.html())){var a=this;$.ajax({url:a.urls.tag,error:function(h,g,f){b.log("Error loading tag area html",h,g,f);b.trigger("error",_l("Tagging failed"),h,g,f)},success:function(f){c.html(f);c.find(".tooltip").tooltip();e.slideDown("fast")}})}else{e.slideDown("fast")}}else{e.slideUp("fast")}return false},displayMessage:function(c,d){var b=this.$el.find("#message-container"),a=$("
    ").addClass(c+"message").text(d);b.html(a)},removeMessage:function(){var a=this.$el.find("#message-container");a.html(null)},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 --git a/static/scripts/packed/mvc/user/user-model.js b/static/scripts/packed/mvc/user/user-model.js
index 6da0b93163a..4ef4801ba42 100644
--- a/static/scripts/packed/mvc/user/user-model.js
+++ b/static/scripts/packed/mvc/user/user-model.js
@@ -1 +1 @@
-var User=BaseModel.extend(LoggableMixin).extend({urlRoot:"api/users",defaults:{id:null,username:"("+_l("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"0 bytes",quota_percent:null},initialize:function(a){this.log("User.initialize:",a);this.on("loaded",function(b,c){this.log(this+" has loaded:",b,c)});this.on("change",function(b,c){this.log(this+" has changed:",b,c.changes)})},isAnonymous:function(){return(!this.get("email"))},loadFromApi:function(d,b){d=d||User.CURRENT_ID_STR;b=b||{};var a=this,c=b.success;b.success=function(f,e){a.trigger("loaded",f,e);if(c){c(f,e)}};if(d===User.CURRENT_ID_STR){b.url=this.urlRoot+"/"+User.CURRENT_ID_STR}return BaseModel.prototype.fetch.call(this,b)},toString:function(){var a=[this.get("username")];if(this.get("id")){a.unshift(this.get("id"));a.push(this.get("email"))}return"User("+a.join(":")+")"}});User.CURRENT_ID_STR="current";User.getCurrentUserFromApi=function(b){var a=new User();a.loadFromApi(User.CURRENT_ID_STR,b);return a};var UserCollection=Backbone.Collection.extend(LoggableMixin).extend({model:User,urlRoot:"api/users"});
\ No newline at end of file
+var User=Backbone.Model.extend(LoggableMixin).extend({urlRoot:"api/users",defaults:{id:null,username:"("+_l("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"",quota_percent:null},initialize:function(a){this.log("User.initialize:",a);this.on("loaded",function(b,c){this.log(this+" has loaded:",b,c)});this.on("change",function(b,c){this.log(this+" has changed:",b,c.changes)})},isAnonymous:function(){return(!this.get("email"))},loadFromApi:function(d,b){d=d||User.CURRENT_ID_STR;b=b||{};var a=this,c=b.success;b.success=function(f,e){a.trigger("loaded",f,e);if(c){c(f,e)}};if(d===User.CURRENT_ID_STR){b.url=this.urlRoot+"/"+User.CURRENT_ID_STR}return BaseModel.prototype.fetch.call(this,b)},toString:function(){var a=[this.get("username")];if(this.get("id")){a.unshift(this.get("id"));a.push(this.get("email"))}return"User("+a.join(":")+")"}});User.CURRENT_ID_STR="current";User.getCurrentUserFromApi=function(b){var a=new User();a.loadFromApi(User.CURRENT_ID_STR,b);return a};var UserCollection=Backbone.Collection.extend(LoggableMixin).extend({model:User,urlRoot:"api/users"});
\ No newline at end of file
diff --git a/static/scripts/packed/mvc/user/user-quotameter.js b/static/scripts/packed/mvc/user/user-quotameter.js
index cc047fec351..f841350c0cb 100644
--- a/static/scripts/packed/mvc/user/user-quotameter.js
+++ b/static/scripts/packed/mvc/user/user-quotameter.js
@@ -1 +1 @@
-var UserQuotaMeter=BaseView.extend(LoggableMixin).extend({options:{warnAtPercent:85,errorAtPercent:100},initialize:function(a){this.log(this+".initialize:",a);_.extend(this.options,a);this.model.bind("change:quota_percent change:total_disk_usage",this.render,this)},update:function(a){this.log(this+" updating user data...",a);this.model.loadFromApi(this.model.get("id"),a);return this},isOverQuota:function(){return(this.model.get("quota_percent")!==null&&this.model.get("quota_percent")>=this.options.errorAtPercent)},_render_quota:function(){var a=this.model.toJSON(),b=a.quota_percent,c=$(UserQuotaMeter.templates.quota(a));if(this.isOverQuota()){c.addClass("progress-danger");c.find("#quota-meter-text").css("color","white");this.trigger("quota:over",a)}else{if(b>=this.options.warnAtPercent){c.addClass("progress-warning");this.trigger("quota:under quota:under:approaching",a)}else{c.addClass("progress-success");this.trigger("quota:under quota:under:ok",a)}}return c},_render_usage:function(){var a=$(UserQuotaMeter.templates.usage(this.model.toJSON()));this.log(this+".rendering usage:",a);return a},render:function(){var a=null;this.log(this+".model.quota_percent:",this.model.get("quota_percent"));if((this.model.get("quota_percent")===null)||(this.model.get("quota_percent")===undefined)){a=this._render_usage()}else{a=this._render_quota()}this.$el.html(a);return this},toString:function(){return"UserQuotaMeter("+this.model+")"}});UserQuotaMeter.templates={quota:Handlebars.templates["template-user-quotaMeter-quota"],usage:Handlebars.templates["template-user-quotaMeter-usage"]};
\ No newline at end of file
+var UserQuotaMeter=Backbone.View.extend(LoggableMixin).extend({options:{warnAtPercent:85,errorAtPercent:100},initialize:function(a){this.log(this+".initialize:",a);_.extend(this.options,a);this.model.bind("change:quota_percent change:total_disk_usage",this.render,this)},update:function(a){this.log(this+" updating user data...",a);this.model.loadFromApi(this.model.get("id"),a);return this},isOverQuota:function(){return(this.model.get("quota_percent")!==null&&this.model.get("quota_percent")>=this.options.errorAtPercent)},_render_quota:function(){var a=this.model.toJSON(),b=a.quota_percent,c=$(UserQuotaMeter.templates.quota(a));if(this.isOverQuota()){c.addClass("progress-danger");c.find("#quota-meter-text").css("color","white");this.trigger("quota:over",a)}else{if(b>=this.options.warnAtPercent){c.addClass("progress-warning");this.trigger("quota:under quota:under:approaching",a)}else{c.addClass("progress-success");this.trigger("quota:under quota:under:ok",a)}}return c},_render_usage:function(){var a=$(UserQuotaMeter.templates.usage(this.model.toJSON()));this.log(this+".rendering usage:",a);return a},render:function(){var a=null;this.log(this+".model.quota_percent:",this.model.get("quota_percent"));if((this.model.get("quota_percent")===null)||(this.model.get("quota_percent")===undefined)){a=this._render_usage()}else{a=this._render_quota()}this.$el.html(a);this.$el.find(".quota-meter-text").tooltip();return this},toString:function(){return"UserQuotaMeter("+this.model+")"}});UserQuotaMeter.templates={quota:Handlebars.templates["template-user-quotaMeter-quota"],usage:Handlebars.templates["template-user-quotaMeter-usage"]};
\ No newline at end of file
diff --git a/static/scripts/packed/templates/compiled/template-user-quotaMeter-quota.js b/static/scripts/packed/templates/compiled/template-user-quotaMeter-quota.js
index 24d09da471f..ede6cdde5bb 100644
--- a/static/scripts/packed/templates/compiled/template-user-quotaMeter-quota.js
+++ b/static/scripts/packed/templates/compiled/template-user-quotaMeter-quota.js
@@ -1 +1 @@
-(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-user-quotaMeter-quota"]=b(function(f,l,e,k,j){this.compilerInfo=[2,">= 1.0.0-rc.3"];e=e||f.helpers;j=j||{};var h="",c,o,g="function",i=this.escapeExpression,n=this,m=e.blockHelperMissing;function d(q,p){return"Using"}h+='
    \n    
    \n    \n    
    \n        ';o={hash:{},inverse:n.noop,fn:n.program(1,d,j),data:j};if(c=e.local){c=c.call(l,o)}else{c=l.local;c=typeof c===g?c.apply(l):c}if(!e.local){c=m.call(l,c,o)}if(c||c===0){h+=c}h+=" ";if(c=e.quota_percent){c=c.call(l,{hash:{},data:j})}else{c=l.quota_percent;c=typeof c===g?c.apply(l):c}h+=i(c)+"%\n    
    \n
    ";return h})})();
\ No newline at end of file
+(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-user-quotaMeter-quota"]=b(function(g,m,f,l,k){this.compilerInfo=[2,">= 1.0.0-rc.3"];f=f||g.helpers;k=k||{};var i="",d,p,h="function",j=this.escapeExpression,o=this,n=f.blockHelperMissing;function e(t,s){var q="",r;q+=' title="Using ';if(r=f.nice_total_disk_usage){r=r.call(t,{hash:{},data:s})}else{r=t.nice_total_disk_usage;r=typeof r===h?r.apply(t):r}q+=j(r)+'"';return q}function c(r,q){return"Using"}i+='
    \n    
    \n    \n    
    \n        ";p={hash:{},inverse:o.noop,fn:o.program(3,c,k),data:k};if(d=f.local){d=d.call(m,p)}else{d=m.local;d=typeof d===h?d.apply(m):d}if(!f.local){d=n.call(m,d,p)}if(d||d===0){i+=d}i+=" ";if(d=f.quota_percent){d=d.call(m,{hash:{},data:k})}else{d=m.quota_percent;d=typeof d===h?d.apply(m):d}i+=j(d)+"%\n    
    \n
    ";return i})})();
\ No newline at end of file
diff --git a/static/scripts/packed/templates/compiled/template-user-quotaMeter-usage.js b/static/scripts/packed/templates/compiled/template-user-quotaMeter-usage.js
index 986020af7a4..25366703cc2 100644
--- a/static/scripts/packed/templates/compiled/template-user-quotaMeter-usage.js
+++ b/static/scripts/packed/templates/compiled/template-user-quotaMeter-usage.js
@@ -1 +1 @@
-(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-user-quotaMeter-usage"]=b(function(f,l,e,k,j){this.compilerInfo=[2,">= 1.0.0-rc.3"];e=e||f.helpers;j=j||{};var h="",c,o,n=this,g="function",m=e.blockHelperMissing,i=this.escapeExpression;function d(q,p){return"Using"}h+='\n
    \n    
    \n        ';o={hash:{},inverse:n.noop,fn:n.program(1,d,j),data:j};if(c=e.local){c=c.call(l,o)}else{c=l.local;c=typeof c===g?c.apply(l):c}if(!e.local){c=m.call(l,c,o)}if(c||c===0){h+=c}h+=" ";if(c=e.nice_total_disk_usage){c=c.call(l,{hash:{},data:j})}else{c=l.nice_total_disk_usage;c=typeof c===g?c.apply(l):c}h+=i(c)+"\n    
    \n
    ";return h})})();
\ No newline at end of file
+(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-user-quotaMeter-usage"]=b(function(g,m,f,l,k){this.compilerInfo=[2,">= 1.0.0-rc.3"];f=f||g.helpers;k=k||{};var i="",c,o=this,h="function",n=f.blockHelperMissing,j=this.escapeExpression;function e(t,s){var p="",r,q;q={hash:{},inverse:o.noop,fn:o.program(2,d,s),data:s};if(r=f.local){r=r.call(t,q)}else{r=t.local;r=typeof r===h?r.apply(t):r}if(!f.local){r=n.call(t,r,q)}if(r||r===0){p+=r}p+=" ";if(r=f.nice_total_disk_usage){r=r.call(t,{hash:{},data:s})}else{r=t.nice_total_disk_usage;r=typeof r===h?r.apply(t):r}p+=j(r);return p}function d(q,p){return"Using"}i+='\n
    \n    
    \n        ';c=f["if"].call(m,m.nice_total_disk_usage,{hash:{},inverse:o.noop,fn:o.program(1,e,k),data:k});if(c||c===0){i+=c}i+="\n    
    \n
    ";return i})})();
\ No newline at end of file
diff --git a/static/scripts/templates/compiled/template-user-quotaMeter-quota.js b/static/scripts/templates/compiled/template-user-quotaMeter-quota.js
index 790a8fd183c..c3feab71c20 100644
--- a/static/scripts/templates/compiled/template-user-quotaMeter-quota.js
+++ b/static/scripts/templates/compiled/template-user-quotaMeter-quota.js
@@ -7,6 +7,17 @@ helpers = helpers || Handlebars.helpers; data = data || {};
 
 function program1(depth0,data) {
   
+  var buffer = "", stack1;
+  buffer += " title=\"Using ";
+  if (stack1 = helpers.nice_total_disk_usage) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
+  else { stack1 = depth0.nice_total_disk_usage; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
+  buffer += escapeExpression(stack1)
+    + "\"";
+  return buffer;
+  }
+
+function program3(depth0,data) {
+  
   
   return "Using";
   }
@@ -16,8 +27,11 @@ function program1(depth0,data) {
   else { stack1 = depth0.quota_percent; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
   buffer += escapeExpression(stack1)
     + "%\">
    \n    "
-    + "\n    
    \n        ";
-  options = {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data};
+    + "\n    
    = 1.0.0-rc.3'];
 helpers = helpers || Handlebars.helpers; data = data || {};
-  var buffer = "", stack1, options, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing, escapeExpression=this.escapeExpression;
+  var buffer = "", stack1, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing, escapeExpression=this.escapeExpression;
 
 function program1(depth0,data) {
   
-  
-  return "Using";
-  }
-
-  buffer += "\n
    \n    
    \n        ";
-  options = {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data};
+  var buffer = "", stack1, options;
+  options = {hash:{},inverse:self.noop,fn:self.program(2, program2, data),data:data};
   if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); }
   else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
   if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); }
@@ -20,8 +16,19 @@ function program1(depth0,data) {
   buffer += " ";
   if (stack1 = helpers.nice_total_disk_usage) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
   else { stack1 = depth0.nice_total_disk_usage; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  buffer += escapeExpression(stack1)
-    + "\n    
    \n
    ";
+  buffer += escapeExpression(stack1);
+  return buffer;
+  }
+function program2(depth0,data) {
+  
+  
+  return "Using";
+  }
+
+  buffer += "\n
    \n    
    \n        ";
+  stack1 = helpers['if'].call(depth0, depth0.nice_total_disk_usage, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data});
+  if(stack1 || stack1 === 0) { buffer += stack1; }
+  buffer += "\n    
    \n
    ";
   return buffer;
   });
 })();
\ No newline at end of file
diff --git a/static/scripts/templates/ui-templates.html b/static/scripts/templates/ui-templates.html
index f5da4af2fb7..3735e747cdc 100644
--- a/static/scripts/templates/ui-templates.html
+++ b/static/scripts/templates/ui-templates.html
@@ -2,7 +2,8 @@
 
    
     
    
     {{! TODO: remove the hardcoded style }}
-    
    
+    
    
         {{#local}}Using{{/local}} {{ quota_percent }}%
     
    
 
    
@@ -12,7 +13,7 @@
 {{! TODO: remove the hardcoded styles }}
 
    
     
    
-        {{#local}}Using{{/local}} {{ nice_total_disk_usage }}
+        {{#if nice_total_disk_usage }}{{#local}}Using{{/local}} {{ nice_total_disk_usage }}{{/if}}
     
    
 
    
 
diff --git a/templates/base.mako b/templates/base.mako
index f00f365ea28..f5084ae8a6d 100644
--- a/templates/base.mako
+++ b/templates/base.mako
@@ -1,6 +1,7 @@
 <% _=n_ %>
 
 
+    
     
         ${self.title()}
         
diff --git a/templates/base/base_panels.mako b/templates/base/base_panels.mako
index 3948e0ed4c1..e1bde686ff1 100644
--- a/templates/base/base_panels.mako
+++ b/templates/base/base_panels.mako
@@ -251,6 +251,7 @@
 
 ## Document
 
+    
     ${self.init()}    
     
         ${self.title()}
diff --git a/templates/webapps/galaxy/base_panels.mako b/templates/webapps/galaxy/base_panels.mako
index 9b3b40ce605..98998c82a4e 100644
--- a/templates/webapps/galaxy/base_panels.mako
+++ b/templates/webapps/galaxy/base_panels.mako
@@ -7,6 +7,53 @@
     ${parent.javascripts()}
 
 
+<%def name="get_user_json()">
+<%
+    """Bootstrapping user API JSON"""
+    #TODO: move into common location (poss. BaseController)
+    if trans.user:
+        user_dict = trans.user.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id,
+                                                                             'total_disk_usage': float } )
+        user_dict['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans )
+    else:
+        usage = 0
+        percent = None
+        try:
+            usage = trans.app.quota_agent.get_usage( trans, history=trans.history )
+            percent = trans.app.quota_agent.get_percent( trans=trans, usage=usage )
+        except AssertionError, assertion:
+            # no history for quota_agent.get_usage assertion
+            pass
+        user_dict = {
+            'total_disk_usage'      : int( usage ),
+            'nice_total_disk_usage' : util.nice_size( usage ),
+            'quota_percent'         : percent
+        }
+%>
+${h.to_json_string( user_dict )}
+
+
+<%def name="late_javascripts()">
+${parent.late_javascripts()}
+
+
+${h.templates( "helpers-common-templates", "template-user-quotaMeter-quota", "template-user-quotaMeter-usage" )}
+${h.js( "mvc/base-mvc", "mvc/user/user-model", "mvc/user/user-quotameter" )}
+
+
+
 ## Masthead
 <%def name="masthead()">
 
@@ -190,44 +237,6 @@
         
     
    
 
-    ## Quota meter
-    <%
-        bar_style = "quota-meter-bar"
-        usage = 0
-        percent = 0
-        quota = None
-        try:
-            usage = trans.app.quota_agent.get_usage( trans=trans )
-            quota = trans.app.quota_agent.get_quota( trans.user )
-            percent = trans.app.quota_agent.get_percent( usage=usage, quota=quota )
-            if percent is not None:
-                if percent >= 100:
-                    bar_style += " quota-meter-bar-error"
-                elif percent >= 85:
-                    bar_style += " quota-meter-bar-warn"
-            else:
-                percent = 0
-        except AssertionError:
-            pass # Probably no history yet
-        tooltip = None
-        if not trans.user and quota and trans.app.config.allow_user_creation:
-            if trans.app.quota_agent.default_registered_quota is None or trans.app.quota_agent.default_unregistered_quota < trans.app.quota_agent.default_registered_quota:
-                tooltip = "Your disk quota is %s.  You can increase your quota by registering a Galaxy account." % util.nice_size( quota )
-    %>
+    
    
 
-    
    
-        %if tooltip:
-        
    
-        %else:
-        
    
-        %endif
-            
    
-            %if quota is not None:
-                
    Using ${percent}%
    
-            %else:
-                
    Using ${util.nice_size( usage )}
    
-            %endif
-        
    
-    
    
-    
 
diff --git a/templates/webapps/galaxy/root/history.mako b/templates/webapps/galaxy/root/history.mako
index 2d9dd0bb82c..7f73c695b1a 100644
--- a/templates/webapps/galaxy/root/history.mako
+++ b/templates/webapps/galaxy/root/history.mako
@@ -118,9 +118,6 @@ ${ unquote_plus( h.to_json_string( url_dict ) ) }
     hda_ext_template    = '<%= file_ext %>'
     meta_type_template  = '<%= file_type %>'
 
-    display_app_name_template = '<%= name %>'
-    display_app_link_template = '<%= link %>'
-
     url_dict = {
         # ................................................................ warning message links
         'purge' : h.url_for( controller='dataset', action='purge_async',
@@ -139,7 +136,8 @@ ${ unquote_plus( h.to_json_string( url_dict ) ) }
             dataset_id=encoded_id_template ),
 
         #TODO: via api
-        'delete' : h.url_for( controller='dataset', action='delete_async', dataset_id=encoded_id_template ),
+        'delete' : h.url_for( controller='dataset', action='delete_async',
+            dataset_id=encoded_id_template ),
 
         # ................................................................ download links (and associated meta files),
         'download' : h.url_for( controller='dataset', action='display',
@@ -178,6 +176,7 @@ ${ unquote_plus( h.to_json_string( url_dict ) ) }
 ## -----------------------------------------------------------------------------
 <%def name="get_current_user()">
 <%
+    #TODO: move to root.history, using base.controller.usesUser, unify that with users api
     user_json = trans.webapp.api_controllers[ 'users' ].show( trans, 'current' )
     return user_json
 %>
@@ -222,6 +221,7 @@ ${h.js(
     
 
diff --git a/templates/webapps/galaxy/root/index.mako b/templates/webapps/galaxy/root/index.mako
index 43c4bda7032..0950b6252bd 100644
--- a/templates/webapps/galaxy/root/index.mako
+++ b/templates/webapps/galaxy/root/index.mako
@@ -2,11 +2,14 @@
 
 <%def name="late_javascripts()">
     ${parent.late_javascripts()}
+