1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/95876f2552d3/ changeset: 95876f2552d3 user: jgoecks date: 2012-02-13 17:08:50 summary: Trackster: for flexibility, use dictionaries in all object constructors. Fixed bugs associated with saving/restoring visualizations. affected #: 4 files

diff -r a00a36e7cf4c3b73a0ee2a411b065213f19cf3df -r 95876f2552d354bf88320521dcf5083f31147bf0 lib/galaxy/visualization/tracks/visual_analytics.py --- a/lib/galaxy/visualization/tracks/visual_analytics.py +++ b/lib/galaxy/visualization/tracks/visual_analytics.py @@ -43,16 +43,16 @@ # TODO: could use this assertion to provide more information. # assert job is not None, 'Requested job has not been loaded.' if not job: - return {} + return None tool = trans.app.toolbox.get_tool( job.tool_id ) # TODO: could use this assertion to provide more information. # assert tool is not None, 'Requested tool has not been loaded.' if not tool: - return {} + return None

# Tool must have a Trackster configuration. if not tool.trackster_conf: - return {} + return None

# Get list of tool parameters that can be interactively modified. tool_params = [] @@ -75,7 +75,6 @@ 'html' : urllib.quote( input.get_html() ) } )

# If tool has parameters that can be interactively modified, return tool. - tool_def = {} if len( tool_params ) != 0: - tool_def = { 'name' : tool.name, 'params' : tool_params } - return tool_def \ No newline at end of file + return { 'name' : tool.name, 'params' : tool_params } + return None \ No newline at end of file

diff -r a00a36e7cf4c3b73a0ee2a411b065213f19cf3df -r 95876f2552d354bf88320521dcf5083f31147bf0 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -679,10 +679,10 @@ * * They optionally have a drag handle class. */ -var Drawable = function(name, view, container, prefs, drag_handle_class) { +var Drawable = function(view, container, obj_dict) { if (!Drawable.id_counter) { Drawable.id_counter = 0; } this.id = Drawable.id_counter++; - this.name = name; + this.name = ('name' in obj_dict ? obj_dict.name : null); this.view = view; this.container = container; this.config = new DrawableConfig({ @@ -690,13 +690,13 @@ params: [ { key: 'name', label: 'Name', type: 'text', default_value: name } ], - saved_values: prefs, + saved_values: obj_dict.prefs, onchange: function() { this.track.set_name(this.track.config.values.name); } }); this.prefs = this.config.values; - this.drag_handle_class = drag_handle_class; + this.drag_handle_class = obj_dict.drag_handle_class; this.is_overview = false; this.action_icons = {};

@@ -808,10 +808,6 @@ * Use from_dict to recreate object. */ to_dict: function() {}, - /** - * Restore object from a dictionary created by to_dict() - */ - from_dict: function(object_dict) {}, update_icons: function() {}, /** * Set drawable name. @@ -889,15 +885,27 @@ /** * A collection of drawable objects. */ -var DrawableCollection = function(obj_type, name, view, container, prefs, drag_handle_class) { - Drawable.call(this, name, view, container, prefs, drag_handle_class); +var DrawableCollection = function(view, container, obj_dict) { + Drawable.call(this, view, container, obj_dict);

// Attribute init. - this.obj_type = obj_type; + this.obj_type = obj_dict.obj_type; this.drawables = []; }; extend(DrawableCollection.prototype, Drawable.prototype, { /** + * Unpack and add drawables to the collection. + */ + unpack_drawables: function(drawables_array) { + // Add drawables to collection. + this.drawables = []; + var drawable; + for (var i = 0; i < drawables_array.length; i++) { + drawable = object_from_template(drawables_array[i], this); + this.add_drawable(drawable); + } + }, + /** * Init each drawable in the collection. */ init: function() { @@ -930,28 +938,6 @@ }; }, /** - * Restore object from a dictionary created by to_dict() - */ - from_dict: function(collection_dict, container) { - var collection = new this.constructor( collection_dict.name, view, - container, collection_dict.prefs, - view.viewport_container, view); - var drawable_dict, - drawable_type, - drawable; - for (var i = 0; i < collection_dict.drawables.length; i++) { - drawable_dict = collection_dict.drawables[i]; - drawable_type = drawable_dict['obj_type']; - // For backward compatibility: - if (!drawable_type) { - drawable_type = drawable_dict['track_type']; - } - drawable = addable_objects[ drawable_type ].prototype.from_dict( drawable_dict, collection ); - collection.add_drawable( drawable ); - } - return collection; - }, - /** * Add a drawable to the end of the collection. */ add_drawable: function(drawable) { @@ -1019,8 +1005,12 @@ /** * A group of drawables that are moveable, visible. */ -var DrawableGroup = function(name, view, container, prefs) { - DrawableCollection.call(this, "DrawableGroup", name, view, container, prefs, "group-handle"); +var DrawableGroup = function(view, container, obj_dict) { + extend(obj_dict, { + obj_type: "DrawableGroup", + drag_handle_class: "group-handle" + }); + DrawableCollection.call(this, view, container, obj_dict);

// Set up containers/moving for group: register both container_div and content div as container // because both are used as containers (container div to recognize container, content_div to @@ -1035,6 +1025,23 @@ this.header_div.after(this.filters_manager.parent_div); // For saving drawables' filter managers when group-level filtering is done: this.saved_filters_managers = []; + + // Add drawables. + if ('drawables' in obj_dict) { + this.unpack_drawables(obj_dict.drawables); + } + + // Restore filters. + if ('filters' in obj_dict) { + // FIXME: Pass collection_dict to DrawableCollection/Drawable will make this easier. + var old_manager = this.filters_manager; + this.filters_manager = new FiltersManager(this, obj_dict['filters']); + old_manager.parent_div.replaceWith(this.filters_manager.parent_div); + + if (obj_dict.filters.visible) { + this.setup_multitrack_filtering(); + } + } };

extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, { @@ -1249,7 +1256,10 @@ var new_track_name = "Composite Track of " + this.drawables.length + " tracks (" + drawables_names.join(", ") + ")";

// Replace this group with composite track. - var composite_track = new CompositeTrack(new_track_name, this.view, this.view, this.drawables); + var composite_track = new CompositeTrack(this.view, this.view, { + name: new_track_name, + drawables: this.drawables + }); var index = this.container.replace_drawable(this, composite_track, true); composite_track.request_draw(); }, @@ -1276,29 +1286,6 @@

return obj_dict; }, - /** - * Restore object from a dictionary created by to_dict() - */ - from_dict: function(collection_dict, container) { - var group = DrawableCollection.prototype.from_dict.call(this, collection_dict, container); - - // Add drawables to group's content div to make them visible. - for (var i = 0; i < group.drawables.length; i++) { - group.content_div.append(group.drawables[i].container_div); - } - - // Handle filters. - // FIXME: Pass collection_dict to DrawableCollection/Drawable will make this easier. - var old_manager = group.filters_manager; - group.filters_manager = new FiltersManager(group, collection_dict['filters']); - old_manager.parent_div.replaceWith(group.filters_manager.parent_div); - - if (collection_dict.filters.visible) { - group.setup_multitrack_filtering(); - } - - return group; - }, request_draw: function(clear_after, force) { for (var i = 0; i < this.drawables.length; i++) { this.drawables[i].request_draw(clear_after, force); @@ -1309,13 +1296,15 @@ /** * View object manages complete viz view, including tracks and user interactions. */ -var View = function(container, title, vis_id, dbkey) { - DrawableCollection.call(this, "View"); - this.container = container; +var View = function(obj_dict) { + extend(obj_dict, { + obj_type: "View" + }); + DrawableCollection.call(this, "View", obj_dict.container, obj_dict); this.chrom = null; - this.vis_id = vis_id; - this.dbkey = dbkey; - this.title = title; + this.vis_id = obj_dict.vis_id; + this.dbkey = obj_dict.dbkey; + this.title = obj_dict.title; this.label_tracks = []; this.tracks_to_be_redrawn = []; this.max_low = 0; @@ -1326,7 +1315,7 @@ // Deferred object that indicates when view's chrom data has been loaded. this.load_chroms_deferred = null; this.init(); - this.canvas_manager = new CanvasManager( container.get(0).ownerDocument ); + this.canvas_manager = new CanvasManager( this.container.get(0).ownerDocument ); this.reset(); }; extend( View.prototype, DrawableCollection.prototype, { @@ -2051,7 +2040,10 @@ }

// Create and init new track. - var new_track = new current_track.constructor(track_name, view, container, "hda"); + var new_track = new current_track.constructor(view, container, { + name: track_name, + hda_ldda: "hda" + }); new_track.init_for_tool_data(); new_track.change_mode(current_track.mode); new_track.set_filters_manager(current_track.filters_manager.copy(new_track)); @@ -2479,7 +2471,7 @@ // // Restore state from dict. // - if (obj_dict) { + if (obj_dict && 'filters' in obj_dict) { // Second condition needed for backward compatibility. var alpha_filter_name = ('alpha_filter' in obj_dict ? obj_dict.alpha_filter : null), height_filter_name = ('height_filter' in obj_dict ? obj_dict.height_filter : null), @@ -3060,18 +3052,21 @@ * -------> ReadTrack * -------> VcfTrack */ -var Track = function(name, view, container, prefs, data_manager, data_url, data_query_wait) { +var Track = function(view, container, obj_dict) { // For now, track's container is always view. - Drawable.call(this, name, view, container, {}, "draghandle"); + extend(obj_dict, { + drag_handle_class: "draghandle" + }); + Drawable.call(this, view, container, obj_dict);

// // Attribute init. // - this.data_url = (data_url ? data_url : default_data_url); + 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 ? data_query_wait : DEFAULT_DATA_QUERY_WAIT); + 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.data_manager = (data_manager ? data_manager : new DataManager(DATA_CACHE_SIZE, this)); + this.data_manager = ('data_manager' in obj_dict ? obj_dict.data_manager : new DataManager(DATA_CACHE_SIZE, this));

// // Create content div, which is where track is displayed, and add to container if available. @@ -3327,8 +3322,8 @@ predraw_init: function() {} });

-var TiledTrack = function(name, view, container, prefs, filters_dict, tool_dict, data_manager) { - Track.call(this, name, view, container, prefs, data_manager); +var TiledTrack = function(view, container, obj_dict) { + Track.call(this, view, container, obj_dict);

var track = this, view = track.view; @@ -3337,9 +3332,9 @@ moveable(track.container_div, track.drag_handle_class, ".group", track);

// Attribute init. - this.filters_manager = new FiltersManager(this, filters_dict); + this.filters_manager = new FiltersManager(this, ('filters' in obj_dict ? obj_dict.filters : null)); this.filters_available = false; - this.tool = (tool_dict !== undefined && obj_length(tool_dict) > 0 ? new Tool(this, tool_dict) : undefined); + this.tool = ('tool' in obj_dict && obj_dict.tool ? new Tool(this, obj_dict.tool) : null); this.tile_cache = new Cache(TILE_CACHE_SIZE);

if (this.header_div) { @@ -3356,6 +3351,10 @@ this.header_div.after(this.dynamic_tool_div); } } + + if (obj_dict.mode) { + this.change_mode(obj_dict.mode); + } }; extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { /** @@ -3363,8 +3362,11 @@ */ copy: function(container) { // Create copy. - var new_track = new this.constructor(this.name, this.view, container, this.hda_ldda, this.dataset_id, this.prefs, - this.filters, this.tool, this.data_manager); + var obj_dict = this.to_dict(); + extend(obj_dict, { + data_manager: this.data_manager + }); + var new_track = new this.constructor(this.view, container, obj_dict); // Misc. init and return. new_track.change_mode(this.mode); new_track.enabled = this.enabled; @@ -3389,22 +3391,11 @@ "dataset_id": this.dataset_id, "prefs": this.prefs, "mode": this.mode, - "filters": this.filters_manager.to_dict() + "filters": this.filters_manager.to_dict(), + "tool": null }; }, /** - * Restore object from a dictionary created by to_dict() - */ - from_dict: function(track_dict, container) { - var track = new this.constructor( - track_dict.name, view, container, track_dict.hda_ldda, track_dict.dataset_id, - track_dict.prefs, track_dict.filters, track_dict.tool); - if (track_dict.mode) { - track.change_mode(track_dict.mode); - } - return track; - }, - /** * Change track's mode. */ change_mode: function(new_mode) { @@ -3767,7 +3758,11 @@ });

var LabelTrack = function (view, container) { - Track.call(this, "label", view, container, false, {} ); + var obj_dict = { + todo: "label", + todo: false + }; + Track.call(this, view, container, obj_dict); this.container_div.addClass( "label-track" ); }; extend(LabelTrack.prototype, Track.prototype, { @@ -3800,21 +3795,18 @@ /** * A tiled track composed of multiple other tracks. */ -var CompositeTrack = function(name, view, container, drawables) { - TiledTrack.call(this, name, view, container); +var CompositeTrack = function(view, container, obj_dict) { + TiledTrack.call(this, view, container, obj_dict);

// Init drawables; each drawable is a copy so that config/preferences // are independent of each other. Also init left offset. this.drawables = []; this.left_offset = 0; - if (drawables) { - var - ids = [], - drawable; - for (var i = 0; i < drawables.length; i++) { - drawable = drawables[i]; - ids.push(drawable.dataset_id); - this.drawables[i] = drawable.copy(); + if ('drawables' in obj_dict) { + var drawable; + for (var i = 0; i < obj_dict.drawables.length; i++) { + drawable = obj_dict.drawables[i]; + this.drawables[i] = object_from_template(drawable);

// Track's left offset is the max of all tracks. if (drawable.left_offset > this.left_offset) { @@ -3858,34 +3850,7 @@ */ to_dict: DrawableCollection.prototype.to_dict, add_drawable: DrawableCollection.prototype.add_drawable, - /** - * Restore object from a dictionary created by to_dict() - */ - // TODO: unify with DrawableCollection.prototype.from_dict? - from_dict: function(collection_dict, container) { - var collection = new this.constructor( collection_dict.name, view, - container, collection_dict.prefs, - view.viewport_container, view); - var drawable_dict, - drawable_type, - drawable; - for (var i = 0; i < collection_dict.drawables.length; i++) { - drawable_dict = collection_dict.drawables[i]; - drawable_type = drawable_dict['obj_type']; - // For backward compatibility: - if (!drawable_type) { - drawable_type = drawable_dict['track_type']; - } - // No container for tracks so that it is not made visible. - drawable = addable_objects[ drawable_type ].prototype.from_dict(drawable_dict); - collection.add_drawable(drawable); - } - - // HACKish: set mode using the first drawable. Should use config object and set mode from there. - collection.set_display_modes(collection.drawables[0].display_modes, collection.drawables[0].mode); - - return collection; - }, + unpack_drawables: DrawableCollection.prototype.unpack_drawables, change_mode: function(new_mode) { TiledTrack.prototype.change_mode.call(this, new_mode); for (var i = 0; i < this.drawables.length; i++) { @@ -3919,8 +3884,9 @@ // FIXME: this function is similar to TiledTrack.draw_helper -- can the two be merged/refactored? var track = this, key = this._gen_tile_cache_key(width, w_scale, tile_index), - tile_low = tile_index * TILE_SIZE * resolution, - tile_high = tile_low + TILE_SIZE * resolution; + tile_bounds = this._get_tile_bounds(tile_index, resolution), + tile_low = tile_bounds[0], + tile_high = tile_bounds[1];

// Init kwargs if necessary to avoid having to check if kwargs defined. if (!kwargs) { kwargs = {}; } @@ -4036,7 +4002,9 @@ show_group: function() { // Create group with individual tracks. var - group = new DrawableGroup(this.name, this.view, this.container), + group = new DrawableGroup(this.view, this.container, { + name: this.name + }), track; for (var i = 0; i < this.drawables.length; i++) { track = this.drawables[i] @@ -4154,11 +4122,11 @@ } });

-var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager) { +var LineTrack = function (view, container, obj_dict) { var track = this; this.display_modes = ["Histogram", "Line", "Filled", "Intensity"]; this.mode = "Histogram"; - TiledTrack.call(this, name, view, container, prefs, filters, tool, data_manager); + TiledTrack.call(this, view, container, obj_dict);

// Cannot subset LineTrack data right now; see note in DataManager about using resolution in key // to address this issue. @@ -4168,9 +4136,9 @@ this.max_height_px = 400; // Default height for new tracks, should be a defined constant? this.height_px = 32; - this.hda_ldda = hda_ldda; - this.dataset_id = dataset_id; - this.original_dataset_id = dataset_id; + this.hda_ldda = obj_dict.hda_ldda; + this.dataset_id = obj_dict.dataset_id; + this.original_dataset_id = this.dataset_id; this.left_offset = 0;

// Define track configuration @@ -4184,7 +4152,7 @@ { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, { key: 'height', type: 'int', default_value: this.height_px, hidden: true } ], - saved_values: prefs, + saved_values: obj_dict.prefs, onchange: function() { track.set_name(track.prefs.name); track.vertical_range = track.prefs.max_value - track.prefs.min_value; @@ -4319,7 +4287,7 @@ } });

-var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager) { +var FeatureTrack = function(view, container, obj_dict) { // // Preinitialization: do things that need to be done before calling Track and TiledTrack // initialization code. @@ -4330,7 +4298,7 @@ // // Initialization. // - TiledTrack.call(this, name, view, container, prefs, filters, tool, data_manager); + TiledTrack.call(this, view, container, obj_dict);

// Define and restore track configuration. this.config = new DrawableConfig( { @@ -4346,7 +4314,7 @@ options: [ { label: 'Line with arrows', value: 'fishbone' }, { label: 'Arcs', value: 'arcs' } ] }, { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, ], - saved_values: prefs, + saved_values: obj_dict.prefs, onchange: function() { track.set_name(track.prefs.name); track.tile_cache.clear(); @@ -4358,9 +4326,9 @@

this.height_px = 0; this.container_div.addClass( "feature-track" ); - this.hda_ldda = hda_ldda; - this.dataset_id = dataset_id; - this.original_dataset_id = dataset_id; + this.hda_ldda = obj_dict.hda_ldda; + this.dataset_id = obj_dict.dataset_id; + this.original_dataset_id = obj_dict.dataset_id; this.show_labels_scale = 0.001; this.showing_details = false; this.summary_draw_height = 30; @@ -4734,8 +4702,8 @@ }, });

-var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager) { - FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager); +var VcfTrack = function(view, container, obj_dict) { + FeatureTrack.call(this, view, container, obj_dict);

this.config = new DrawableConfig( { track: this, @@ -4747,7 +4715,7 @@ { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true }, { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, ], - saved_values: prefs, + saved_values: obj_dict.prefs, onchange: function() { this.track.set_name(this.track.prefs.name); this.track.tile_cache.clear(); @@ -4761,8 +4729,8 @@

extend(VcfTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype);

-var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters, data_manager) { - FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, data_manager); +var ReadTrack = function (view, container, obj_dict) { + FeatureTrack.call(this, view, container, obj_dict);

var block_color = get_random_color(), @@ -4780,7 +4748,7 @@ { key: 'histogram_max', label: 'Histogram maximum', type: 'float', default_value: null, help: 'Clear value to set automatically' }, { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, ], - saved_values: prefs, + saved_values: obj_dict.prefs, onchange: function() { this.track.set_name(this.track.prefs.name); this.track.tile_cache.clear();

diff -r a00a36e7cf4c3b73a0ee2a411b065213f19cf3df -r 95876f2552d354bf88320521dcf5083f31147bf0 static/scripts/trackster_ui.js --- a/static/scripts/trackster_ui.js +++ b/static/scripts/trackster_ui.js @@ -29,16 +29,24 @@ };

/** - * Create object from a dictionary. + * Create new object from a template. A template can be either an object dictionary or an + * object itself. */ -var object_from_dict = function(track_dict, container) { - var - drawable_type = track_dict['obj_type']; - // For backward compatibility: - if (!drawable_type) { - drawable_type = track_dict['track_type']; +var object_from_template = function(template, container) { + if ('copy' in template) { + // Template is an object. + return template.copy(container); } - return addable_objects[ drawable_type ].prototype.from_dict(track_dict, container); + else { + // Template is a dictionary. + var + drawable_type = template['obj_type']; + // For backward compatibility: + if (!drawable_type) { + drawable_type = template['track_type']; + } + return new addable_objects[ drawable_type ](view, container, template); + } };

/** @@ -55,10 +63,10 @@ /** * Create a complete Trackster visualization. Returns view. */ -var create_visualization = function(parent_elt, title, id, dbkey, viewport_config, drawables_config, bookmarks_config) { +var create_visualization = function(view_config, viewport_config, drawables_config, bookmarks_config) {

// Create view. - view = new View(parent_elt, title, id, dbkey); + view = new View(view_config); view.editor = true; $.when( view.load_chroms_deferred ).then(function() { // Viewport config. @@ -81,7 +89,7 @@ drawable_type, drawable; for (var i = 0; i < drawables_config.length; i++) { - view.add_drawable( object_from_dict( drawables_config[i], view ) ); + view.add_drawable( object_from_template( drawables_config[i], view ) ); } }

diff -r a00a36e7cf4c3b73a0ee2a411b065213f19cf3df -r 95876f2552d354bf88320521dcf5083f31147bf0 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -168,8 +168,12 @@ $("#right-border").click(function() { view.resize_window(); });

%if config: - view = create_visualization( $("#browser-container"), "${config.get('title') | h}", - "${config.get('vis_id')}", "${config.get('dbkey')}", + view = create_visualization( { + container: $("#browser-container"), + title: "${config.get('title') | h}", + vis_id: "${config.get('vis_id')}", + dbkey: "${config.get('dbkey')}" + }, JSON.parse('${ h.to_json_string( config.get( 'viewport', dict() ) ) }'), JSON.parse('${ h.to_json_string( config['tracks'] ).replace("'", "\'") }'), JSON.parse('${ h.to_json_string( config['bookmarks'] ) }') @@ -225,7 +229,7 @@ $("#add-tracks-icon").click( function() { add_tracks(); } );

$("#add-group-icon").click( function() { - view.add_drawable( new DrawableGroup("New Group", view, view) ); + view.add_drawable( new DrawableGroup(view, view, { name: "New Group" }) ); });

$("#save-icon").click( function() {

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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