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Visualization framework improvements.

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This commit is contained in:
Jeremy Goecks
2012-06-15 17:43:54 -04:00
parent 6150366728
commit c1ea2ba186
5 changed files with 117 additions and 62 deletions
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static/scripts/mvc/tools.js
+10
View File
@@ -67,6 +67,16 @@ var Tool = BaseModel.extend({
}).set('value', value);
},
/**
* Set many input values at once.
*/
set_input_values: function(inputs_dict) {
var self = this;
_.each(_.keys(inputs_dict), function(input_name) {
self.set_input_value(input_name, inputs_dict[input_name]);
});
},
/**
* Run tool; returns a Deferred that resolves to the tool's output(s).
*/
static/scripts/viz/trackster.js
+8 -56
View File
@@ -176,56 +176,6 @@ var trackster_module = function(require, exports) {
var extend = require('class').extend,
slotting = require('slotting'),
painters = require('painters');
// ---- Canvas management and extensions ----
/**
* Canvas manager is used to create canvases, for browsers, this deals with
* backward comparibility using excanvas, as well as providing a pattern cache
*/
var CanvasManager = function( document, default_font ) {
this.document = document;
this.default_font = default_font !== undefined ? default_font : "9px Monaco, Lucida Console, monospace";
this.dummy_canvas = this.new_canvas();
this.dummy_context = this.dummy_canvas.getContext('2d');
this.dummy_context.font = this.default_font;
this.char_width_px = this.dummy_context.measureText("A").width;
this.patterns = {};
// FIXME: move somewhere to make this more general
this.load_pattern( 'right_strand', "/visualization/strand_right.png" );
this.load_pattern( 'left_strand', "/visualization/strand_left.png" );
this.load_pattern( 'right_strand_inv', "/visualization/strand_right_inv.png" );
this.load_pattern( 'left_strand_inv', "/visualization/strand_left_inv.png" );
}
extend( CanvasManager.prototype, {
load_pattern: function( key, path ) {
var patterns = this.patterns,
dummy_context = this.dummy_context,
image = new Image();
image.src = galaxy_paths.attributes.image_path + path;
image.onload = function() {
patterns[key] = dummy_context.createPattern( image, "repeat" );
}
},
get_pattern: function( key ) {
return this.patterns[key];
},
new_canvas: function() {
var canvas = this.document.createElement("canvas");
// If using excanvas in IE, we need to explicately attach the canvas
// methods to the DOM element
if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); }
// Keep a reference back to the manager
canvas.manager = this;
return canvas;
}
});
// ---- Web UI specific utilities ----
@@ -2985,18 +2935,20 @@ var Track = function(view, container, obj_dict) {
this.data_url = ('data_url' in obj_dict ? obj_dict.data_url : default_data_url);
this.data_url_extra_params = {}
this.data_query_wait = ('data_query_wait' in obj_dict ? obj_dict.data_query_wait : DEFAULT_DATA_QUERY_WAIT);
this.dataset_check_url = converted_datasets_state_url;
this.dataset_check_url = ('converted_datasets_state_url' in obj_dict ? obj_dict.converted_datasets_state_url : converted_datasets_state_url);
// A little ugly creating data manager right now due to transition to Backbone-based objects.
var dataset = new Dataset({
id: obj_dict.dataset_id,
hda_ldda: obj_dict.hda_ldda
});
var track = this,
dataset = new Dataset({
id: obj_dict.dataset_id,
hda_ldda: obj_dict.hda_ldda
});
this.data_manager = ('data_manager' in obj_dict ?
obj_dict.data_manager :
new GenomeDataManager({
dataset: dataset,
data_url: default_data_url,
data_url: track.data_url,
dataset_state_url: track.dataset_check_url,
data_mode_compatible: this.data_and_mode_compatible,
can_subset: this.can_subset,
}));
static/scripts/viz/trackster_ui.js
+2 -2
View File
@@ -36,7 +36,7 @@ var add_bookmark = function(position, annotation) {
* Create new object from a template. A template can be either an object dictionary or an
* object itself.
*/
var object_from_template = function(template, container) {
var object_from_template = function(template, view, container) {
if ('copy' in template) {
// Template is an object.
return template.copy(container);
@@ -93,7 +93,7 @@ var create_visualization = function(view_config, viewport_config, drawables_conf
drawable_type,
drawable;
for (var i = 0; i < drawables_config.length; i++) {
view.add_drawable( object_from_template( drawables_config[i], view ) );
view.add_drawable( object_from_template( drawables_config[i], view, view ) );
}
}
static/scripts/viz/visualization.js
+92 -3
View File
@@ -1,5 +1,7 @@
/**
* Model, view, and controller objects for Galaxy tools and tool panel.
* Model, view, and controller objects for Galaxy visualization framework.
*
* Required libraries: Backbone, jQuery
*
* Models have no references to views, instead using events to indicate state
* changes; this is advantageous because multiple views can use the same object
@@ -45,14 +47,66 @@ var ServerStateDeferred = Backbone.Model.extend({
}
});
// TODO: move to Backbone
/**
* Canvas manager is used to create canvases, for browsers, this deals with
* backward comparibility using excanvas, as well as providing a pattern cache
*/
var CanvasManager = function(default_font) {
this.default_font = default_font !== undefined ? default_font : "9px Monaco, Lucida Console, monospace";
this.dummy_canvas = this.new_canvas();
this.dummy_context = this.dummy_canvas.getContext('2d');
this.dummy_context.font = this.default_font;
this.char_width_px = this.dummy_context.measureText("A").width;
this.patterns = {};
// FIXME: move somewhere to make this more general
this.load_pattern( 'right_strand', "/visualization/strand_right.png" );
this.load_pattern( 'left_strand', "/visualization/strand_left.png" );
this.load_pattern( 'right_strand_inv', "/visualization/strand_right_inv.png" );
this.load_pattern( 'left_strand_inv', "/visualization/strand_left_inv.png" );
}
_.extend( CanvasManager.prototype, {
load_pattern: function( key, path ) {
var patterns = this.patterns,
dummy_context = this.dummy_context,
image = new Image();
image.src = galaxy_paths.attributes.image_path + path;
image.onload = function() {
patterns[key] = dummy_context.createPattern( image, "repeat" );
}
},
get_pattern: function( key ) {
return this.patterns[key];
},
new_canvas: function() {
var canvas = $("<canvas/>")[0];
// If using excanvas in IE, we need to explicately attach the canvas
// methods to the DOM element
if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); }
// Keep a reference back to the manager
canvas.manager = this;
return canvas;
}
});
/**
* Generic cache that handles key/value pairs.
*/
var Cache = Backbone.Model.extend({
defaults: {
num_elements: 20,
obj_cache: {},
key_ary: []
obj_cache: null,
key_ary: null
},
initialize: function(options) {
this.clear();
},
get_elt: function(key) {
@@ -114,9 +168,36 @@ var GenomeDataManager = Cache.extend({
dataset: null,
filters_manager: null,
data_url: null,
dataset_state_url: null,
data_mode_compatible: function(entry, mode) { return true; },
can_subset: function(entry) { return false; }
}),
/**
* Returns deferred that resolves to true when dataset is ready (or false if dataset
* cannot be used).
*/
data_is_ready: function() {
var dataset = this.get('dataset'),
ready_deferred = $.Deferred(),
ss_deferred = new ServerStateDeferred({
ajax_settings: {
url: this.get('dataset_state_url'),
data: {
dataset_id: dataset.id,
hda_ldda: dataset.get('hda_ldda')
},
dataType: "json"
},
interval: 5000,
success_fn: function(response) { return response !== "pending"; }
});
$.when(ss_deferred.go()).then(function(response) {
ready_deferred.resolve(response === "ok" || response === "data" );
});
return ready_deferred;
},
/**
* Load data from server; returns AJAX object so that use of Deferred is possible.
@@ -366,6 +447,10 @@ var GenomeRegion = Backbone.Model.extend({
end: this.get('end')
});
},
length: function() {
return this.get('end') - this.get('start');
},
/** Returns region in canonical form chrom:start-end */
toString: function() {
@@ -438,6 +523,10 @@ var GenomeRegion = Backbone.Model.extend({
}
});
var GenomeRegionCollection = Backbone.Collection.extend({
model: GenomeRegion
});
/**
* A genome browser bookmark.
*/
templates/base_panels.mako
+5 -1
View File
@@ -53,7 +53,11 @@
var galaxy_paths = new GalaxyPaths({
root_path: '${h.url_for( "/" )}',
image_path: '${h.url_for( "/static/images" )}',
tool_url: '${h.url_for( controller="/api/tools" )}'
tool_url: '${h.url_for( controller="/api/tools" )}',
data_url: '${h.url_for( controller="tracks", action="data" )}',
raw_data_url: '${h.url_for( controller="tracks", action="raw_data" )}',
converted_datasets_state_url: '${h.url_for( controller="tracks", action="converted_datasets_state" )}',
dataset_state_url: '${h.url_for( controller="tracks", action="dataset_state" )}'
});
</script>
</%def>