diff --git a/client/galaxy/scripts/base.js b/client/galaxy/scripts/base.js
index 24a5e6eb63b..2664386ab2d 100644
--- a/client/galaxy/scripts/base.js
+++ b/client/galaxy/scripts/base.js
@@ -1,4 +1,4 @@
-define( ["libs/backbone/backbone"], function( Backbone ) {
+define( [], function() {
var Base = function() {
if( this.initialize ) {
diff --git a/client/galaxy/scripts/viz/trackster.js b/client/galaxy/scripts/viz/trackster.js
index 6da2b057a0b..02d162ca472 100644
--- a/client/galaxy/scripts/viz/trackster.js
+++ b/client/galaxy/scripts/viz/trackster.js
@@ -34,7 +34,7 @@ require(
define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization", "mvc/ui/icon-button" ],
function(_, base, tracks, visualization, mod_icon_btn) {
/**
- * User interface controls for trackster
+ * User interface controls for trackster
*/
var TracksterUI = base.Base.extend({
initialize: function( baseURL ) {
@@ -47,10 +47,10 @@ var TracksterUI = base.Base.extend({
save_viz: function() {
// show dialog
Galaxy.modal.show({title: "Saving...", body: "progress" });
-
+
// Save bookmarks.
var bookmarks = [];
- $(".bookmark").each(function() {
+ $(".bookmark").each(function() {
bookmarks.push({
position: $(this).children(".position").text(),
annotation: $(this).children(".annotation").text()
@@ -96,22 +96,22 @@ var TracksterUI = base.Base.extend({
/**
* Create button menu
- */
+ */
createButtonMenu: function() {
var self = this,
menu = mod_icon_btn.create_icon_buttons_menu([
- { icon_class: 'plus-button', title: 'Add tracks', on_click: function() {
- visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey },
+ { icon_class: 'plus-button', title: 'Add tracks', on_click: function() {
+ visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey },
function(new_tracks) {
_.each(new_tracks, function(track) {
view.add_drawable( tracks.object_from_template(track, view, view) );
});
});
} },
- { icon_class: 'block--plus', title: 'Add group', on_click: function() {
+ { icon_class: 'block--plus', title: 'Add group', on_click: function() {
view.add_drawable( new tracks.DrawableGroup(view, view, { name: "New Group" }) );
} },
- { icon_class: 'bookmarks', title: 'Bookmarks', on_click: function() {
+ { icon_class: 'bookmarks', title: 'Bookmarks', on_click: function() {
// HACK -- use style to determine if panel is hidden and hide/show accordingly.
force_right_panel(($("div#right").css("right") == "0px" ? "hide" : "show"));
} },
@@ -122,7 +122,7 @@ var TracksterUI = base.Base.extend({
window.location = self.baseURL + 'visualization/circster?id=' + view.vis_id;
}
},
- { icon_class: 'disk--arrow', title: 'Save', on_click: function() {
+ { icon_class: 'disk--arrow', title: 'Save', on_click: function() {
self.save_viz();
} },
{
@@ -132,8 +132,8 @@ var TracksterUI = base.Base.extend({
self.handle_unsaved_changes(view);
}
}
- ],
- {
+ ],
+ {
tooltip_config: { placement: 'bottom' }
});
this.buttonMenu = menu;
@@ -146,16 +146,16 @@ var TracksterUI = base.Base.extend({
add_bookmarks: function() {
var self = this,
baseURL = this.baseURL;
-
+
// show modal while loading history
Galaxy.modal.show({title: "Select dataset for new bookmarks", body: "progress" });
-
+
$.ajax({
url: this.baseURL + "/visualization/list_histories",
data: { "f-dbkey": view.dbkey },
error: function() { alert( "Grid failed" ); },
success: function(table_html) {
-
+
// show modal to select bookmarks
Galaxy.modal.show(
{
@@ -167,7 +167,7 @@ var TracksterUI = base.Base.extend({
{
Galaxy.modal.hide();
},
-
+
"Insert": function()
{
// Just use the first selected
@@ -238,7 +238,7 @@ var TracksterUI = base.Base.extend({
* Create a complete Trackster visualization. Returns view.
*/
create_visualization: function(view_config, viewport_config, drawables_config, bookmarks_config, editable) {
-
+
// Create view.
var self = this,
view = new tracks.TracksterView(_.extend(view_config, {header: false}));
@@ -250,7 +250,7 @@ var TracksterUI = base.Base.extend({
start = viewport_config.start,
end = viewport_config.end,
overview_drawable_name = viewport_config.overview;
-
+
if (chrom && (start !== undefined) && end) {
view.change_chrom(chrom, start, end);
}
@@ -263,7 +263,7 @@ var TracksterUI = base.Base.extend({
// No viewport, so use first chromosome.
view.change_chrom(chrom_info[0].chrom);
}
-
+
// Add drawables to view.
if (drawables_config) {
// FIXME: can from_dict() be used to create view and add drawables?
@@ -274,7 +274,7 @@ var TracksterUI = base.Base.extend({
view.add_drawable( tracks.object_from_template( drawables_config[i], view, view ) );
}
}
-
+
// Set overview.
var overview_drawable;
for (var i = 0; i < view.drawables.length; i++) {
@@ -283,7 +283,7 @@ var TracksterUI = base.Base.extend({
break;
}
}
-
+
// Load bookmarks.
if (bookmarks_config) {
var bookmark;
@@ -299,7 +299,7 @@ var TracksterUI = base.Base.extend({
// Final initialization.
this.set_up_router({view: view});
-
+
return view;
},
@@ -322,7 +322,7 @@ var TracksterUI = base.Base.extend({
if ($(e.srcElement).is(':input')) {
return;
}
-
+
// Key codes: left == 37, up == 38, right == 39, down == 40
switch(e.which) {
case 37:
@@ -365,8 +365,8 @@ var TracksterUI = base.Base.extend({
}
}
});
-
- }
+
+ }
else {
window.location = galaxy_config.root + 'visualization';
}
@@ -374,7 +374,7 @@ var TracksterUI = base.Base.extend({
});
-var TracksterView = base.Backbone.View.extend(
+var TracksterView = Backbone.View.extend(
{
// initalize trackster
initialize : function ()
@@ -387,14 +387,14 @@ var TracksterView = base.Backbone.View.extend(
// attach the button menu to the panel header and float it left
ui.buttonMenu.$el.attr("style", "float: right");
-
+
// add to center panel
$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);
// configure right panel
$("#right .unified-panel-title").append("Bookmarks");
$("#right .unified-panel-icons").append("");
-
+
// resize view when showing/hiding right panel (bookmarks for now).
$("#right-border").click(function() { view.resize_window(); });
@@ -457,7 +457,7 @@ var TracksterView = base.Backbone.View.extend(
"Create": function() { self.create_browser($("#new-title").val(), $("#new-dbkey").val()); Galaxy.modal.hide(); }
}
});
-
+
// select default
if (galaxy_config.app.default_dbkey) {
$("#new-dbkey").val( galaxy_config.app.default_dbkey );
@@ -472,7 +472,7 @@ var TracksterView = base.Backbone.View.extend(
}
});
},
-
+
// new browser form
template_view_new: function(response)
{
@@ -494,7 +494,7 @@ var TracksterView = base.Backbone.View.extend(
for (var i = 0; i < response.length; i++) {
html += '';
}
-
+
// close selection/finalize template
html += '' +
'' +
@@ -505,11 +505,11 @@ var TracksterView = base.Backbone.View.extend(
'Add a Custom Build' +
'' +
'';
-
+
// return
return html;
},
-
+
// create
create_browser : function(name, dbkey)
{
@@ -521,10 +521,10 @@ var TracksterView = base.Backbone.View.extend(
name: name,
dbkey: dbkey
}, galaxy_config.app.gene_region);
-
+
// initialize editor
this.init_editor();
-
+
// modify view setting
view.editor = true;
},
@@ -534,7 +534,7 @@ var TracksterView = base.Backbone.View.extend(
{
// set title
$("#center .unified-panel-title").text(view.config.get_value('name') + " (" + view.dbkey + ")");
-
+
// add dataset
if (galaxy_config.app.add_dataset)
$.ajax({
diff --git a/static/maps/base.js.map b/static/maps/base.js.map
index 2009ec6c3f6..aeb3ad7f662 100644
--- a/static/maps/base.js.map
+++ b/static/maps/base.js.map
@@ -1 +1 @@
-{"version":3,"file":"base.js","sources":["../src/base.js"],"names":["define","Backbone","Base","this","initialize","apply","arguments","extend","Model"],"mappings":"AAAAA,QAAS,0BAA2B,SAAUC,GAE7C,GAAIC,GAAO,WACNC,KAAKC,YACRD,KAAKC,WAAWC,MAAMF,KAAMG,WAK9B,OAFAJ,GAAKK,OAASN,EAASO,MAAMD,QAG5BL,KAAMA,EACND,SAAUA"}
\ No newline at end of file
+{"version":3,"file":"base.js","sources":["../src/base.js"],"names":["define","Base","this","initialize","apply","arguments","extend","Backbone","Model"],"mappings":"AAAAA,UAAY,WAEX,GAAIC,GAAO,WACNC,KAAKC,YACRD,KAAKC,WAAWC,MAAMF,KAAMG,WAK9B,OAFAJ,GAAKK,OAASC,SAASC,MAAMF,QAG5BL,KAAMA,EACNM,SAAUA"}
\ No newline at end of file
diff --git a/static/maps/viz/trackster.js.map b/static/maps/viz/trackster.js.map
index 537dc0c06d4..83d0ceaa2fe 100644
--- a/static/maps/viz/trackster.js.map
+++ b/static/maps/viz/trackster.js.map
@@ -1 +1 @@
-{"version":3,"file":"trackster.js","sources":["../../src/viz/trackster.js"],"names":["ui","view","browser_router","require","mod_utils","cssLoadFile","define","_","base","tracks","visualization","mod_icon_btn","TracksterUI","Base","extend","initialize","baseURL","this","save_viz","Galaxy","modal","show","title","body","bookmarks","$","each","push","position","children","text","annotation","overview_track_name","overview_drawable","config","get_value","viz_config","to_dict","viewport","chrom","start","low","end","high","overview","ajax","url","galaxy_config","root","type","dataType","data","id","vis_id","dbkey","vis_json","JSON","stringify","success","vis_info","hide","has_changes","window","history","pushState","location","hash","error","buttons","Cancel","createButtonMenu","self","menu","create_icon_buttons_menu","icon_class","on_click","select_datasets","f-dbkey","new_tracks","track","add_drawable","object_from_template","DrawableGroup","name","force_right_panel","css","handle_unsaved_changes","tooltip_config","placement","buttonMenu","add_bookmarks","alert","table_html","Insert","first","val","attr","hda_id","ldda_id","then","i","length","row","add_bookmark","editable","bookmarks_container","new_bookmark","addClass","appendTo","position_div","annotation_div","click","go_to","delete_icon_container","prependTo","slideUp","remove","make_text_editable","num_rows","use_textarea","help_text","create_visualization","view_config","viewport_config","drawables_config","bookmarks_config","TracksterView","header","editor","when","load_chroms_deferred","chrom_info","overview_drawable_name","undefined","change_chrom","drawables","set_overview","bookmark","set_up_router","options","TrackBrowserRouter","Backbone","init_keyboard_nav","document","keyup","e","srcElement","is","which","move_fraction","Math","round","viewport_container","height","scrollTop","Leave 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\ No newline at end of file
diff --git a/static/scripts/base.js b/static/scripts/base.js
index 57760d577b8..751a061d68a 100644
--- a/static/scripts/base.js
+++ b/static/scripts/base.js
@@ -1,2 +1,2 @@
-define(["libs/backbone/backbone"],function(a){var b=function(){this.initialize&&this.initialize.apply(this,arguments)};return b.extend=a.Model.extend,{Base:b,Backbone:a}});
+define([],function(){var a=function(){this.initialize&&this.initialize.apply(this,arguments)};return a.extend=Backbone.Model.extend,{Base:a,Backbone:Backbone}});
//# sourceMappingURL=../maps/base.js.map
\ No newline at end of file
diff --git a/static/scripts/viz/trackster.js b/static/scripts/viz/trackster.js
index 50849c9f3d1..2703449f2b3 100644
--- a/static/scripts/viz/trackster.js
+++ b/static/scripts/viz/trackster.js
@@ -1,2 +1,2 @@
-var ui=null,view=null,browser_router=null;require(["utils/utils","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating"],function(a){a.cssLoadFile("static/style/jquery.rating.css"),a.cssLoadFile("static/style/autocomplete_tagging.css"),a.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css"),a.cssLoadFile("static/style/library.css"),a.cssLoadFile("static/style/trackster.css")}),define(["libs/underscore","base","viz/trackster/tracks","viz/visualization","mvc/ui/icon-button"],function(a,b,c,d,e){var f=b.Base.extend({initialize:function(a){this.baseURL=a},save_viz:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var a=[];$(".bookmark").each(function(){a.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var b=view.overview_drawable?view.overview_drawable.config.get_value("name"):null,c={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:b},bookmarks:a};return $.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.config.get_value("name"),dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(c)}}).success(function(a){Galaxy.modal.hide(),view.vis_id=a.vis_id,view.has_changes=!1,window.history.pushState({},"",a.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})},createButtonMenu:function(){var b=this,f=e.create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){d.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(b){a.each(b,function(a){view.add_drawable(c.object_from_template(a,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new c.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel("0px"==$("div#right").css("right")?"hide":"show")}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=b.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){b.save_viz()}},{icon_class:"cross-circle",title:"Close",on_click:function(){b.handle_unsaved_changes(view)}}],{tooltip_config:{placement:"bottom"}});return this.buttonMenu=f,f},add_bookmarks:function(){{var a=this;this.baseURL}Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"}),$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(b){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:b,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var b,c=$(this).val();b="id"===$(this).attr("name")?{hda_id:c}:{ldda_id:c},$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:b,dataType:"json"}).then(function(b){for(i=0;i").addClass("bookmark").appendTo(d),f=$("").addClass("position").appendTo(e),g=($("").text(a).appendTo(f).click(function(){return view.go_to(a),!1}),$("").text(b).appendTo(e));if(c){{var h=$("").addClass("delete-icon-container").prependTo(e).click(function(){return e.slideUp("fast"),e.remove(),view.has_changes=!0,!1});$("").addClass("icon-button delete").appendTo(h)}g.make_text_editable({num_rows:3,use_textarea:!0,help_text:"Edit bookmark note"}).addClass("annotation")}return view.has_changes=!0,e},create_visualization:function(b,d,e,f,g){var h=this,i=new c.TracksterView(a.extend(b,{header:!1}));return i.editor=!0,$.when(i.load_chroms_deferred).then(function(a){if(d){var b=d.chrom,j=d.start,k=d.end,l=d.overview;b&&void 0!==j&&k?i.change_chrom(b,j,k):i.change_chrom(a[0].chrom)}else i.change_chrom(a[0].chrom);if(e)for(var m=0;m