From 372c2e9e43854b0e5e576abcead50e22f00923d9 Mon Sep 17 00:00:00 2001 From: carlfeberhard Date: Thu, 12 Nov 2015 14:52:11 -0500 Subject: [PATCH] Webpack: move data.js into dataset/data.js; pack scripts --- client/galaxy/scripts/layout/scratchbook.js | 2 +- .../galaxy/scripts/mvc/{ => dataset}/data.js | 0 client/galaxy/scripts/mvc/tools/tools.js | 2 +- client/galaxy/scripts/viz/phyloviz.js | 4 +- client/galaxy/scripts/viz/sweepster.js | 2 +- client/galaxy/scripts/viz/trackster/tracks.js | 2 +- client/galaxy/scripts/viz/visualization.js | 158 +++++++++--------- static/maps/galaxy.tools.js.map | 2 +- static/maps/layout/scratchbook.js.map | 2 +- static/maps/mvc/app/app-analysis.js.map | 2 +- static/maps/mvc/data.js.map | 1 - static/maps/mvc/dataset/data.js.map | 1 + static/maps/mvc/tools/tools.js.map | 2 +- static/maps/onload.js.map | 2 +- static/maps/ui/scroll-panel.js.map | 2 +- static/maps/viz/phyloviz.js.map | 2 +- static/maps/viz/sweepster.js.map | 2 +- static/maps/viz/trackster/tracks.js.map | 2 +- static/maps/viz/visualization.js.map | 2 +- static/scripts/galaxy.tools.js | 2 +- static/scripts/layout/scratchbook.js | 2 +- static/scripts/mvc/app/app-analysis.js | 2 +- static/scripts/mvc/{ => dataset}/data.js | 2 +- static/scripts/mvc/tools/tools.js | 4 +- static/scripts/onload.js | 2 +- static/scripts/ui/scroll-panel.js | 2 +- static/scripts/viz/phyloviz.js | 2 +- static/scripts/viz/sweepster.js | 2 +- static/scripts/viz/trackster/tracks.js | 5 +- static/scripts/viz/visualization.js | 2 +- templates/webapps/galaxy/dataset/display.mako | 2 +- .../galaxy/dataset/tabular_chunked.mako | 2 +- 32 files changed, 112 insertions(+), 111 deletions(-) rename client/galaxy/scripts/mvc/{ => dataset}/data.js (100%) delete mode 100644 static/maps/mvc/data.js.map create mode 100644 static/maps/mvc/dataset/data.js.map rename static/scripts/mvc/{ => dataset}/data.js (99%) diff --git a/client/galaxy/scripts/layout/scratchbook.js b/client/galaxy/scripts/layout/scratchbook.js index b4640e794c8..13a992c2093 100644 --- a/client/galaxy/scripts/layout/scratchbook.js +++ b/client/galaxy/scripts/layout/scratchbook.js @@ -77,7 +77,7 @@ var GalaxyFrame = Backbone.View.extend({ */ add_dataset: function(dataset_id) { var self = this; - require(['mvc/data'], function(DATA) { + require(['mvc/dataset/data'], function(DATA) { var dataset = new DATA.Dataset({ id: dataset_id }); $.when( dataset.fetch() ).then( function() { // Construct frame config based on dataset's type. diff --git a/client/galaxy/scripts/mvc/data.js b/client/galaxy/scripts/mvc/dataset/data.js similarity index 100% rename from client/galaxy/scripts/mvc/data.js rename to client/galaxy/scripts/mvc/dataset/data.js diff --git a/client/galaxy/scripts/mvc/tools/tools.js b/client/galaxy/scripts/mvc/tools/tools.js index 3a7548b3859..4cbe0097ad0 100644 --- a/client/galaxy/scripts/mvc/tools/tools.js +++ b/client/galaxy/scripts/mvc/tools/tools.js @@ -5,7 +5,7 @@ define([ "libs/underscore", "viz/trackster/util", - "mvc/data", + "mvc/dataset/data", "mvc/tools/tools-form", "templates/tool_form.handlebars", "templates/tool_link.handlebars", diff --git a/client/galaxy/scripts/viz/phyloviz.js b/client/galaxy/scripts/viz/phyloviz.js index 0a1c3fd372c..15a17a0909e 100644 --- a/client/galaxy/scripts/viz/phyloviz.js +++ b/client/galaxy/scripts/viz/phyloviz.js @@ -1,7 +1,7 @@ define([ 'libs/d3', 'viz/visualization', - 'mvc/data', + 'mvc/dataset/data', 'mvc/ui/icon-button' ], function(d3, visualization_mod, data_mod, mod_icon_btn) { @@ -204,7 +204,7 @@ var PhyloTree = visualization_mod.Visualization.extend({ this.set("dataset", new data_mod.Dataset({ id: options.dataset_id })); - + }, root : {}, // Root has to be its own independent object because it is not part of the viz_config diff --git a/client/galaxy/scripts/viz/sweepster.js b/client/galaxy/scripts/viz/sweepster.js index a125cd34852..36f512fba73 100644 --- a/client/galaxy/scripts/viz/sweepster.js +++ b/client/galaxy/scripts/viz/sweepster.js @@ -10,7 +10,7 @@ define([ "viz/visualization", "viz/trackster/tracks", "mvc/tools/tools", - "mvc/data", + "mvc/dataset/data", "utils/config", "mvc/ui/icon-button" ], function(_, d3, util, visualization, tracks, tools, data, config, mod_icon_btn) { diff --git a/client/galaxy/scripts/viz/trackster/tracks.js b/client/galaxy/scripts/viz/trackster/tracks.js index 64d85a1ce06..0d33d661bad 100644 --- a/client/galaxy/scripts/viz/trackster/tracks.js +++ b/client/galaxy/scripts/viz/trackster/tracks.js @@ -6,7 +6,7 @@ define([ "viz/trackster/slotting", "viz/trackster/painters", "viz/trackster/filters", - "mvc/data", + "mvc/dataset/data", "mvc/tools/tools", "utils/config", "ui/editable-text", diff --git a/client/galaxy/scripts/viz/visualization.js b/client/galaxy/scripts/viz/visualization.js index d6ea5967e26..4c9298e1355 100644 --- a/client/galaxy/scripts/viz/visualization.js +++ b/client/galaxy/scripts/viz/visualization.js @@ -1,7 +1,7 @@ -define( ["libs/underscore", "mvc/data", "viz/trackster/util", "utils/config"], function(_, data_mod, util_mod, config_mod) { +define( ["libs/underscore", "mvc/dataset/data", "viz/trackster/util", "utils/config"], function(_, data_mod, util_mod, config_mod) { /** - * Mixin for returning custom JSON representation from toJSON. Class attribute to_json_keys defines a set of attributes + * Mixin for returning custom JSON representation from toJSON. Class attribute to_json_keys defines a set of attributes * to include in the representation; to_json_mappers defines mappers for returned objects. */ var CustomToJSON = { @@ -25,8 +25,8 @@ var CustomToJSON = { /** * Model, view, and controller objects for Galaxy visualization framework. * - * Models have no references to views, instead using events to indicate state - * changes; this is advantageous because multiple views can use the same object + * Models have no references to views, instead using events to indicate state + * changes; this is advantageous because multiple views can use the same object * and models can be used without views. */ @@ -66,13 +66,13 @@ var select_datasets = function(dataset_url, add_track_async_url, filters, succes dataType: "json" }); }); - // To preserve order, wait until there are definitions for all tracks and then add + // To preserve order, wait until there are definitions for all tracks and then add // them sequentially. $.when.apply($, requests).then(function() { // jQuery always returns an Array for arguments, so need to look at first element - // to determine whether multiple requests were made and consequently how to + // to determine whether multiple requests were made and consequently how to // map arguments to track definitions. - var track_defs = (arguments[0] instanceof Array ? + var track_defs = (arguments[0] instanceof Array ? $.map(arguments, function(arg) { return arg[0]; }) : [ arguments[0] ] ); @@ -94,13 +94,13 @@ var select_datasets = function(dataset_url, add_track_async_url, filters, succes */ 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 @@ -135,13 +135,13 @@ _.extend( CanvasManager.prototype, { }); /** - * Generic cache that handles key/value pairs. Keys can be any object that can be + * Generic cache that handles key/value pairs. Keys can be any object that can be * converted to a String and compared. - */ + */ var Cache = Backbone.Model.extend({ defaults: { num_elements: 20, - // Objects in cache; indexes into cache are strings of keys. + // Objects in cache; indexes into cache are strings of keys. obj_cache: null, // key_ary contains keys for objects in cache. key_ary: null @@ -153,7 +153,7 @@ var Cache = Backbone.Model.extend({ /** * Get an element from the cache using its key. - */ + */ get_elt: function(key) { var obj_cache = this.attributes.obj_cache, key_ary = this.attributes.key_ary, @@ -178,7 +178,7 @@ var Cache = Backbone.Model.extend({ return obj_cache[key_str]; }, - + /** * Put an element into the cache. */ @@ -206,16 +206,16 @@ var Cache = Backbone.Model.extend({ obj_cache[key_str] = value; return value; }, - - /** - * Move key to end of cache. Keys are removed from the front, so moving a key to the end + + /** + * Move key to end of cache. Keys are removed from the front, so moving a key to the end * delays the key's removal. */ move_key_to_end: function(key, index) { this.attributes.key_ary.splice(index, 1); this.attributes.key_ary.push(key); }, - + /** * Clear all elements from the cache. */ @@ -223,7 +223,7 @@ var Cache = Backbone.Model.extend({ this.attributes.obj_cache = {}; this.attributes.key_ary = []; }, - + /** Returns the number of elements in the cache. */ size: function() { return this.attributes.key_ary.length; @@ -231,8 +231,8 @@ var Cache = Backbone.Model.extend({ /** Returns key most recently added to cache. */ most_recently_added: function() { - return this.size() === 0 ? null : - // Most recent key is at the end of key array. + return this.size() === 0 ? null : + // Most recent key is at the end of key array. this.attributes.key_ary[this.attributes.key_ary.length - 1]; } }); @@ -289,9 +289,9 @@ var GenomeDataManager = Cache.extend({ data_is_ready: function() { var dataset = this.get('dataset'), ready_deferred = $.Deferred(), - // If requesting raw data, query dataset state; if requesting (converted) data, + // If requesting raw data, query dataset state; if requesting (converted) data, // need to query converted datasets state. - query_type = (this.get('data_type') === 'raw_data' ? 'state' : + query_type = (this.get('data_type') === 'raw_data' ? 'state' : this.get('data_type') === 'data' ? 'converted_datasets_state' : "error" ), ss_deferred = new util_mod.ServerStateDeferred({ ajax_settings: { @@ -324,7 +324,7 @@ var GenomeDataManager = Cache.extend({ }; return $.getJSON(dataset.url(), params); }, - + /** * Load data from server and manages data entries. Adds a Deferred to manager * for region; when data becomes available, replaces Deferred with data. @@ -335,16 +335,16 @@ var GenomeDataManager = Cache.extend({ var dataset = this.get('dataset'), params = { "data_type": this.get('data_type'), - "chrom": region.get('chrom'), - "low": region.get('start'), - "high": region.get('end'), + "chrom": region.get('chrom'), + "low": region.get('start'), + "high": region.get('end'), "mode": mode, "resolution": resolution, "hda_ldda": dataset.get('hda_ldda') }; $.extend(params, extra_params); - + // Add track filters to params. var filters_manager = this.get('filters_manager'); if (filters_manager) { @@ -355,7 +355,7 @@ var GenomeDataManager = Cache.extend({ } params.filter_cols = JSON.stringify(filter_names); } - + // Do request. var manager = this, entry = $.getJSON(dataset.url(), params, function (result) { @@ -367,14 +367,14 @@ var GenomeDataManager = Cache.extend({ this.set_data(region, entry); return entry; }, - + /** * Get data from dataset. */ get_data: function(region, mode, resolution, extra_params) { // Look for entry and return if it's a deferred or if data available is compatible with mode. var entry = this.get_elt(region); - if ( entry && + if ( entry && ( util_mod.is_deferred(entry) || this.get('data_mode_compatible')(entry, mode) ) ) { return entry; } @@ -389,14 +389,14 @@ var GenomeDataManager = Cache.extend({ entry_region, is_subregion; for (var i = 0; i < key_ary.length; i++) { entry_region = key_ary[i]; - + if (entry_region.contains(region)) { is_subregion = true; // This entry has data in the requested range. Return if data // is compatible and can be subsetted. entry = obj_cache[entry_region.toString()]; - if ( util_mod.is_deferred(entry) || + if ( util_mod.is_deferred(entry) || ( this.get('data_mode_compatible')(entry, mode) && this.get('can_subset')(entry) ) ) { this.move_key_to_end(entry_region, i); @@ -412,7 +412,7 @@ var GenomeDataManager = Cache.extend({ } } - // FIXME: There _may_ be instances where region is a subregion of another entry but cannot be + // FIXME: There _may_ be instances where region is a subregion of another entry but cannot be // subsetted. For these cases, do not increase length because region will never be found (and // an infinite loop will occur.) // If needed, extend region to make it minimum size. @@ -442,20 +442,20 @@ var GenomeDataManager = Cache.extend({ return this.load_data(region, mode, resolution, extra_params); }, - + /** * Alias for set_elt for readbility. */ set_data: function(region, entry) { - this.set_elt(region, entry); + this.set_elt(region, entry); }, - + /** "Deep" data request; used as a parameter for DataManager.get_more_data() */ DEEP_DATA_REQ: "deep", - + /** "Broad" data request; used as a parameter for DataManager.get_more_data() */ BROAD_DATA_REQ: "breadth", - + /** * Gets more data for a region using either a depth-first or a breadth-first approach. */ @@ -465,7 +465,7 @@ var GenomeDataManager = Cache.extend({ console.log('ERROR: problem with getting more data: current data is not compatible'); return; } - + // // Set parameters based on request type. // @@ -480,7 +480,7 @@ var GenomeDataManager = Cache.extend({ query_low = (cur_data.max_high ? cur_data.max_high : cur_data.data[cur_data.data.length - 1][2]) + 1; } var query_region = region.copy().set('start', query_low); - + // // Get additional data, append to current data, and set new data. Use a custom deferred object // to signal when new data is available. @@ -605,7 +605,7 @@ var GenomeDataManager = Cache.extend({ var subset_fns = { bigwig: function(data, subregion) { return _.filter(data, function(data_point) { - return data_point[0] >= subregion.get('start') && + return data_point[0] >= subregion.get('start') && data_point[0] <= subregion.get('end'); }); }, @@ -640,12 +640,12 @@ var GenomeReferenceDataManager = GenomeDataManager.extend({ load_data: function(region, mode, resolution, extra_params) { // Fetch data if region is not too large. - return ( region.length() <= 100000 ? + return ( region.length() <= 100000 ? GenomeDataManager.prototype.load_data.call(this, region, mode, resolution, extra_params) : { data: null, region: region } ); } }); - + /** * A genome build. */ @@ -659,20 +659,20 @@ var Genome = Backbone.Model.extend({ initialize: function(options) { this.id = options.dbkey; }, - + /** * Shorthand for getting to chromosome information. */ get_chroms_info: function() { - return this.attributes.chroms_info.chrom_info; + return this.attributes.chroms_info.chrom_info; }, - /** + /** * Returns a GenomeRegion object denoting a complete chromosome. */ get_chrom_region: function(chr_name) { // FIXME: use findWhere in underscore 1.4 - var chrom_info = _.find(this.get_chroms_info(), function(chrom_info) { + var chrom_info = _.find(this.get_chroms_info(), function(chrom_info) { return chrom_info.chrom === chr_name; }); return new GenomeRegion({ @@ -684,7 +684,7 @@ var Genome = Backbone.Model.extend({ /** Returns the length of a chromosome. */ get_chrom_len: function(chr_name) { // FIXME: use findWhere in underscore 1.4 - return _.find(this.get_chroms_info(), function(chrom_info) { + return _.find(this.get_chroms_info(), function(chrom_info) { return chrom_info.chrom === chr_name; }).len; } @@ -711,7 +711,7 @@ var GenomeRegion = Backbone.Model.extend({ this.attributes.start === region.get('start') && this.attributes.end === region.get('end'); }, - + /** * If from_str specified, use it to initialize attributes. */ @@ -732,27 +732,27 @@ var GenomeRegion = Backbone.Model.extend({ // Set str_val on attribute change. this.on('change', function() { - this.attributes.str_val = this.get('chrom') + ":" + this.get('start') + "-" + this.get('end'); + this.attributes.str_val = this.get('chrom') + ":" + this.get('start') + "-" + this.get('end'); }, this); }, - + copy: function() { return new GenomeRegion({ chrom: this.get('chrom'), start: this.get('start'), - end: this.get('end') + end: this.get('end') }); }, length: function() { return this.get('end') - this.get('start'); }, - + /** Returns region in canonical form chrom:start-end */ toString: function() { return this.attributes.str_val; }, - + toJSON: function() { return { chrom: this.get('chrom'), @@ -760,9 +760,9 @@ var GenomeRegion = Backbone.Model.extend({ end: this.get('end') }; }, - + /** - * Compute the type of overlap between this region and another region. The overlap is computed relative to the given/second region; + * Compute the type of overlap between this region and another region. The overlap is computed relative to the given/second region; * hence, OVERLAP_START indicates that the first region overlaps the start (but not the end) of the second region. */ compute_overlap: function(a_region) { @@ -770,12 +770,12 @@ var GenomeRegion = Backbone.Model.extend({ first_start = this.get('start'), second_start = a_region.get('start'), first_end = this.get('end'), second_end = a_region.get('end'), overlap; - + // Compare chroms. if (first_chrom && second_chrom && first_chrom !== second_chrom) { return GenomeRegion.overlap_results.DIF_CHROMS; } - + // Compare regions. if (first_start < second_start) { if (first_end < second_start) { @@ -800,8 +800,8 @@ var GenomeRegion = Backbone.Model.extend({ } } else { // first_start === second_start - overlap = (first_end >= second_end ? - GenomeRegion.overlap_results.CONTAINS : + overlap = (first_end >= second_end ? + GenomeRegion.overlap_results.CONTAINS : GenomeRegion.overlap_results.CONTAINED_BY); } @@ -827,7 +827,7 @@ var GenomeRegion = Backbone.Model.extend({ return this; }, - + /** * Returns true if this region contains a given region. */ @@ -839,18 +839,18 @@ var GenomeRegion = Backbone.Model.extend({ * Returns true if regions overlap. */ overlaps: function(a_region) { - return _.intersection( [this.compute_overlap(a_region)], - [GenomeRegion.overlap_results.DIF_CHROMS, GenomeRegion.overlap_results.BEFORE, GenomeRegion.overlap_results.AFTER] ).length === 0; + return _.intersection( [this.compute_overlap(a_region)], + [GenomeRegion.overlap_results.DIF_CHROMS, GenomeRegion.overlap_results.BEFORE, GenomeRegion.overlap_results.AFTER] ).length === 0; } }, { overlap_results: { DIF_CHROMS: 1000, - BEFORE: 1001, - CONTAINS: 1002, - OVERLAP_START: 1003, - OVERLAP_END: 1004, - CONTAINED_BY: 1005, + BEFORE: 1001, + CONTAINS: 1002, + OVERLAP_START: 1003, + OVERLAP_END: 1004, + CONTAINED_BY: 1005, AFTER: 1006 } }); @@ -892,7 +892,7 @@ var BackboneTrack = Backbone.Model.extend(CustomToJSON).extend({ initialize: function(options) { this.set('dataset', new data_mod.Dataset(options.dataset)); - // -- Set up config settings. -- + // -- Set up config settings. -- var models = [ { key: 'name', default_value: this.get('dataset').get('name') }, { key: 'color' }, @@ -959,10 +959,10 @@ var Visualization = Backbone.Model.extend({ }, urlRoot: galaxy_config.root + "api/visualizations", - + /** * POSTs visualization's JSON to its URL using the parameter 'vis_json' - * Note: This is necessary because (a) Galaxy requires keyword args and + * Note: This is necessary because (a) Galaxy requires keyword args and * (b) Galaxy does not handle PUT now. */ save: function() { @@ -970,7 +970,7 @@ var Visualization = Backbone.Model.extend({ url: this.url(), type: "POST", dataType: "json", - data: { + data: { vis_json: JSON.stringify(this) } }); @@ -994,7 +994,7 @@ var GenomeVisualization = Visualization.extend(CustomToJSON).extend({ var models = []; this.set('config', config_mod.ConfigSettingCollection.from_models_and_saved_values(models, options.prefs)); - + // Clear track and data definitions to avoid storing large objects. this.unset('tracks'); this.get('drawables').each(function(d) { @@ -1039,22 +1039,22 @@ var GenomeVisualization = Visualization.extend(CustomToJSON).extend({ /** * Router for track browser. */ -var TrackBrowserRouter = Backbone.Router.extend({ +var TrackBrowserRouter = Backbone.Router.extend({ initialize: function(options) { this.view = options.view; - + // Can't put regular expression in routes dictionary. // NOTE: parentheses are used to denote parameters returned to callback. this.route(/([\w]+)$/, 'change_location'); this.route(/([\w\+]+\:[\d,]+-[\d,]+)$/, 'change_location'); - + // Handle navigate events from view. var self = this; self.view.on("navigate", function(new_loc) { self.navigate(new_loc); }); }, - + change_location: function(new_loc) { this.view.go_to(new_loc); } diff --git a/static/maps/galaxy.tools.js.map b/static/maps/galaxy.tools.js.map index 3ebcebd65ea..4c3b8d640d7 100644 --- a/static/maps/galaxy.tools.js.map +++ b/static/maps/galaxy.tools.js.map @@ -1 +1 @@ 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