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Restore trackster options

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This commit is contained in:
guerler
2017-07-11 15:16:36 -04:00
parent 9b1ec4bea2
commit ccc5fc2837
6 changed files with 79 additions and 109 deletions
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client/galaxy/scripts/viz/trackster.js
+64 -94
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@@ -8,9 +8,7 @@ var view = null;
var browser_router = null;
// load required libraries
require(
[
// load js libraries
require([
'utils/utils',
'libs/jquery/jquery.event.drag',
'libs/jquery/jquery.event.hover',
@@ -20,10 +18,8 @@ require(
'libs/farbtastic',
'libs/jquery/jquery.form',
'libs/jquery/jquery.rating',
"ui/editable-text",
], function(mod_utils, mod_icon_btn)
{
// load css
'ui/editable-text',
], function(mod_utils) {
mod_utils.cssLoadFile("static/style/jquery.rating.css");
mod_utils.cssLoadFile("static/style/autocomplete_tagging.css");
mod_utils.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");
@@ -37,8 +33,9 @@ define([
"viz/trackster/tracks",
"viz/visualization",
"mvc/ui/icon-button",
"utils/query-string-parsing"
], function(_, tracks, visualization, mod_icon_btn, query_string) {
"utils/query-string-parsing",
"mvc/grid/grid-view"
], function(_, tracks, visualization, mod_icon_btn, query_string, GridView) {
/**
* Base Object/Model for inhertiance.
@@ -265,8 +262,7 @@ var TracksterUI = Base.extend({
/**
* Set up location router to use hashes as track browser locations.
*/
set_up_router : function(options)
{
set_up_router : function(options) {
new visualization.TrackBrowserRouter(options);
Backbone.history.start();
},
@@ -333,11 +329,9 @@ var TracksterUI = Base.extend({
});
var TracksterView = Backbone.View.extend(
{
var TracksterView = Backbone.View.extend( {
// initalize trackster
initialize : function ()
{
initialize : function () {
// load ui
ui = new TracksterUI(Galaxy.root);
@@ -377,77 +371,68 @@ var TracksterView = Backbone.View.extend(
dataset_params = {
dbkey : dbkey,
dataset_id : query_string.get( 'dataset_id' ),
hda_ldda : query_string.get( 'hda_ldda' )
hda_ldda : query_string.get( 'hda_ldda' ),
gene_region : query_string.get( 'gene_region' ),
};
if (dbkey){
listTracksParams[ 'f-dbkey' ] = dbkey;
}
$.ajax({
url: Galaxy.root + 'visualization/list_tracks?' + $.param( listTracksParams ),
dataType: "html",
error: function() { alert( "Could not add this dataset to browser." ); },
success: function(table_html) {
console.debug( 'success' );
function view_in_saved(){
// Show new modal with saved visualizations.
Galaxy.modal.show({
title : "Add Data to Saved Visualization",
body : table_html,
buttons : {
"Cancel": function() {
// go back to the first choice
show_choice();
},
"Add to visualization": function() {
$(parent.document).find('input[name=id]:checked').each(function() {
var vis_id = $(this).val();
dataset_params.id = vis_id;
window.location = Galaxy.root + "visualization/trackster?" + $.param(dataset_params);
});
}
}
});
Galaxy.modal.show({
title : "View Data in a New or Saved Visualization?",
// either have text in here or have to remove body and the header/footer margins
body : (
"<p><ul style='list-style: disc inside none'>You can add this dataset as:" +
"<li>a new track to one of your existing, saved Trackster " +
"sessions if they share the genome build: <b>" + ( dbkey || "Not available." ) + "</b></li>" +
"<li>or create a new session with this dataset as the only track</li>" +
"</ul></p>"
),
buttons : {
"Cancel": function() {
window.location = Galaxy.root + "visualization/list";
},
"View in saved visualization": function() {
self.view_in_saved( dataset_params );
},
"View in new visualization": function() {
self.view_new();
}
function show_choice(){
Galaxy.modal.show({
title : "View Data in a New or Saved Visualization?",
// either have text in here or have to remove body and the header/footer margins
body : (
// TODO: yay. inline styles. thanks, galaxy
'<p><ul style="list-style: disc inside none">You can add this dataset as:' +
"<li>a new track to one of your existing, saved Trackster " +
"sessions if they share the genome build: <b>" + dbkey + "</b></li>" +
"<li>or create a new session with this dataset as the only track</li>" +
"</ul></p>"
),
buttons : {
"Cancel": function() {
window.location = Galaxy.root + "visualization/list";
},
"View in saved visualization": function() {
view_in_saved();
},
"View in new visualization": function() {
self.view_new();
}
}
});
}
show_choice();
}
});
},
// view
view_existing : function ()
{
view_in_saved : function( dataset_params ) {
var tracks_grid = new GridView( {
url_base : Galaxy.root + 'visualization/list_tracks',
dict_format : true,
embedded : true
});
Galaxy.modal.show({
title : "Add Data to Saved Visualization",
body : tracks_grid.$el,
buttons : {
"Cancel": function() {
window.location = Galaxy.root + "visualization/list";
},
"Add to visualization": function() {
$(parent.document).find('input[name=id]:checked').each(function() {
dataset_params.id = $(this).val();
window.location = Galaxy.root + "visualization/trackster?" + $.param(dataset_params);
});
}
}
});
},
// view
view_existing : function () {
// get config
var viz_config = galaxy_config.app.viz_config;
// view
view = ui.create_visualization(
{
view = ui.create_visualization( {
container: $("#center .unified-panel-body"),
name: viz_config.title,
vis_id: viz_config.vis_id,
@@ -459,26 +444,16 @@ var TracksterView = Backbone.View.extend(
},
// view
view_new : function ()
{
// availability of default database key
/*if (galaxy_config.app.default_dbkey !== undefined)
{
this.create_browser("Unnamed", galaxy_config.app.default_dbkey);
return;
}*/
view_new : function () {
// reference this
var self = this;
// ajax
$.ajax(
{
$.ajax( {
url: Galaxy.root + "api/genomes?chrom_info=True",
data: {},
error: function() { alert( "Couldn't create new browser." ); },
success: function(response)
{
success: function(response) {
// show dialog
Galaxy.modal.show({
title : "New Visualization",
@@ -506,8 +481,7 @@ var TracksterView = Backbone.View.extend(
},
// new browser form
template_view_new: function(response)
{
template_view_new: function(response) {
// start template
var html = '<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;">' +
'<div class="form-row">' +
@@ -543,12 +517,10 @@ var TracksterView = Backbone.View.extend(
},
// create
create_browser : function(name, dbkey)
{
create_browser : function(name, dbkey) {
$(document).trigger("convert_to_values");
view = ui.create_visualization (
{
view = ui.create_visualization ({
container: $("#center .unified-panel-body"),
name: name,
dbkey: dbkey
@@ -562,8 +534,7 @@ var TracksterView = Backbone.View.extend(
},
// initialization for editor-specific functions.
init_editor : function ()
{
init_editor : function () {
// set title
$("#center .unified-panel-title").text(view.config.get_value('name') + " (" + view.dbkey + ")");
@@ -577,8 +548,7 @@ var TracksterView = Backbone.View.extend(
});
// initialize icons
$("#add-bookmark-button").click(function()
{
$("#add-bookmark-button").click(function() {
// add new bookmark.
var position = view.chrom + ":" + view.low + "-" + view.high,
annotation = "Bookmark description";
static/maps/viz/trackster.js.map
+1 -1
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static/scripts/bundled/analysis.bundled.js
+11 -11
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static/scripts/bundled/analysis.bundled.js.map
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static/scripts/bundled/libs.bundled.js.map
+1 -1
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static/scripts/viz/trackster.js
+1 -1
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