1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/040555fcc6b5/ changeset: 040555fcc6b5 user: jgoecks date: 2012-09-21 16:12:01 summary: Add requireJS support for data, visualization, tools and update dependencies. affected #: 11 files

diff -r d824b236fe80ffea89cae979112580935abfa7c4 -r 040555fcc6b5341e2878c0d4ec33f54c712273c2 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -1,3 +1,4 @@ +define(["libs/backbone/backbone-relational"], function() { /** * A dataset. In Galaxy, datasets are associated with a history, so * this object is also known as a HistoryDatasetAssociation. @@ -17,3 +18,9 @@ model: Dataset });

+return { + Dataset: Dataset, + DatasetCollection: DatasetCollection +}; + +});

diff -r d824b236fe80ffea89cae979112580935abfa7c4 -r 040555fcc6b5341e2878c0d4ec33f54c712273c2 static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -6,39 +6,8 @@ * and models can be used without views. */

-// FIXME: copied from visualization module; remove once a module has been created from tools. -var ServerStateDeferred = Backbone.Model.extend({ - defaults: { - ajax_settings: {}, - interval: 1000, - success_fn: function(result) { return true; } - }, - - /** - * Returns a deferred that resolves when success function returns true. - */ - go: function() { - var deferred = $.Deferred(), - self = this, - ajax_settings = self.get('ajax_settings'), - success_fn = self.get('success_fn'), - interval = self.get('interval'), - _go = function() { - $.ajax(ajax_settings).success(function(result) { - if (success_fn(result)) { - // Result is good, so resolve. - deferred.resolve(result); - } - else { - // Result not good, try again. - setTimeout(_go, interval); - } - }); - }; - _go(); - return deferred; - } -}); + define( ["libs/underscore", "viz/trackster/util", "mvc/data", "libs/backbone/backbone-relational" ], + function(_, util, data) {

/** * Simple base model for any visible element. Includes useful attributes and ability @@ -64,6 +33,47 @@ });

/** + * A tool input. + */ +var ToolInput = Backbone.RelationalModel.extend({ + defaults: { + name: null, + label: null, + type: null, + value: null, + num_samples: 5 + }, + + initialize: function() { + this.attributes.html = unescape(this.attributes.html); + }, + + copy: function() { + return new ToolInput(this.toJSON()); + }, + + /** + * Returns samples from a tool input. + */ + get_samples: function() { + var type = this.get('type'), + samples = null; + if (type === 'number') { + samples = d3.scale.linear() + .domain([this.get('min'), this.get('max')]) + .ticks(this.get('num_samples')); + } + else if (type === 'select') { + samples = _.map(this.get('options'), function(option) { + return option[0]; + }); + } + + return samples; + } +}); + +/** * A Galaxy tool. */ var Tool = BaseModel.extend({ @@ -78,7 +88,7 @@ { type: Backbone.HasMany, key: 'inputs', - relatedModel: 'ToolInput', + relatedModel: ToolInput, reverseRelation: { key: 'tool', includeInJSON: false @@ -176,7 +186,7 @@ // deferred to ensure that job is run. Also use deferred that // resolves to outputs from tool. var run_deferred = $.Deferred(), - ss_deferred = new ServerStateDeferred({ + ss_deferred = new util.ServerStateDeferred({ ajax_settings: { url: this.urlRoot, data: JSON.stringify(payload), @@ -192,54 +202,13 @@

// Run job and resolve run_deferred to tool outputs. $.when(ss_deferred.go()).then(function(result) { - run_deferred.resolve(new DatasetCollection().reset(result)); + run_deferred.resolve(new data.DatasetCollection().reset(result)); }); return run_deferred; } });

/** - * A tool input. - */ -var ToolInput = Backbone.RelationalModel.extend({ - defaults: { - name: null, - label: null, - type: null, - value: null, - num_samples: 5 - }, - - initialize: function() { - this.attributes.html = unescape(this.attributes.html); - }, - - copy: function() { - return new ToolInput(this.toJSON()); - }, - - /** - * Returns samples from a tool input. - */ - get_samples: function() { - var type = this.get('type'), - samples = null; - if (type === 'number') { - samples = d3.scale.linear() - .domain([this.get('min'), this.get('max')]) - .ticks(this.get('num_samples')); - } - else if (type === 'select') { - samples = _.map(this.get('options'), function(option) { - return option[0]; - }); - } - - return samples; - } -}); - -/** * Wrap collection of tools for fast access/manipulation. */ var ToolCollection = Backbone.Collection.extend({ @@ -723,4 +692,15 @@ $('#left').width("650px"); }); } -}); \ No newline at end of file +}); + +// Exports +return { + Tool: Tool, + ToolSearch: ToolSearch, + ToolPanel: ToolPanel, + ToolPanelView: ToolPanelView, + ToolFormView: ToolFormView +}; + +});

diff -r d824b236fe80ffea89cae979112580935abfa7c4 -r 040555fcc6b5341e2878c0d4ec33f54c712273c2 static/scripts/viz/sweepster.js --- a/static/scripts/viz/sweepster.js +++ b/static/scripts/viz/sweepster.js @@ -3,7 +3,8 @@ * genomic visualization. */

-define( ["libs/d3", "viz/trackster/util", "viz/visualization", "viz/trackster/tracks"], function( d3, util, visualization, tracks ) { +define(["libs/d3", "viz/trackster/util", "viz/visualization", "viz/trackster/tracks", "mvc/tools", "mvc/data"], + function(d3, util, visualization, tracks, tools, data) {

/** * A collection of tool input settings. Object is useful for keeping a list of settings @@ -318,12 +319,12 @@ { type: Backbone.HasOne, key: 'dataset', - relatedModel: Dataset + relatedModel: data.Dataset }, { type: Backbone.HasOne, key: 'tool', - relatedModel: Tool + relatedModel: tools.Tool }, { type: Backbone.HasMany, @@ -571,7 +572,7 @@

render: function() { // Start with tool form view. - var tool_form_view = new ToolFormView({ + var tool_form_view = new tools.ToolFormView({ model: this.model.get('tool') }); tool_form_view.render();

diff -r d824b236fe80ffea89cae979112580935abfa7c4 -r 040555fcc6b5341e2878c0d4ec33f54c712273c2 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1,4 +1,6 @@ -define( ["libs/underscore", "viz/visualization", "viz/trackster/util", "viz/trackster/slotting", "viz/trackster/painters" ], function( _, visualization, util, slotting, painters ) { +define( ["libs/underscore", "viz/visualization", "viz/trackster/util", + "viz/trackster/slotting", "viz/trackster/painters", "mvc/data" ], + function( _, visualization, util, slotting, painters, data ) {

var extend = _.extend; var get_random_color = util.get_random_color; @@ -878,7 +880,7 @@ // Deferred object that indicates when view's chrom data has been loaded. this.load_chroms_deferred = null; this.init(); - this.canvas_manager = new CanvasManager( this.container.get(0).ownerDocument ); + this.canvas_manager = new visualization.CanvasManager( this.container.get(0).ownerDocument ); this.reset(); }; _.extend( View.prototype, Backbone.Events); @@ -1749,7 +1751,7 @@ this.run(url_params, new_track, // Success callback. function(track_data) { - new_track.set_dataset(new Dataset(track_data)); + new_track.set_dataset(new data.Dataset(track_data)); new_track.tiles_div.text("Running job."); new_track.init(); } @@ -1761,7 +1763,7 @@ run: function(url_params, new_track, success_callback) { // Run tool. url_params.inputs = this.get_param_values_dict(); - var ss_deferred = new ServerStateDeferred({ + var ss_deferred = new util.ServerStateDeferred({ ajax_settings: { url: galaxy_paths.get('tool_url'), data: JSON.stringify(url_params), @@ -2655,7 +2657,7 @@ .css({'height': ERROR_PADDING-1, 'width': canvas.width}).prependTo(this.html_elt);

// Handle message; only message currently is that only the first N elements are displayed. - var tile_region = new GenomeRegion({ + var tile_region = new visualization.GenomeRegion({ chrom: track.view.chrom, start: this.low, end: this.high @@ -2817,7 +2819,7 @@ // // Attribute init. // - this.dataset = new Dataset({ + this.dataset = new data.Dataset({ id: obj_dict.dataset_id, hda_ldda: obj_dict.hda_ldda }); @@ -2928,13 +2930,13 @@ ok_fn = function() { var regions_to_use = $('select[name="regions"] option:selected').val(), regions, - view_region = new GenomeRegion({ + view_region = new visualization.GenomeRegion({ chrom: view.chrom, start: view.low, end: view.high }), bookmarked_regions = _.map($(".bookmark"), function(elt) { - return new GenomeRegion({from_str: $(elt).children(".position").text()}); + return new visualization.GenomeRegion({from_str: $(elt).children(".position").text()}); });

// Get regions for visualization. @@ -3634,7 +3636,7 @@ tile_length = Math.ceil( TILE_SIZE * resolution ), // Tile high cannot be larger than view.max_high, which the chromosome length. tile_high = (tile_low + tile_length <= this.view.max_high ? tile_low + tile_length : this.view.max_high); - return new GenomeRegion({ + return new visualization.GenomeRegion({ chrom: this.view.chrom, start: tile_low, end: tile_high @@ -3691,7 +3693,7 @@ self.data_query_wait = DEFAULT_DATA_QUERY_WAIT;

// Reset data URL when dataset indexing has completed/when not pending. - var ss_deferred = new ServerStateDeferred({ + var ss_deferred = new util.ServerStateDeferred({ url: self.dataset_state_url, url_params: {dataset_id : self.dataset_id, hda_ldda: self.hda_ldda}, interval: self.data_query_wait,

diff -r d824b236fe80ffea89cae979112580935abfa7c4 -r 040555fcc6b5341e2878c0d4ec33f54c712273c2 static/scripts/viz/trackster/util.js --- a/static/scripts/viz/trackster/util.js +++ b/static/scripts/viz/trackster/util.js @@ -3,6 +3,43 @@ exports = {};

/** + * Implementation of a server-state based deferred. Server is repeatedly polled, and when + * condition is met, deferred is resolved. + */ +exports.ServerStateDeferred = Backbone.Model.extend({ + defaults: { + ajax_settings: {}, + interval: 1000, + success_fn: function(result) { return true; } + }, + + /** + * Returns a deferred that resolves when success function returns true. + */ + go: function() { + var deferred = $.Deferred(), + self = this, + ajax_settings = self.get('ajax_settings'), + success_fn = self.get('success_fn'), + interval = self.get('interval'), + _go = function() { + $.ajax(ajax_settings).success(function(result) { + if (success_fn(result)) { + // Result is good, so resolve. + deferred.resolve(result); + } + else { + // Result not good, try again. + setTimeout(_go, interval); + } + }); + }; + _go(); + return deferred; + } +}); + +/** * Returns a random color in hexadecimal format that is sufficiently different from a single color * or set of colors. * @param colors a color or list of colors in the format '#RRGGBB'

diff -r d824b236fe80ffea89cae979112580935abfa7c4 -r 040555fcc6b5341e2878c0d4ec33f54c712273c2 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -1,4 +1,4 @@ -(function(){ +define( ["mvc/data", "viz/trackster/util" ], function(data, util) {

/** * Model, view, and controller objects for Galaxy visualization framework. @@ -20,45 +20,6 @@ // --------- Models ---------

/** - * Implementation of a server-state based deferred. Server is repeatedly polled, and when - * condition is met, deferred is resolved. - */ -var ServerStateDeferred = Backbone.Model.extend({ - defaults: { - ajax_settings: {}, - interval: 1000, - success_fn: function(result) { return true; } - }, - - /** - * Returns a deferred that resolves when success function returns true. - */ - go: function() { - var deferred = $.Deferred(), - self = this, - ajax_settings = self.get('ajax_settings'), - success_fn = self.get('success_fn'), - interval = self.get('interval'), - _go = function() { - $.ajax(ajax_settings).success(function(result) { - if (success_fn(result)) { - // Result is good, so resolve. - deferred.resolve(result); - } - else { - // Result not good, try again. - setTimeout(_go, interval); - } - }); - }; - _go(); - return deferred; - } -}); - -// 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 */ @@ -189,7 +150,7 @@ data_is_ready: function() { var dataset = this.get('dataset'), ready_deferred = $.Deferred(), - ss_deferred = new ServerStateDeferred({ + ss_deferred = new util.ServerStateDeferred({ ajax_settings: { url: this.get('dataset').url(), data: { @@ -622,7 +583,7 @@ * A track of data in a genome visualization. */ // TODO: rename to Track and merge with Trackster's Track object. -var BackboneTrack = Dataset.extend({ +var BackboneTrack = data.Dataset.extend({

initialize: function(options) { // Dataset id is unique ID for now. @@ -783,39 +744,23 @@ }); };

-// ---- Exports ---- +return { + BrowserBookmark: BrowserBookmark, + BrowserBookmarkCollection: BrowserBookmarkCollection, + Cache: Cache, + CanvasManager: CanvasManager, + Genome: Genome, + GenomeDataManager: GenomeDataManager, + GenomeRegion: GenomeRegion, + GenomeRegionCollection: GenomeRegionCollection, + GenomeVisualization: GenomeVisualization, + GenomeWideBigWigData: GenomeWideBigWigData, + GenomeWideSummaryTreeData: GenomeWideSummaryTreeData, + ReferenceTrackDataManager: ReferenceTrackDataManager, + TrackBrowserRouter: TrackBrowserRouter, + TrackConfig: TrackConfig, + Visualization: Visualization, + add_datasets: add_datasets +};

-var exports = (function() { - if ( typeof module !== 'undefined' && module.exports ) { - // CommonJS - return module.exports; - } else if ( typeof define === 'function' && define.amd ) { - // AMD - exports = {}; - define( function() { return exports; } ); - return exports; - } else { - // Browser global - return window; - } -})(); - -exports.BrowserBookmark = BrowserBookmark; -exports.BrowserBookmarkCollection = BrowserBookmarkCollection; -exports.Cache = Cache; -exports.CanvasManager = CanvasManager; -exports.Genome = Genome; -exports.GenomeDataManager = GenomeDataManager; -exports.GenomeRegion = GenomeRegion; -exports.GenomeRegionCollection = GenomeRegionCollection; -exports.GenomeVisualization = GenomeVisualization; -exports.GenomeWideBigWigData = GenomeWideBigWigData; -exports.GenomeWideSummaryTreeData = GenomeWideSummaryTreeData; -exports.ReferenceTrackDataManager = ReferenceTrackDataManager; -exports.ServerStateDeferred = ServerStateDeferred; -exports.TrackBrowserRouter = TrackBrowserRouter; -exports.TrackConfig = TrackConfig; -exports.Visualization = Visualization; -exports.add_datasets = add_datasets; - -}).call(this); \ No newline at end of file +}); \ No newline at end of file

diff -r d824b236fe80ffea89cae979112580935abfa7c4 -r 040555fcc6b5341e2878c0d4ec33f54c712273c2 templates/root/tool_menu.mako --- a/templates/root/tool_menu.mako +++ b/templates/root/tool_menu.mako @@ -17,7 +17,7 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.templates( "tool_link", "panel_section", "tool_search" )} - ${h.js( "galaxy.autocom_tagging", "mvc/tools" )} + ${h.js( "libs/require", "galaxy.autocom_tagging" )}

<% # Set up for creating tool panel. @@ -29,51 +29,64 @@ %><script type="text/javascript"> - // Init. on document load. - var tool_panel, tool_panel_view, tool_search; - $(function() { - // Set up search. - tool_search = new ToolSearch( {spinner_url: "${h.url_for('/static/images/loading_small_white_bg.gif')}", - search_url: "${h.url_for( controller='root', action='tool_search' )}", - hidden: ${tool_search_hidden} } ); - - // Set up tool panel. - tool_panel = new ToolPanel( { tool_search: tool_search } ); - tool_panel.reset( tool_panel.parse( ${h.to_json_string( dictified_panel )} ) ); - - // Set up tool panel view and initialize. - tool_panel_view = new ToolPanelView( {collection: tool_panel} ); - tool_panel_view.render(); - $('body').prepend(tool_panel_view.$el); - - // Minsize init hint. - $( "a[minsizehint]" ).click( function() { - if ( parent.handle_minwidth_hint ) { - parent.handle_minwidth_hint( $(this).attr( "minsizehint" ) ); + + require.config({ + baseUrl: "${h.url_for('/static/scripts')}", + shim: { + "libs/underscore": { exports: "_" } } + }); + + require(["mvc/tools"], function(tools) { + + // Init. on document load. + var tool_panel, tool_panel_view, tool_search; + $(function() { + // Set up search. + tool_search = new tools.ToolSearch( + { spinner_url: "${h.url_for('/static/images/loading_small_white_bg.gif')}", + search_url: "${h.url_for( controller='root', action='tool_search' )}", + hidden: ${tool_search_hidden} } ); + + // Set up tool panel. + tool_panel = new tools.ToolPanel( { tool_search: tool_search } ); + tool_panel.reset( tool_panel.parse( ${h.to_json_string( dictified_panel )} ) ); + + // Set up tool panel view and initialize. + tool_panel_view = new tools.ToolPanelView( {collection: tool_panel} ); + tool_panel_view.render(); + $('body').prepend(tool_panel_view.$el); + + // Minsize init hint. + $( "a[minsizehint]" ).click( function() { + if ( parent.handle_minwidth_hint ) { + parent.handle_minwidth_hint( $(this).attr( "minsizehint" ) ); + } + }); + + // Log clicks on tools. + /* + $("div.toolTitle > a").click( function() { + var tool_title = $(this).attr('id').split("-")[1]; + var section_title = $.trim( $(this).parents("div.toolSectionWrapper").find("div.toolSectionTitle").text() ); + var search_active = $(this).parents("div.toolTitle").hasClass("search_match"); + + // Log action. + galaxy_async.log_user_action("tool_menu_click." + tool_title, section_title, + JSON.stringify({"search_active" : search_active})); + }); + */ + + $( '.tooltip' ).tooltip(); + + // TODO: is this necessary? + $( "a[minsizehint]" ).click( function() { + if ( parent.handle_minwidth_hint ) { + parent.handle_minwidth_hint( $(this).attr( "minsizehint" ) ); + } + }); }); - - // Log clicks on tools. - /* - $("div.toolTitle > a").click( function() { - var tool_title = $(this).attr('id').split("-")[1]; - var section_title = $.trim( $(this).parents("div.toolSectionWrapper").find("div.toolSectionTitle").text() ); - var search_active = $(this).parents("div.toolTitle").hasClass("search_match"); - - // Log action. - galaxy_async.log_user_action("tool_menu_click." + tool_title, section_title, - JSON.stringify({"search_active" : search_active})); - }); - */ - - $( '.tooltip' ).tooltip(); - - // TODO: is this necessary? - $( "a[minsizehint]" ).click( function() { - if ( parent.handle_minwidth_hint ) { - parent.handle_minwidth_hint( $(this).attr( "minsizehint" ) ); - } - }); + }); </script></%def>

diff -r d824b236fe80ffea89cae979112580935abfa7c4 -r 040555fcc6b5341e2878c0d4ec33f54c712273c2 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -32,10 +32,12 @@ baseUrl: "${h.url_for('/static/scripts') }", shim: { "libs/underscore": { exports: "_" }, - "libs/backbone/backbone": { exports: "Backbone" } + "libs/backbone/backbone": { exports: "Backbone" }, + "libs/backbone/backbone-relational": ["libs/backbone/backbone"] } }); - require( ["base", "viz/trackster_ui","viz/trackster/util","viz/trackster/tracks"], function( base, trackster_ui, util, tracks ) { + require( ["base", "viz/visualization", "viz/trackster_ui", "viz/trackster/tracks"], + function( base, visualization, trackster_ui, tracks ) {

// // Place URLs here so that url_for can be used to generate them. @@ -54,7 +56,7 @@ * Set up router. */ var set_up_router = function(options) { - browser_router = new TrackBrowserRouter(options); + browser_router = new visualization.TrackBrowserRouter(options); Backbone.history.start(); };

diff -r d824b236fe80ffea89cae979112580935abfa7c4 -r 040555fcc6b5341e2878c0d4ec33f54c712273c2 templates/visualization/circster.mako --- a/templates/visualization/circster.mako +++ b/templates/visualization/circster.mako @@ -16,7 +16,7 @@ <%def name="javascripts()"> ${parent.javascripts()}

- ${h.js( "libs/require", "mvc/data" )} + ${h.js( "libs/require" )}

<script type="text/javascript">

diff -r d824b236fe80ffea89cae979112580935abfa7c4 -r 040555fcc6b5341e2878c0d4ec33f54c712273c2 templates/visualization/sweepster.mako --- a/templates/visualization/sweepster.mako +++ b/templates/visualization/sweepster.mako @@ -108,19 +108,19 @@

${h.templates( "tool_link", "panel_section", "tool_search", "tool_form" )} ${h.js( "libs/require", "libs/jquery/jquery-ui-1.8.23.custom.min" )} - ${h.js( "mvc/data", "mvc/tools" )} - + <script type="text/javascript"> require.config({ baseUrl: "${h.url_for('/static/scripts')}", shim: { "libs/underscore": { exports: "_" }, "libs/d3": { exports: "d3" }, - "libs/backbone/backbone": { exports: "Backbone" } + "libs/backbone/backbone": { exports: "Backbone" }, + "libs/backbone/backbone-relational": ["libs/backbone/backbone"] } });

- require(["libs/d3", "viz/visualization", "viz/sweepster"], function(d3, visualization, sweepster) { + require(["libs/d3", "viz/sweepster"], function(d3, sweepster) {

var viz; $(function() {

diff -r d824b236fe80ffea89cae979112580935abfa7c4 -r 040555fcc6b5341e2878c0d4ec33f54c712273c2 templates/visualization/trackster_common.mako --- a/templates/visualization/trackster_common.mako +++ b/templates/visualization/trackster_common.mako @@ -11,7 +11,7 @@

## Render needed JavaScript files. <%def name="render_trackster_js_files()"> - ${h.js( "galaxy.panels", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery-ui-1.8.23.custom.min", "mvc/data", "viz/visualization", "libs/require", "libs/farbtastic" )} + ${h.js( "galaxy.panels", "libs/jquery/jstorage", "libs/jquery/jquery.event.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel", "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/require", "libs/farbtastic" )} </%def>

## Render a block of JavaScript that contains all necessary variables for Trackster.

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

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