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commit/galaxy-central: jgoecks: Add requireJS support for data, visualization, tools and update dependencies.
by Bitbucket 21 Sep '12

21 Sep '12

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Workflows: Viewing and Downloading of workflows with missing tools now handled gracefully.
by Bitbucket 20 Sep '12

20 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d824b236fe80/ changeset: d824b236fe80 user: dannon date: 2012-09-20 23:10:52 summary: Workflows: Viewing and Downloading of workflows with missing tools now handled gracefully. affected #: 3 files diff -r 501641b6f680b88f5e1ef78e1b8080853d59dea8 -r d824b236fe80ffea89cae979112580935abfa7c4 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -668,14 +668,19 @@ if step.type == 'tool' or step.type is None: # Restore the tool state for the step module = module_factory.from_workflow_step( trans, step ) - #Check if tool was upgraded - step.upgrade_messages = module.check_and_update_state() - # Any connected input needs to have value DummyDataset (these - # are not persisted so we need to do it every time) - module.add_dummy_datasets( connections=step.input_connections ) - # Store state with the step - step.module = module - step.state = module.state + if module: + #Check if tool was upgraded + step.upgrade_messages = module.check_and_update_state() + # Any connected input needs to have value DummyDataset (these + # are not persisted so we need to do it every time) + module.add_dummy_datasets( connections=step.input_connections ) + # Store state with the step + step.module = module + step.state = module.state + else: + step.upgrade_messages = "Unknown Tool ID" + step.module = None + step.state = None # Error dict if step.tool_errors: errors[step.id] = step.tool_errors diff -r 501641b6f680b88f5e1ef78e1b8080853d59dea8 -r d824b236fe80ffea89cae979112580935abfa7c4 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -214,14 +214,12 @@ raise web.httpexceptions.HTTPNotFound() # Security check raises error if user cannot access workflow. self.security_check( trans, stored_workflow, False, True ) - # Get data for workflow's steps. self.get_stored_workflow_steps( trans, stored_workflow ) # Get annotations. stored_workflow.annotation = self.get_item_annotation_str( trans.sa_session, stored_workflow.user, stored_workflow ) for step in stored_workflow.latest_workflow.steps: step.annotation = self.get_item_annotation_str( trans.sa_session, stored_workflow.user, step ) - # Get rating data. user_item_rating = 0 if trans.get_user(): @@ -1010,6 +1008,10 @@ # Stream workflow to file. stored_dict = self._workflow_to_dict( trans, stored ) + if not stored_dict: + #This workflow has a tool that's missing from the distribution + trans.response.status = 400 + return "Workflow cannot be exported due to missing tools." valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' sname = stored.name sname = ''.join(c in valid_chars and c or '_' for c in sname)[0:150] @@ -1661,6 +1663,8 @@ for step in workflow.steps: # Load from database representation module = module_factory.from_workflow_step( trans, step ) + if not module: + return None # Get user annotation. step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) annotation_str = "" diff -r 501641b6f680b88f5e1ef78e1b8080853d59dea8 -r d824b236fe80ffea89cae979112580935abfa7c4 templates/workflow/display.mako --- a/templates/workflow/display.mako +++ b/templates/workflow/display.mako @@ -87,10 +87,14 @@ tool = trans.app.toolbox.get_tool( step.tool_id ) %><div class="toolForm"> + %if tool: <div class="toolFormTitle">Step ${int(step.order_index)+1}: ${tool.name}</div><div class="toolFormBody"> ${do_inputs( tool.inputs, step.state.inputs, "", step )} </div> + %else: + <div class="toolFormTitle">Step ${int(step.order_index)+1}: Unknown Tool with id '${step.tool_id}'</div> + %endif </div> %else: ## TODO: always input dataset? Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Add utility function to circster that determines whether an element is visible.
by Bitbucket 20 Sep '12

20 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/501641b6f680/ changeset: 501641b6f680 user: jgoecks date: 2012-09-20 21:39:57 summary: Add utility function to circster that determines whether an element is visible. affected #: 1 file diff -r b7fdcf887f2da2e4ba19b5894f56b3807e98bdf4 -r 501641b6f680b88f5e1ef78e1b8080853d59dea8 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -3,8 +3,32 @@ // General backbone style inheritence var Base = function() { this.initialize && this.initialize.apply(this, arguments); }; Base.extend = Backbone.Model.extend; +var SVGUtils = Backbone.Model.extend({ + + /** + * Returns true if element is visible. + */ + is_visible: function(svg_elt, svg) { + var eltBRect = svg_elt.getBoundingClientRect(), + svgBRect = $('svg')[0].getBoundingClientRect(); + + if (// To the left of screen? + eltBRect.right < 0 || + // To the right of screen? + eltBRect.left > svgBRect.right || + // Above screen? + eltBRect.bottom < 0 || + // Below screen? + eltBRect.top > svgBRect.bottom) { + return false; + } + return true; + } + +}); + /** - * Renders a full circster visualization + * Renders a full circster visualization. */ var CircsterView = Backbone.View.extend({ className: 'circster', @@ -23,7 +47,7 @@ height = self.$el.height(), // Compute radius start based on model, will be centered // and fit entirely inside element by default - init_radius_start = ( Math.min(width,height)/2 - + init_radius_start = ( Math.min(width, height)/2 - this.model.get('tracks').length * (this.dataset_arc_height + this.track_gap) ); // Set up SVG element. @@ -38,6 +62,13 @@ svg.attr("transform", "translate(" + d3.event.translate + ")" + " scale(" + d3.event.scale + ")"); + var utils = new SVGUtils(); + var visible_elts = d3.selectAll('path').filter(function(d, i) { + return utils.is_visible(this, svg); + }); + visible_elts.each(function(d, i) { + console.log(this.attr('title')); + }); })) .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")") .append('svg:g'); @@ -57,7 +88,7 @@ total_gap: self.total_gap }); - track_renderer.render( svg ); + track_renderer.render(svg); }); } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Display warning or error message if attempting to install tool dependencies defined in a tool shed repository when the tool_dependency_dir config setting is not set in the Galaxy config.
by Bitbucket 20 Sep '12

20 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b7fdcf887f2d/ changeset: b7fdcf887f2d user: greg date: 2012-09-20 20:41:33 summary: Display warning or error message if attempting to install tool dependencies defined in a tool shed repository when the tool_dependency_dir config setting is not set in the Galaxy config. affected #: 1 file diff -r 92b2699573b9c2c8439e1e53a03c9e01ae1c4f15 -r b7fdcf887f2da2e4ba19b5894f56b3807e98bdf4 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -963,17 +963,23 @@ kwd[ 'message' ] = 'All selected tool dependencies are already uninstalled.' kwd[ 'status' ] = 'error' elif operation == "install": - tool_dependencies_for_installation = [] - for tool_dependency_id in tool_dependency_ids: - tool_dependency = get_tool_dependency( trans, tool_dependency_id ) - if tool_dependency.status in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED, - trans.model.ToolDependency.installation_status.UNINSTALLED ]: - tool_dependencies_for_installation.append( tool_dependency ) - if tool_dependencies_for_installation: - self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation ) + if trans.app.config.tool_dependency_dir: + tool_dependencies_for_installation = [] + for tool_dependency_id in tool_dependency_ids: + tool_dependency = get_tool_dependency( trans, tool_dependency_id ) + if tool_dependency.status in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED, + trans.model.ToolDependency.installation_status.UNINSTALLED ]: + tool_dependencies_for_installation.append( tool_dependency ) + if tool_dependencies_for_installation: + self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation ) + else: + kwd[ 'message' ] = 'All selected tool dependencies are already installed.' + kwd[ 'status' ] = 'error' else: - kwd[ 'message' ] = 'All selected tool dependencies are already installed.' - kwd[ 'status' ] = 'error' + message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (universe_wsgi.ini) ' + message += ' and restart your Galaxy server to install tool dependencies.' + kwd[ 'message' ] = message + kwd[ 'status' ] = 'error' return self.tool_dependency_grid( trans, **kwd ) @web.expose @web.require_admin @@ -1186,6 +1192,10 @@ else: readme_text = '' if trans.app.config.tool_dependency_dir is None: + if includes_tool_dependencies: + message = "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b>" + message += " setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository." + status = "warning" checked = False else: checked = True Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Workflows: Fix for 0ba260ea43c4 to correctly display error message when attempting to run a workflow missing tools.
by Bitbucket 20 Sep '12

20 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/92b2699573b9/ changeset: 92b2699573b9 user: dannon date: 2012-09-20 20:11:19 summary: Workflows: Fix for 0ba260ea43c4 to correctly display error message when attempting to run a workflow missing tools. affected #: 1 file diff -r dd1711a3518a27f6426cdf4d9def2efae29149c0 -r 92b2699573b9c2c8439e1e53a03c9e01ae1c4f15 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1497,7 +1497,11 @@ step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) if missing_tools: stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored ) - return trans.fill_template("workflow/run.mako", steps=[], workflow=stored, missing_tools = missing_tools) + return trans.fill_template("workflow/run.mako", + steps=[], + workflow=stored, + hide_fixed_params=hide_fixed_params, + missing_tools = missing_tools) # Render the form stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored ) return trans.fill_template( Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fixes for viewing tool metadata in a tool shed repository for tools the require data index (.loc) files.
by Bitbucket 20 Sep '12

20 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/dd1711a3518a/ changeset: dd1711a3518a user: greg date: 2012-09-20 19:43:42 summary: Fixes for viewing tool metadata in a tool shed repository for tools the require data index (.loc) files. affected #: 3 files diff -r 3184303c13918a8b4734e46e1ac956d0e44ecba2 -r dd1711a3518a27f6426cdf4d9def2efae29149c0 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -341,6 +341,17 @@ correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_file_name ) invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) ) return invalid_files_and_errors_tups +def concat_messages( msg1, msg2 ): + if msg1: + if msg2: + message = '%s %s' % ( msg1, msg2 ) + else: + message = msg1 + elif msg2: + message = msg2 + else: + message = '' + return message def config_elems_to_xml_file( app, config_elems, config_filename, tool_path ): # Persist the current in-memory list of config_elems to a file named by the value of config_filename. fd, filename = tempfile.mkstemp() @@ -352,6 +363,16 @@ os.close( fd ) shutil.move( filename, os.path.abspath( config_filename ) ) os.chmod( config_filename, 0644 ) +def copy_disk_sample_files_to_dir( trans, repo_files_dir, dest_path ): + sample_files = [] + for root, dirs, files in os.walk( repo_files_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name.endswith( '.sample' ): + relative_path = os.path.join( root, name ) + copy_sample_file( trans.app, relative_path, dest_path=dest_path ) + sample_files.append( name ) + return sample_files def clean_repository_clone_url( repository_clone_url ): if repository_clone_url.find( '@' ) > 0: # We have an url that includes an authenticated user, something like: @@ -1399,12 +1420,13 @@ if missing_data_table_entry: # The repository must contain a tool_data_table_conf.xml.sample file that includes all required entries for all tools in the repository. sample_tool_data_table_conf = get_config_from_disk( 'tool_data_table_conf.xml.sample', relative_install_dir ) - # Add entries to the ToolDataTableManager's in-memory data_tables dictionary as well as the list of data_table_elems and the list of - # data_table_elem_names. - error, correction_msg = handle_sample_tool_data_table_conf_file( app, sample_tool_data_table_conf, persist=True ) - if error: - # TODO: Do more here than logging an exception. - log.debug( correction_msg ) + if sample_tool_data_table_conf: + # Add entries to the ToolDataTableManager's in-memory data_tables dictionary as well as the list of data_table_elems and the list of + # data_table_elem_names. + error, message = handle_sample_tool_data_table_conf_file( app, sample_tool_data_table_conf, persist=True ) + if error: + # TODO: Do more here than logging an exception. + log.debug( message ) # Reload the tool into the local list of repository_tools_tups. repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid ) repository_tools_tups[ index ] = ( tup_path, guid, repository_tool ) @@ -1436,9 +1458,21 @@ repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid ) repository_tools_tups[ index ] = ( tup_path, guid, repository_tool ) return repository_tools_tups, sample_files_copied +def handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir ): + # Copy all sample files from disk to a temporary directory since the sample files may be in multiple directories. + message = '' + sample_files = copy_disk_sample_files_to_dir( trans, repo_files_dir, work_dir ) + if sample_files: + if 'tool_data_table_conf.xml.sample' in sample_files: + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = os.path.join( work_dir, 'tool_data_table_conf.xml' ) + error, message = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) + tool, valid, message2 = load_tool_from_config( trans.app, tool_config_filepath ) + message = concat_messages( message, message2 ) + return tool, valid, message def handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ): tool = None - message = None + message = '' ctx = get_changectx_for_changeset( repo, changeset_revision ) # We're not currently doing anything with the returned list of deleted_sample_files here. It is intended to help handle sample files that are in # the manifest, but have been deleted from disk. @@ -1448,13 +1482,14 @@ if 'tool_data_table_conf.xml.sample' in sample_files: # Load entries into the tool_data_tables if the tool requires them. tool_data_table_config = os.path.join( work_dir, 'tool_data_table_conf.xml' ) - error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) - if error: - # TODO: Do more here than logging an exception. - log.debug( correction_msg ) + if tool_data_table_config: + error, message = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) + if error: + log.debug( message ) manifest_ctx, ctx_file = get_ctx_file_path_from_manifest( tool_config_filename, repo, changeset_revision ) if manifest_ctx and ctx_file: - tool, message = load_tool_from_tmp_config( trans, repo, manifest_ctx, ctx_file, work_dir ) + tool, message2 = load_tool_from_tmp_config( trans, repo, manifest_ctx, ctx_file, work_dir ) + message = concat_messages( message, message2 ) return tool, message def handle_sample_tool_data_table_conf_file( app, filename, persist=False ): """ diff -r 3184303c13918a8b4734e46e1ac956d0e44ecba2 -r dd1711a3518a27f6426cdf4d9def2efae29149c0 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -7,8 +7,9 @@ from galaxy.util.hash_util import * from galaxy.util.shed_util import check_tool_input_params, clone_repository, copy_sample_file, generate_metadata_for_changeset_revision from galaxy.util.shed_util import get_changectx_for_changeset, get_config_from_disk, get_configured_ui, get_file_context_from_ctx, get_named_tmpfile_from_ctx -from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_tmp_config, handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH -from galaxy.util.shed_util import load_tool_from_config, reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path +from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_disk, handle_sample_files_and_load_tool_from_tmp_config +from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH, load_tool_from_config, reset_tool_data_tables +from galaxy.util.shed_util import reversed_upper_bounded_changelog, strip_path from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -258,16 +259,6 @@ else: return 'subset' return 'not equal and not subset' -def copy_disk_sample_files_to_dir( trans, repo_files_dir, dest_path ): - sample_files = [] - for root, dirs, files in os.walk( repo_files_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name.endswith( '.sample' ): - relative_path = os.path.join( root, name ) - copy_sample_file( trans.app, relative_path, dest_path=dest_path ) - sample_files.append( name ) - return sample_files def copy_file_from_disk( filename, repo_dir, dir ): file_path = None found = False @@ -628,15 +619,8 @@ work_dir = tempfile.mkdtemp() can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, tool_config_filepath, changeset_revision ) if can_use_disk_file: - # Copy all sample files from disk to a temporary directory since the sample files may be in multiple directories. - sample_files = copy_disk_sample_files_to_dir( trans, repo_files_dir, work_dir ) - if sample_files: - trans.app.config.tool_data_path = work_dir - if 'tool_data_table_conf.xml.sample' in sample_files: - # Load entries into the tool_data_tables if the tool requires them. - tool_data_table_config = os.path.join( work_dir, 'tool_data_table_conf.xml' ) - error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) - tool, valid, message = load_tool_from_config( trans.app, tool_config_filepath ) + trans.app.config.tool_data_path = work_dir + tool, valid, message = handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir ) if tool is not None: invalid_files_and_errors_tups = check_tool_input_params( trans.app, repo_files_dir, @@ -645,11 +629,12 @@ sample_files, webapp='community' ) if invalid_files_and_errors_tups: - message = generate_message_for_invalid_tools( invalid_files_and_errors_tups, - repository, - metadata_dict=None, - as_html=True, - displaying_invalid_tool=True ) + message2 = generate_message_for_invalid_tools( invalid_files_and_errors_tups, + repository, + metadata_dict=None, + as_html=True, + displaying_invalid_tool=True ) + message = concat_messages( message, message2 ) status = 'error' else: tool, message = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ) diff -r 3184303c13918a8b4734e46e1ac956d0e44ecba2 -r dd1711a3518a27f6426cdf4d9def2efae29149c0 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -10,9 +10,9 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.model.orm import * from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_repository_file_contents -from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_tmp_config, INITIAL_CHANGELOG_HASH, load_tool_from_config, NOT_TOOL_CONFIGS -from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, reversed_upper_bounded_changelog, strip_path -from galaxy.util.shed_util import to_html_escaped, update_repository, url_join +from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_disk, handle_sample_files_and_load_tool_from_tmp_config, INITIAL_CHANGELOG_HASH +from galaxy.util.shed_util import load_tool_from_config, NOT_TOOL_CONFIGS, open_repository_files_folder, reversed_lower_upper_bounded_changelog +from galaxy.util.shed_util import reversed_upper_bounded_changelog, strip_path, to_html_escaped, update_repository, url_join from galaxy.tool_shed.encoding_util import * from common import * @@ -2293,20 +2293,21 @@ if 'tools' in metadata: for tool_metadata_dict in metadata[ 'tools' ]: if tool_metadata_dict[ 'id' ] == tool_id: + work_dir = tempfile.mkdtemp() relative_path_to_tool_config = tool_metadata_dict[ 'tool_config' ] guid = tool_metadata_dict[ 'guid' ] full_path_to_tool_config = os.path.abspath( relative_path_to_tool_config ) - full_path_to_dir, tool_tool_config_filename = os.path.split( full_path_to_tool_config ) + full_path_to_dir, tool_config_filename = os.path.split( full_path_to_tool_config ) can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, full_path_to_tool_config, changeset_revision ) if can_use_disk_file: - trans.app.config.tool_data_path = full_path_to_dir - # Load entries into the tool_data_tables if the tool requires them. - tool_data_table_config = get_config_from_disk( 'tool_data_table_conf.xml.sample', full_path_to_dir ) - error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) - tool, valid, message = load_tool_from_config( trans.app, full_path_to_tool_config ) + trans.app.config.tool_data_path = work_dir + tool, valid, message = handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, full_path_to_tool_config, work_dir ) + if message: + status = 'error' else: - work_dir = tempfile.mkdtemp() tool, message = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ) + if message: + status = 'error' break if guid: tool_lineage = self.get_versions_of_tool( trans, repository, repository_metadata, guid ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for viewing tool metadata defined for tools in a repository that use the Galaxy ToolDataTableManager.
by Bitbucket 20 Sep '12

20 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3184303c1391/ changeset: 3184303c1391 user: greg date: 2012-09-20 16:58:05 summary: Fix for viewing tool metadata defined for tools in a repository that use the Galaxy ToolDataTableManager. affected #: 3 files diff -r be1f6ebb8d6bd3864e5ca08c59f8edaa4f471004 -r 3184303c13918a8b4734e46e1ac956d0e44ecba2 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1053,12 +1053,75 @@ if converter_path and display_path: break return converter_path, display_path +def get_ctx_file_path_from_manifest( filename, repo, changeset_revision ): + """Get the ctx file path for the latest revision of filename from the repository manifest up to the value of changeset_revision.""" + stripped_filename = strip_path( filename ) + for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): + manifest_changeset_revision = str( repo.changectx( changeset ) ) + manifest_ctx = repo.changectx( changeset ) + for ctx_file in manifest_ctx.files(): + ctx_file_name = strip_path( ctx_file ) + if ctx_file_name == stripped_filename: + return manifest_ctx, ctx_file + return None, None def get_ctx_rev( tool_shed_url, name, owner, changeset_revision ): url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % ( name, owner, changeset_revision ) ) response = urllib2.urlopen( url ) ctx_rev = response.read() response.close() return ctx_rev +def get_file_context_from_ctx( ctx, filename ): + # We have to be careful in determining if we found the correct file because multiple files with the same name may be in different directories + # within ctx if the files were moved within the change set. For example, in the following ctx.files() list, the former may have been moved to + # the latter: ['tmap_wrapper_0.0.19/tool_data_table_conf.xml.sample', 'tmap_wrapper_0.3.3/tool_data_table_conf.xml.sample']. Another scenario + # is that the file has been deleted. + deleted = False + filename = strip_path( filename ) + for ctx_file in ctx.files(): + ctx_file_name = strip_path( ctx_file ) + if filename == ctx_file_name: + try: + # If the file was moved, its destination will be returned here. + fctx = ctx[ ctx_file ] + return fctx + except LookupError, e: + # Set deleted for now, and continue looking in case the file was moved instead of deleted. + deleted = True + if deleted: + return 'DELETED' + return None +def get_list_of_copied_sample_files( repo, ctx, dir ): + """ + Find all sample files (files in the repository with the special .sample extension) in the reversed repository manifest up to ctx. Copy + each discovered file to dir and return the list of filenames. If a .sample file was added in a changeset and then deleted in a later + changeset, it will be returned in the deleted_sample_files list. The caller will set the value of app.config.tool_data_path to dir in + order to load the tools and generate metadata for them. + """ + deleted_sample_files = [] + sample_files = [] + for changeset in reversed_upper_bounded_changelog( repo, ctx ): + changeset_ctx = repo.changectx( changeset ) + for ctx_file in changeset_ctx.files(): + ctx_file_name = strip_path( ctx_file ) + # If we decide in the future that files deleted later in the changelog should not be used, we can use the following if statement. + # if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files and ctx_file_name not in deleted_sample_files: + if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files: + fctx = get_file_context_from_ctx( changeset_ctx, ctx_file ) + if fctx in [ 'DELETED' ]: + # Since the possibly future used if statement above is commented out, the same file that was initially added will be + # discovered in an earlier changeset in the change log and fall through to the else block below. In other words, if + # a file named blast2go.loc.sample was added in change set 0 and then deleted in changeset 3, the deleted file in changeset + # 3 will be handled here, but the later discovered file in changeset 0 will be handled in the else block below. In this + # way, the file contents will always be found for future tools even though the file was deleted. + if ctx_file_name not in deleted_sample_files: + deleted_sample_files.append( ctx_file_name ) + else: + sample_files.append( ctx_file_name ) + tmp_ctx_file_name = os.path.join( dir, ctx_file_name.replace( '.sample', '' ) ) + fh = open( tmp_ctx_file_name, 'wb' ) + fh.write( fctx.data() ) + fh.close() + return sample_files, deleted_sample_files def get_named_tmpfile_from_ctx( ctx, filename, dir ): filename = strip_path( filename ) for ctx_file in ctx.files(): @@ -1373,6 +1436,26 @@ repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid ) repository_tools_tups[ index ] = ( tup_path, guid, repository_tool ) return repository_tools_tups, sample_files_copied +def handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ): + tool = None + message = None + ctx = get_changectx_for_changeset( repo, changeset_revision ) + # We're not currently doing anything with the returned list of deleted_sample_files here. It is intended to help handle sample files that are in + # the manifest, but have been deleted from disk. + sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) + if sample_files: + trans.app.config.tool_data_path = work_dir + if 'tool_data_table_conf.xml.sample' in sample_files: + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = os.path.join( work_dir, 'tool_data_table_conf.xml' ) + error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) + if error: + # TODO: Do more here than logging an exception. + log.debug( correction_msg ) + manifest_ctx, ctx_file = get_ctx_file_path_from_manifest( tool_config_filename, repo, changeset_revision ) + if manifest_ctx and ctx_file: + tool, message = load_tool_from_tmp_config( trans, repo, manifest_ctx, ctx_file, work_dir ) + return tool, message def handle_sample_tool_data_table_conf_file( app, filename, persist=False ): """ Parse the incoming filename and add new entries to the in-memory app.tool_data_tables dictionary. If persist is True (should only occur) @@ -1492,6 +1575,31 @@ valid = False error_message = str( e ) return tool, valid, error_message +def load_tool_from_tmp_config( trans, repo, ctx, ctx_file, work_dir ): + tool = None + message = '' + tmp_tool_config = get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) + if tmp_tool_config: + element_tree = util.parse_xml( tmp_tool_config ) + element_tree_root = element_tree.getroot() + # Look for code files required by the tool config. + tmp_code_files = [] + for code_elem in element_tree_root.findall( 'code' ): + code_file_name = code_elem.get( 'file' ) + tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) + if tmp_code_file_name: + tmp_code_files.append( tmp_code_file_name ) + tool, valid, message = load_tool_from_config( trans.app, tmp_tool_config ) + for tmp_code_file in tmp_code_files: + try: + os.unlink( tmp_code_file ) + except: + pass + try: + os.unlink( tmp_tool_config ) + except: + pass + return tool, message def open_repository_files_folder( trans, folder_path ): try: files_list = get_repository_files( trans, folder_path ) diff -r be1f6ebb8d6bd3864e5ca08c59f8edaa4f471004 -r 3184303c13918a8b4734e46e1ac956d0e44ecba2 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -6,9 +6,9 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.util.hash_util import * from galaxy.util.shed_util import check_tool_input_params, clone_repository, copy_sample_file, generate_metadata_for_changeset_revision -from galaxy.util.shed_util import get_changectx_for_changeset, get_config_from_disk, get_configured_ui, get_named_tmpfile_from_ctx -from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH, load_tool_from_config, reset_tool_data_tables -from galaxy.util.shed_util import reversed_upper_bounded_changelog, strip_path +from galaxy.util.shed_util import get_changectx_for_changeset, get_config_from_disk, get_configured_ui, get_file_context_from_ctx, get_named_tmpfile_from_ctx +from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_tmp_config, handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH +from galaxy.util.shed_util import load_tool_from_config, reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -392,37 +392,6 @@ return trans.sa_session.query( trans.model.Category ) \ .filter( trans.model.Category.table.c.deleted==False ) \ .order_by( trans.model.Category.table.c.name ).all() -def get_file_context_from_ctx( ctx, filename ): - # We have to be careful in determining if we found the correct file because multiple files with the same name may be in different directories - # within ctx if the files were moved within the change set. For example, in the following ctx.files() list, the former may have been moved to - # the latter: ['tmap_wrapper_0.0.19/tool_data_table_conf.xml.sample', 'tmap_wrapper_0.3.3/tool_data_table_conf.xml.sample']. Another scenario - # is that the file has been deleted. - deleted = False - filename = strip_path( filename ) - for ctx_file in ctx.files(): - ctx_file_name = strip_path( ctx_file ) - if filename == ctx_file_name: - try: - # If the file was moved, its destination will be returned here. - fctx = ctx[ ctx_file ] - return fctx - except LookupError, e: - # Set deleted for now, and continue looking in case the file was moved instead of deleted. - deleted = True - if deleted: - return 'DELETED' - return None -def get_ctx_file_path_from_manifest( filename, repo, changeset_revision ): - """Get the ctx file path for the latest revision of filename from the repository manifest up to the value of changeset_revision.""" - stripped_filename = strip_path( filename ) - for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): - manifest_changeset_revision = str( repo.changectx( changeset ) ) - manifest_ctx = repo.changectx( changeset ) - for ctx_file in manifest_ctx.files(): - ctx_file_name = strip_path( ctx_file ) - if ctx_file_name == stripped_filename: - return manifest_ctx, ctx_file - return None, None def get_latest_repository_metadata( trans, decoded_repository_id ): """Get last metadata defined for a specified repository from the database""" return trans.sa_session.query( trans.model.RepositoryMetadata ) \ @@ -450,38 +419,6 @@ fh.close() return tmp_filename return None -def get_list_of_copied_sample_files( repo, ctx, dir ): - """ - Find all sample files (files in the repository with the special .sample extension) in the reversed repository manifest up to ctx. Copy - each discovered file to dir and return the list of filenames. If a .sample file was added in a changeset and then deleted in a later - changeset, it will be returned in the deleted_sample_files list. The caller will set the value of app.config.tool_data_path to dir in - order to load the tools and generate metadata for them. - """ - deleted_sample_files = [] - sample_files = [] - for changeset in reversed_upper_bounded_changelog( repo, ctx ): - changeset_ctx = repo.changectx( changeset ) - for ctx_file in changeset_ctx.files(): - ctx_file_name = strip_path( ctx_file ) - # If we decide in the future that files deleted later in the changelog should not be used, we can use the following if statement. - # if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files and ctx_file_name not in deleted_sample_files: - if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files: - fctx = get_file_context_from_ctx( changeset_ctx, ctx_file ) - if fctx in [ 'DELETED' ]: - # Since the possibly future used if statement above is commented out, the same file that was initially added will be - # discovered in an earlier changeset in the change log and fall through to the else block below. In other words, if - # a file named blast2go.loc.sample was added in change set 0 and then deleted in changeset 3, the deleted file in changeset - # 3 will be handled here, but the later discovered file in changeset 0 will be handled in the else block below. In this - # way, the file contents will always be found for future tools even though the file was deleted. - if ctx_file_name not in deleted_sample_files: - deleted_sample_files.append( ctx_file_name ) - else: - sample_files.append( ctx_file_name ) - tmp_ctx_file_name = os.path.join( dir, ctx_file_name.replace( '.sample', '' ) ) - fh = open( tmp_ctx_file_name, 'wb' ) - fh.write( fctx.data() ) - fh.close() - return sample_files, deleted_sample_files def get_parent_id( trans, id, old_id, version, guid, changeset_revisions ): parent_id = None # Compare from most recent to oldest. @@ -715,54 +652,15 @@ displaying_invalid_tool=True ) status = 'error' else: - # The desired version of the tool config is no longer on disk, so create a temporary work environment and copy the tool config and dependent files. - ctx = get_changectx_for_changeset( repo, changeset_revision ) - # We're not currently doing anything with the returned list of deleted_sample_files here. It is intended to help handle sample files that are in - # the manifest, but have been deleted from disk. - sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) - if sample_files: - trans.app.config.tool_data_path = work_dir - if 'tool_data_table_conf.xml.sample' in sample_files: - # Load entries into the tool_data_tables if the tool requires them. - tool_data_table_config = os.path.join( work_dir, 'tool_data_table_conf.xml' ) - error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) - manifest_ctx, ctx_file = get_ctx_file_path_from_manifest( tool_config_filename, repo, changeset_revision ) - if manifest_ctx and ctx_file: - tool, message = load_tool_from_tmp_config( trans, repo, manifest_ctx, ctx_file, work_dir ) + tool, message = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ) try: shutil.rmtree( work_dir ) except: pass - if sample_files: - trans.app.config.tool_data_path = original_tool_data_path + trans.app.config.tool_data_path = original_tool_data_path # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. reset_tool_data_tables( trans.app ) return repository, tool, message -def load_tool_from_tmp_config( trans, repo, ctx, ctx_file, work_dir ): - tool = None - message = '' - tmp_tool_config = get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) - if tmp_tool_config: - element_tree = util.parse_xml( tmp_tool_config ) - element_tree_root = element_tree.getroot() - # Look for code files required by the tool config. - tmp_code_files = [] - for code_elem in element_tree_root.findall( 'code' ): - code_file_name = code_elem.get( 'file' ) - tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) - if tmp_code_file_name: - tmp_code_files.append( tmp_code_file_name ) - tool, valid, message = load_tool_from_config( trans.app, tmp_tool_config ) - for tmp_code_file in tmp_code_files: - try: - os.unlink( tmp_code_file ) - except: - pass - try: - os.unlink( tmp_tool_config ) - except: - pass - return tool, message def new_tool_metadata_required( trans, repository, metadata_dict ): """ Compare the last saved metadata for each tool in the repository with the new metadata in metadata_dict to determine if a new repository_metadata diff -r be1f6ebb8d6bd3864e5ca08c59f8edaa4f471004 -r 3184303c13918a8b4734e46e1ac956d0e44ecba2 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -9,9 +9,10 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.util.json import from_json_string, to_json_string from galaxy.model.orm import * -from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_repository_file_contents, INITIAL_CHANGELOG_HASH -from galaxy.util.shed_util import load_tool_from_config, NOT_TOOL_CONFIGS, open_repository_files_folder, reversed_lower_upper_bounded_changelog -from galaxy.util.shed_util import reversed_upper_bounded_changelog, strip_path, to_html_escaped, update_repository, url_join +from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_repository_file_contents +from galaxy.util.shed_util import handle_sample_files_and_load_tool_from_tmp_config, INITIAL_CHANGELOG_HASH, load_tool_from_config, NOT_TOOL_CONFIGS +from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, reversed_upper_bounded_changelog, strip_path +from galaxy.util.shed_util import to_html_escaped, update_repository, url_join from galaxy.tool_shed.encoding_util import * from common import * @@ -2283,6 +2284,7 @@ tool_lineage = [] tool = None guid = None + original_tool_data_path = trans.app.config.tool_data_path revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) if repository_metadata: @@ -2293,16 +2295,18 @@ if tool_metadata_dict[ 'id' ] == tool_id: relative_path_to_tool_config = tool_metadata_dict[ 'tool_config' ] guid = tool_metadata_dict[ 'guid' ] - full_path = os.path.abspath( relative_path_to_tool_config ) - can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, full_path, changeset_revision ) + full_path_to_tool_config = os.path.abspath( relative_path_to_tool_config ) + full_path_to_dir, tool_tool_config_filename = os.path.split( full_path_to_tool_config ) + can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, full_path_to_tool_config, changeset_revision ) if can_use_disk_file: - tool, valid, message = load_tool_from_config( trans.app, full_path ) + trans.app.config.tool_data_path = full_path_to_dir + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = get_config_from_disk( 'tool_data_table_conf.xml.sample', full_path_to_dir ) + error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) + tool, valid, message = load_tool_from_config( trans.app, full_path_to_tool_config ) else: - # We're attempting to load a tool using a config that no longer exists on disk. work_dir = tempfile.mkdtemp() - manifest_ctx, ctx_file = get_ctx_file_path_from_manifest( relative_path_to_tool_config, repo, changeset_revision ) - if manifest_ctx and ctx_file: - tool, message = load_tool_from_tmp_config( trans, repo, manifest_ctx, ctx_file, work_dir ) + tool, message = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ) break if guid: tool_lineage = self.get_versions_of_tool( trans, repository, repository_metadata, guid ) @@ -2312,6 +2316,7 @@ selected_value=changeset_revision, add_id_to_name=False, downloadable_only=False ) + trans.app.config.tool_data_path = original_tool_data_path return trans.fill_template( "/webapps/community/repository/view_tool_metadata.mako", repository=repository, tool=tool, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Circster: render wiggle data as a single path rather than many small paths.
by Bitbucket 19 Sep '12

19 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/be1f6ebb8d6b/ changeset: be1f6ebb8d6b user: jgoecks date: 2012-09-20 00:31:30 summary: Circster: render wiggle data as a single path rather than many small paths. affected #: 1 file diff -r 6390e1f3a72300974c113f927b80eec98b32fe94 -r be1f6ebb8d6bd3864e5ca08c59f8edaa4f471004 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -69,15 +69,10 @@ this.options = options; }, - render: function( svg ) { - + render: function( svg ) { + // Draw background arcs for each chromosome. var genome_arcs = this.chroms_layout(), - chroms_arcs = this.genome_data_layout(); - - // -- Render. -- - - // Draw background arcs for each chromosome. - var radius_start = this.options.radius_start, + radius_start = this.options.radius_start, radius_end = this.options.radius_end, base_arc = svg.append("g").attr("id", "inner-arc"), arc_gen = d3.svg.arc() @@ -91,24 +86,13 @@ .style("fill", "#ccc") .append("title").text(function(d) { return d.data.chrom; }); - // For each chromosome, draw dataset. + // Render data. + this.render_data(svg); + var prefs = this.options.track.get('prefs'), block_color = prefs.block_color; - - _.each(chroms_arcs, function(chrom_layout) { - if (!chrom_layout) { return; } - - var group = svg.append("g"), - arc_gen = d3.svg.arc().innerRadius(radius_start), - dataset_elts = group.selectAll("path") - .data(chrom_layout).enter() - ; - //.style("stroke", block_color) - //.style("fill", block_color) - - dataset_elts.append("path").attr("d", arc_gen).style("stroke", block_color); - - }); + if (!block_color) { block_color = prefs.color; } + svg.selectAll('path.chrom-data').style('stroke', block_color).style('fill', block_color); }, /** @@ -131,12 +115,15 @@ }, /** - * Returns layouts for drawing a chromosome's data. + * Render chromosome data and attach elements to svg. */ - chrom_data_layout: function(chrom_arc, chrom_data, inner_radius, outer_radius, max) { + render_chrom_data: function(chrom_arc, chrom_data, inner_radius, outer_radius, max) { }, - genome_data_layout: function() { + /** + * Render data as elements attached to svg. + */ + render_data: function(svg) { var self = this, chrom_arcs = this.chroms_layout(), dataset = this.options.track.get('genome_wide_data'), @@ -150,7 +137,9 @@ chroms_data_layout = _.map(layout_and_data, function(chrom_info) { var chrom_arc = chrom_info[0], chrom_data = chrom_info[1]; - return self.chrom_data_layout(chrom_arc, chrom_data, r_start, r_end, dataset.get('min'), dataset.get('max')); + return self.render_chrom_data(svg, chrom_arc, chrom_data, + r_start, r_end, + dataset.get('min'), dataset.get('max')); }); return chroms_data_layout; @@ -165,7 +154,9 @@ /** * Returns layouts for drawing a chromosome's data. */ - chrom_data_layout: function(chrom_arc, chrom_data, inner_radius, outer_radius, min, max) { + render_chrom_data: function(svg, chrom_arc, chrom_data, inner_radius, outer_radius, min, max) { + // FIXME: draw as area: + /* // If no chrom data, return null. if (!chrom_data || typeof chrom_data === "string") { return null; @@ -189,6 +180,7 @@ }); return arcs; + */ } }); @@ -198,32 +190,49 @@ var CircsterBigWigTrackRenderer = CircsterTrackRenderer.extend({ /** - * Returns layouts for drawing a chromosome's data. + * Render chromosome data and attach elements to svg. */ - chrom_data_layout: function(chrom_arc, chrom_data, inner_radius, outer_radius, min, max) { + render_chrom_data: function(svg, chrom_arc, chrom_data, inner_radius, outer_radius, min, max) { var data = chrom_data.data; if (data.length === 0) { return; } - - var scale = d3.scale.linear() - .domain( [min, max] ) - .range( [inner_radius, outer_radius] ), - arc_layout = d3.layout.pie().value(function(d, i) { - // If at end of data, draw nothing. - if (i + 1 === data.length) { return 0; } - // Layout is from current position to next position. - return data[i+1][0] - data[i][0]; - }) - .startAngle(chrom_arc.startAngle) - .endAngle(chrom_arc.endAngle), - arcs = arc_layout(data); - - // Use scale to assign outer radius. - _.each(data, function(datum, index) { - arcs[index].outerRadius = scale(datum[1]); - }); - - return arcs; + // Radius scaler. + var radius = d3.scale.linear() + .domain([min, max]) + .range([inner_radius, outer_radius]); + + // Scaler for placing data points across arc. + var angle = d3.scale.linear() + .domain([0, data.length]) + .range([chrom_arc.startAngle, chrom_arc.endAngle]); + + // FIXME: + // *area is not necessary as long as 0 is used as the inner radius. + // *could provide fill as an option. + + // Use both a line and area; area creates definition and line ensures that something is + // always drawn. + var line = d3.svg.line.radial() + .interpolate("linear-closed") + .radius(function(d) { return radius(d[1]); }) + .angle(function(d, i) { return angle(i); }); + + var area = d3.svg.area.radial() + .interpolate(line.interpolate()) + .innerRadius(radius(0)) + .outerRadius(line.radius()) + .angle(line.angle()); + + // Render data. + var parent = svg.datum(data); + + parent.append("path") + .attr("class", "chrom-data") + .attr("d", area); + + parent.append("path") + .attr("class", "chrom-data") + .attr("d", line); } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix and enhance the features for resetting a repository that encounted errors during the cloning process so the Galaxy admin can make another attempt to install it.
by Bitbucket 19 Sep '12

19 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6390e1f3a723/ changeset: 6390e1f3a723 user: greg date: 2012-09-19 22:35:49 summary: Fix and enhance the features for resetting a repository that encounted errors during the cloning process so the Galaxy admin can make another attempt to install it. affected #: 11 files diff -r da9d740fce314d67b51ff4f9d80b34bd37d3fd84 -r 6390e1f3a72300974c113f927b80eec98b32fe94 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -244,57 +244,58 @@ owner=self.repository_owner, dist_to_shed=True ) update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) - clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev ) - self.handle_repository_contents( tool_shed_repository=tool_shed_repository, - repository_clone_url=repository_clone_url, - relative_install_dir=relative_install_dir, - repository_elem=repository_elem, - install_dependencies=install_dependencies ) - self.app.sa_session.refresh( tool_shed_repository ) - metadata_dict = tool_shed_repository.metadata - if 'tools' in metadata_dict: - update_tool_shed_repository_status( self.app, - tool_shed_repository, - self.app.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) - # Get the tool_versions from the tool shed for each tool in the installed change set. - url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ - ( tool_shed_url, tool_shed_repository.name, self.repository_owner, installed_changeset_revision ) - response = urllib2.urlopen( url ) - text = response.read() - response.close() - if text: - tool_version_dicts = from_json_string( text ) - handle_tool_versions( self.app, tool_version_dicts, tool_shed_repository ) - else: - # Set the tool versions since they seem to be missing for this repository in the tool shed. - # CRITICAL NOTE: These default settings may not properly handle all parent/child associations. - for tool_dict in metadata_dict[ 'tools' ]: - flush_needed = False - tool_id = tool_dict[ 'guid' ] - old_tool_id = tool_dict[ 'id' ] - tool_version = tool_dict[ 'version' ] - tool_version_using_old_id = get_tool_version( self.app, old_tool_id ) - tool_version_using_guid = get_tool_version( self.app, tool_id ) - if not tool_version_using_old_id: - tool_version_using_old_id = self.app.model.ToolVersion( tool_id=old_tool_id, - tool_shed_repository=tool_shed_repository ) - self.app.sa_session.add( tool_version_using_old_id ) - self.app.sa_session.flush() - if not tool_version_using_guid: - tool_version_using_guid = self.app.model.ToolVersion( tool_id=tool_id, - tool_shed_repository=tool_shed_repository ) - self.app.sa_session.add( tool_version_using_guid ) - self.app.sa_session.flush() - # Associate the two versions as parent / child. - tool_version_association = get_tool_version_association( self.app, - tool_version_using_old_id, - tool_version_using_guid ) - if not tool_version_association: - tool_version_association = self.app.model.ToolVersionAssociation( tool_id=tool_version_using_guid.id, - parent_id=tool_version_using_old_id.id ) - self.app.sa_session.add( tool_version_association ) - self.app.sa_session.flush() - update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.INSTALLED ) + cloned_ok, error_message = clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev ) + if cloned_ok: + self.handle_repository_contents( tool_shed_repository=tool_shed_repository, + repository_clone_url=repository_clone_url, + relative_install_dir=relative_install_dir, + repository_elem=repository_elem, + install_dependencies=install_dependencies ) + self.app.sa_session.refresh( tool_shed_repository ) + metadata_dict = tool_shed_repository.metadata + if 'tools' in metadata_dict: + update_tool_shed_repository_status( self.app, + tool_shed_repository, + self.app.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) + # Get the tool_versions from the tool shed for each tool in the installed change set. + url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( tool_shed_url, tool_shed_repository.name, self.repository_owner, installed_changeset_revision ) + response = urllib2.urlopen( url ) + text = response.read() + response.close() + if text: + tool_version_dicts = from_json_string( text ) + handle_tool_versions( self.app, tool_version_dicts, tool_shed_repository ) + else: + # Set the tool versions since they seem to be missing for this repository in the tool shed. + # CRITICAL NOTE: These default settings may not properly handle all parent/child associations. + for tool_dict in metadata_dict[ 'tools' ]: + flush_needed = False + tool_id = tool_dict[ 'guid' ] + old_tool_id = tool_dict[ 'id' ] + tool_version = tool_dict[ 'version' ] + tool_version_using_old_id = get_tool_version( self.app, old_tool_id ) + tool_version_using_guid = get_tool_version( self.app, tool_id ) + if not tool_version_using_old_id: + tool_version_using_old_id = self.app.model.ToolVersion( tool_id=old_tool_id, + tool_shed_repository=tool_shed_repository ) + self.app.sa_session.add( tool_version_using_old_id ) + self.app.sa_session.flush() + if not tool_version_using_guid: + tool_version_using_guid = self.app.model.ToolVersion( tool_id=tool_id, + tool_shed_repository=tool_shed_repository ) + self.app.sa_session.add( tool_version_using_guid ) + self.app.sa_session.flush() + # Associate the two versions as parent / child. + tool_version_association = get_tool_version_association( self.app, + tool_version_using_old_id, + tool_version_using_guid ) + if not tool_version_association: + tool_version_association = self.app.model.ToolVersionAssociation( tool_id=tool_version_using_guid.id, + parent_id=tool_version_using_old_id.id ) + self.app.sa_session.add( tool_version_association ) + self.app.sa_session.flush() + update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.INSTALLED ) @property def non_shed_tool_panel_configs( self ): # Get the non-shed related tool panel config file names from the Galaxy config - the default is tool_conf.xml. diff -r da9d740fce314d67b51ff4f9d80b34bd37d3fd84 -r 6390e1f3a72300974c113f927b80eec98b32fe94 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -380,10 +380,11 @@ pull=True, noupdate=False, rev=util.listify( str( ctx_rev ) ) ) - return True + return True, None except Exception, e: - log.debug( 'Encountered an exception while cloning the repository: %s' % e ) - return False + error_message = 'Error cloning repository: %s' % str( e ) + log.debug( error_message ) + return False, error_message def copy_sample_file( app, filename, dest_path=None ): """Copy xxx.sample to dest_path/xxx.sample and dest_path/xxx. The default value for dest_path is ~/tool-data.""" if dest_path is None: diff -r da9d740fce314d67b51ff4f9d80b34bd37d3fd84 -r 6390e1f3a72300974c113f927b80eec98b32fe94 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -63,8 +63,9 @@ columns = [ NameColumn( "Name", key="name", - link=( lambda item: iff( item.status == model.ToolShedRepository.installation_status.ERROR, \ - None, dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ) ), + link=( lambda item: iff( item.status in [ model.ToolShedRepository.installation_status.CLONING ], + None, + dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ) ), attach_popup=True ), DescriptionColumn( "Description" ), OwnerColumn( "Owner" ), @@ -90,25 +91,25 @@ [ model.ToolShedRepository.installation_status.ERROR, model.ToolShedRepository.installation_status.NEW ] ), async_compatible=False, url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='get updates' ) ), + grids.GridOperation( "Install", + allow_multiple=False, + condition=( lambda item: not item.deleted and item.status == model.ToolShedRepository.installation_status.NEW ), + async_compatible=False, + url_args=dict( controller='admin_toolshed', action='manage_repository', operation='install' ) ), grids.GridOperation( "Deactivate or uninstall", allow_multiple=False, condition=( lambda item: not item.deleted and item.status not in \ [ model.ToolShedRepository.installation_status.ERROR, model.ToolShedRepository.installation_status.NEW ] ), async_compatible=False, url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='deactivate or uninstall' ) ), - grids.GridOperation( "Uninstall", - allow_multiple=False, - condition=( lambda item: ( item.status == model.ToolShedRepository.installation_status.ERROR ) ), - async_compatible=False, - url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='uninstall' ) ), grids.GridOperation( "Reset to install", allow_multiple=False, condition=( lambda item: ( item.status == model.ToolShedRepository.installation_status.ERROR ) ), async_compatible=False, - url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='reset status to new' ) ), + url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='reset to install' ) ), grids.GridOperation( "Activate or reinstall", allow_multiple=False, - condition=( lambda item: ( item.deleted or item.uninstalled ) ), + condition=( lambda item: item.deleted ), async_compatible=False, url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='activate or reinstall' ) ) ] standard_filters = [] @@ -354,16 +355,9 @@ return self.manage_repository( trans, **kwd ) if operation == "get updates": return self.check_for_updates( trans, **kwd ) - if operation == "uninstall": - kwd[ 'deactivate_or_uninstall_repository_button' ] = 'Deactivate or Uninstall' - kwd[ 'remove_from_disk' ] = [u'true', u'true'] - return self.deactivate_or_uninstall_repository( trans, **kwd ) - if operation == "reset status to new": - repository = get_repository( trans, kwd[ 'id' ] ) - repository.status = model.ToolShedRepository.installation_status.NEW - repository.deleted = False - repository.uninstalled = True - trans.app.model.context.current.flush() + if operation == "reset to install": + kwd[ 'reset_repository' ] = True + return self.reset_to_install( trans, **kwd ) if operation == "activate or reinstall": repository = get_repository( trans, kwd[ 'id' ] ) if repository.uninstalled: @@ -386,9 +380,19 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) tool_dependency = get_tool_dependency( trans, kwd[ 'id' ] ) + in_error_state = tool_dependency.status == trans.model.ToolDependency.installation_status.ERROR + can_uninstall = tool_dependency.status in [ trans.model.ToolDependency.installation_status.ERROR, + trans.model.ToolDependency.installation_status.INSTALLED ] + if in_error_state: + message = "This tool dependency is not installed correctly (see the <b>Tool dependency installation error</b> below). " + message += "Choose <b>Uninstall this tool dependency</b> from the <b>Repository Actions</b> menu, correct problems " + message += "if necessary, and try installing the dependency again." + status = "error" return trans.fill_template( '/admin/tool_shed_repository/browse_tool_dependency.mako', repository=tool_dependency.tool_shed_repository, tool_dependency=tool_dependency, + in_error_state=in_error_state, + can_uninstall=can_uninstall, message=message, status=status ) @web.expose @@ -428,7 +432,10 @@ remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk ) tool_shed_repository = get_repository( trans, kwd[ 'id' ] ) shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) - repository_install_dir = os.path.abspath ( relative_install_dir ) if relative_install_dir is not None else None + if relative_install_dir: + repository_install_dir = os.path.abspath( relative_install_dir ) + else: + repository_install_dir = None errors = '' if params.get( 'deactivate_or_uninstall_repository_button', False ): if tool_shed_repository.includes_tools: @@ -448,12 +455,8 @@ log.debug( "Removed repository installation directory: %s" % str( repository_install_dir ) ) removed = True except Exception, e: - if repository_install_dir is not None: - removed = False - log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) ) - else: - log.debug( "Repository installation directory does not exist." ) - removed = True + log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) ) + removed = False if removed: tool_shed_repository.uninstalled = True # Remove all installed tool dependencies. @@ -636,67 +639,72 @@ description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name ) - result = clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev ) - if not result: - update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.ERROR ) - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='monitor_repository_installation', - tool_shed_repository_ids=[ trans.security.encode_id( tool_shed_repository.id ) ] ) ) - if reinstalling: - # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated. - current_changeset_revision, current_ctx_rev = get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) - if current_ctx_rev != ctx_rev: - repo = hg.repository( get_configured_ui(), path=os.path.abspath( relative_install_dir ) ) - pull_repository( repo, repository_clone_url, current_changeset_revision ) - update_repository( repo, ctx_rev=current_ctx_rev ) - self.handle_repository_contents( trans, - tool_shed_repository=tool_shed_repository, - tool_path=tool_path, - repository_clone_url=repository_clone_url, - relative_install_dir=relative_install_dir, - tool_shed=tool_shed_repository.tool_shed, - tool_section=tool_section, - shed_tool_conf=kwd.get( 'shed_tool_conf', '' ), - reinstalling=reinstalling ) - trans.sa_session.refresh( tool_shed_repository ) - metadata = tool_shed_repository.metadata - if 'tools' in metadata: - # Get the tool_versions from the tool shed for each tool in the installed change set. - update_tool_shed_repository_status( trans.app, - tool_shed_repository, - trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) - tool_shed_url = get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) - url = url_join( tool_shed_url, - '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ - ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) ) - response = urllib2.urlopen( url ) - text = response.read() - response.close() - if text: - tool_version_dicts = from_json_string( text ) - handle_tool_versions( trans.app, tool_version_dicts, tool_shed_repository ) - else: - message += "Version information for the tools included in the <b>%s</b> repository is missing. " % name - message += "Reset all of this repository's metadata in the tool shed, then set the installed tool versions " - message += "from the installed repository's <b>Repository Actions</b> menu. " - status = 'error' - if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata: - work_dir = tempfile.mkdtemp() - # Install tool dependencies. - update_tool_shed_repository_status( trans.app, - tool_shed_repository, - trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) - # Get the tool_dependencies.xml file from the repository. - tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', relative_install_dir ) - installed_tool_dependencies = handle_tool_dependencies( app=trans.app, - tool_shed_repository=tool_shed_repository, - tool_dependencies_config=tool_dependencies_config, - tool_dependencies=tool_shed_repository.tool_dependencies ) - try: - shutil.rmtree( work_dir ) - except: - pass - update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.INSTALLED ) + cloned_ok, error_message = clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev ) + if cloned_ok: + if reinstalling: + # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated. + current_changeset_revision, current_ctx_rev = get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) + if current_ctx_rev != ctx_rev: + repo = hg.repository( get_configured_ui(), path=os.path.abspath( relative_install_dir ) ) + pull_repository( repo, repository_clone_url, current_changeset_revision ) + update_repository( repo, ctx_rev=current_ctx_rev ) + self.handle_repository_contents( trans, + tool_shed_repository=tool_shed_repository, + tool_path=tool_path, + repository_clone_url=repository_clone_url, + relative_install_dir=relative_install_dir, + tool_shed=tool_shed_repository.tool_shed, + tool_section=tool_section, + shed_tool_conf=kwd.get( 'shed_tool_conf', '' ), + reinstalling=reinstalling ) + trans.sa_session.refresh( tool_shed_repository ) + metadata = tool_shed_repository.metadata + if 'tools' in metadata: + # Get the tool_versions from the tool shed for each tool in the installed change set. + update_tool_shed_repository_status( trans.app, + tool_shed_repository, + trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) + tool_shed_url = get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) + url = url_join( tool_shed_url, + '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) ) + response = urllib2.urlopen( url ) + text = response.read() + response.close() + if text: + tool_version_dicts = from_json_string( text ) + handle_tool_versions( trans.app, tool_version_dicts, tool_shed_repository ) + else: + message += "Version information for the tools included in the <b>%s</b> repository is missing. " % name + message += "Reset all of this repository's metadata in the tool shed, then set the installed tool versions " + message += "from the installed repository's <b>Repository Actions</b> menu. " + status = 'error' + if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata: + work_dir = tempfile.mkdtemp() + # Install tool dependencies. + update_tool_shed_repository_status( trans.app, + tool_shed_repository, + trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) + # Get the tool_dependencies.xml file from the repository. + tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', relative_install_dir ) + installed_tool_dependencies = handle_tool_dependencies( app=trans.app, + tool_shed_repository=tool_shed_repository, + tool_dependencies_config=tool_dependencies_config, + tool_dependencies=tool_shed_repository.tool_dependencies ) + try: + shutil.rmtree( work_dir ) + except: + pass + update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.INSTALLED ) + else: + # An error occurred while cloning the repository, so reset everything necessary to enable another attempt. + self.set_repository_attributes( trans, + tool_shed_repository, + status=trans.model.ToolShedRepository.installation_status.ERROR, + error_message=error_message, + deleted=False, + uninstalled=False, + remove_from_disk=True ) tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', @@ -776,17 +784,39 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository_id = kwd[ 'id' ] + operation = kwd.get( 'operation', None ) repository = get_repository( trans, repository_id ) - if repository.status in [ trans.model.ToolShedRepository.installation_status.NEW, - trans.model.ToolShedRepository.installation_status.CLONING, - trans.model.ToolShedRepository.installation_status.ERROR ]: + in_error_state = repository.status == trans.model.ToolShedRepository.installation_status.ERROR + can_install = repository.status == trans.model.ToolShedRepository.installation_status.NEW + if repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING ]: return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', **kwd ) ) + if can_install and operation == 'install': + # Send a request to the tool shed to install the repository. + tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) + url = url_join( tool_shed_url, + 'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s&webapp=galaxy' % \ + ( repository.name, + repository.owner, + repository.installed_changeset_revision, + ( url_for( '/', qualified=True ) ) ) ) + return trans.response.send_redirect( url ) description = util.restore_text( params.get( 'description', repository.description ) ) shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) - repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) - if params.get( 'edit_repository_button', False ): + if relative_install_dir: + repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) + else: + repo_files_dir = None + if in_error_state: + message = "This repository is not installed correctly (see the <b>Repository installation error</b> below). Choose " + message += "<b>Reset to install</b> from the <b>Repository Actions</b> menu, correct problems if necessary, and try " + message += "installing the repository again." + status = "error" + elif can_install: + message = "This repository is not installed. You can install it by choosing <b>Install</b> from the <b>Repository Actions</b> menu." + status = "error" + elif params.get( 'edit_repository_button', False ): if description != repository.description: repository.description = description trans.sa_session.add( repository ) @@ -809,6 +839,8 @@ message = "Repository metadata has been reset." return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', repository=repository, + in_error_state=in_error_state, + can_install=can_install, description=description, repo_files_dir=repo_files_dir, message=message, @@ -890,7 +922,7 @@ url_args=dict( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( tool_shed_repository.id ) ) ), - grids.GridAction( label='Get updates', + grids.GridAction( label='Get repository updates', url_args=dict( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( tool_shed_repository.id ) ) ), @@ -1390,6 +1422,41 @@ status=status ) @web.expose @web.require_admin + def reset_to_install( self, trans, **kwd ): + # An error occurred while cloning the repository, so reset everything necessary to enable another attempt. + repository = get_repository( trans, kwd[ 'id' ] ) + if kwd.get( 'reset_repository', False ): + self.set_repository_attributes( trans, + repository, + status=trans.model.ToolShedRepository.installation_status.NEW, + error_message=None, + deleted=False, + uninstalled=False, + remove_from_disk=True ) + new_kwd = {} + new_kwd[ 'message' ] = "You can now attempt to install the repository named <b>%s</b> again." % repository.name + new_kwd[ 'status' ] = "done" + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='browse_repositories', + **new_kwd ) ) + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='manage_repository', + **kwd ) ) + def set_repository_attributes( self, trans, repository, status, error_message, deleted, uninstalled, remove_from_disk=False ): + if remove_from_disk: + relative_install_dir = repository.repo_path( trans.app ) + if relative_install_dir: + clone_dir = os.path.abspath( relative_install_dir ) + shutil.rmtree( clone_dir ) + log.debug( "Removed repository installation directory: %s" % str( clone_dir ) ) + repository.error_message = error_message + repository.status = status + repository.deleted = deleted + repository.uninstalled = uninstalled + trans.sa_session.add( repository ) + trans.sa_session.flush() + @web.expose + @web.require_admin def set_tool_versions( self, trans, **kwd ): # Get the tool_versions from the tool shed for each tool in the installed change set. repository = get_repository( trans, kwd[ 'id' ] ) diff -r da9d740fce314d67b51ff4f9d80b34bd37d3fd84 -r 6390e1f3a72300974c113f927b80eec98b32fe94 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -875,59 +875,60 @@ current_changeset_revision = str( repo.changectx( changeset ) ) ctx = repo.changectx( changeset ) log.debug( "Cloning repository revision: %s", str( ctx.rev() ) ) - clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) ) - log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) - current_metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, - repository_clone_url=repository_clone_url, - relative_install_dir=repo_dir, - repository_files_dir=work_dir, - resetting_all_metadata_on_repository=True, - webapp='community' ) - if current_metadata_dict: - if not metadata_changeset_revision and not metadata_dict: - # We're at the first change set in the change log. - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict - if ancestor_changeset_revision: - # Compare metadata from ancestor and current. The value of comparison will be one of: - # 'no metadata' - no metadata for either ancestor or current, so continue from current - # 'equal' - ancestor metadata is equivalent to current metadata, so continue from current - # 'subset' - ancestor metadata is a subset of current metadata, so continue from current - # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current metadata, so persist ancestor metadata. - comparison = compare_changeset_revisions( ancestor_changeset_revision, - ancestor_metadata_dict, - current_changeset_revision, - current_metadata_dict ) - if comparison in [ 'no metadata', 'equal', 'subset' ]: + cloned_ok, error_message = clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) ) + if cloned_ok: + log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) + current_metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, + repository_clone_url=repository_clone_url, + relative_install_dir=repo_dir, + repository_files_dir=work_dir, + resetting_all_metadata_on_repository=True, + webapp='community' ) + if current_metadata_dict: + if not metadata_changeset_revision and not metadata_dict: + # We're at the first change set in the change log. + metadata_changeset_revision = current_changeset_revision + metadata_dict = current_metadata_dict + if ancestor_changeset_revision: + # Compare metadata from ancestor and current. The value of comparison will be one of: + # 'no metadata' - no metadata for either ancestor or current, so continue from current + # 'equal' - ancestor metadata is equivalent to current metadata, so continue from current + # 'subset' - ancestor metadata is a subset of current metadata, so continue from current + # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current metadata, so persist ancestor metadata. + comparison = compare_changeset_revisions( ancestor_changeset_revision, + ancestor_metadata_dict, + current_changeset_revision, + current_metadata_dict ) + if comparison in [ 'no metadata', 'equal', 'subset' ]: + ancestor_changeset_revision = current_changeset_revision + ancestor_metadata_dict = current_metadata_dict + elif comparison == 'not equal and not subset': + metadata_changeset_revision = ancestor_changeset_revision + metadata_dict = ancestor_metadata_dict + repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + changeset_revisions.append( metadata_changeset_revision ) + ancestor_changeset_revision = current_changeset_revision + ancestor_metadata_dict = current_metadata_dict + else: + # We're at the beginning of the change log. ancestor_changeset_revision = current_changeset_revision ancestor_metadata_dict = current_metadata_dict - elif comparison == 'not equal and not subset': - metadata_changeset_revision = ancestor_changeset_revision - metadata_dict = ancestor_metadata_dict + if not ctx.children(): + metadata_changeset_revision = current_changeset_revision + metadata_dict = current_metadata_dict + # We're at the end of the change log. repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict - else: - # We're at the beginning of the change log. - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict - if not ctx.children(): - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict - # We're at the end of the change log. - repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) - changeset_revisions.append( metadata_changeset_revision ) - ancestor_changeset_revision = None - ancestor_metadata_dict = None - elif ancestor_metadata_dict: - # We reach here only if current_metadata_dict is empty and ancestor_metadata_dict is not. - if not ctx.children(): - # We're at the end of the change log. - repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) - changeset_revisions.append( metadata_changeset_revision ) - ancestor_changeset_revision = None - ancestor_metadata_dict = None + ancestor_changeset_revision = None + ancestor_metadata_dict = None + elif ancestor_metadata_dict: + # We reach here only if current_metadata_dict is empty and ancestor_metadata_dict is not. + if not ctx.children(): + # We're at the end of the change log. + repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + changeset_revisions.append( metadata_changeset_revision ) + ancestor_changeset_revision = None + ancestor_metadata_dict = None if os.path.exists( work_dir ): try: shutil.rmtree( work_dir ) diff -r da9d740fce314d67b51ff4f9d80b34bd37d3fd84 -r 6390e1f3a72300974c113f927b80eec98b32fe94 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1020,10 +1020,11 @@ repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) encoded_repository_ids.append( trans.security.encode_id( repository_metadata.repository.id ) ) changeset_revisions.append( repository_metadata.changeset_revision ) + new_kwd[ 'repository_ids' ] = encoded_repository_ids + new_kwd[ 'changeset_revisions' ] = changeset_revisions return trans.response.send_redirect( web.url_for( controller='repository', action='install_repositories_by_revision', - repository_ids=encoded_repository_ids, - changeset_revisions=changeset_revisions ) ) + **new_kwd ) ) else: # This can only occur when there is a multi-select grid with check boxes and an operation, # and the user clicked the operation button without checking any of the check boxes. @@ -1106,10 +1107,12 @@ repository_metadata = get_repository_metadata_by_id( trans, item_id ) encoded_repository_ids.append( trans.security.encode_id( repository_metadata.repository.id ) ) changeset_revisions.append( repository_metadata.changeset_revision ) + new_kwd = {} + new_kwd[ 'repository_ids' ] = encoded_repository_ids + new_kwd[ 'changeset_revisions' ] = changeset_revisions return trans.response.send_redirect( web.url_for( controller='repository', action='install_repositories_by_revision', - repository_ids=encoded_repository_ids, - changeset_revisions=changeset_revisions ) ) + **new_kwd ) ) else: # This can only occur when there is a multi-select grid with check boxes and an operation, # and the user clicked the operation button without checking any of the check boxes. @@ -1188,7 +1191,7 @@ repo_info_dicts = [] for tup in zip( util.listify( repository_ids ), util.listify( changeset_revisions ) ): repository_id, changeset_revision = tup - repository_clone_url = generate_clone_url( trans, repository_id ) + repository_clone_url = generate_clone_url( trans, repository_id ) repository = get_repository( trans, repository_id ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) metadata = repository_metadata.metadata @@ -1414,9 +1417,22 @@ message=message, status=status ) @web.expose - def install_repositories_by_revision( self, trans, repository_ids, changeset_revisions, **kwd ): - """Send the list of repository_ids and changeset_revisions to Galaxy so it can begin the installation process.""" - galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) + def install_repositories_by_revision( self, trans, **kwd ): + """ + Send the list of repository_ids and changeset_revisions to Galaxy so it can begin the installation process. If the value of + repository_ids is not received, then the name and owner of a single repository must be received to install a single repository. + """ + repository_ids = kwd.get( 'repository_ids', None ) + changeset_revisions = kwd.get( 'changeset_revisions', None ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + galaxy_url = kwd.get( 'galaxy_url', None ) + if not repository_ids: + repository = get_repository_by_name_and_owner( trans, name, owner ) + repository_ids = trans.security.encode_id( repository.id ) + if not galaxy_url: + # If galaxy_url is not in the request, it had to have been stored in a cookie by the tool shed. + galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) # Redirect back to local Galaxy to perform install. url = url_join( galaxy_url, 'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \ diff -r da9d740fce314d67b51ff4f9d80b34bd37d3fd84 -r 6390e1f3a72300974c113f927b80eec98b32fe94 templates/admin/tool_shed_repository/browse_repository.mako --- a/templates/admin/tool_shed_repository/browse_repository.mako +++ b/templates/admin/tool_shed_repository/browse_repository.mako @@ -18,7 +18,7 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a> - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get repository updates</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or uninstall repository</a> %if repository.tool_dependencies: <% tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in repository.tool_dependencies ] %> diff -r da9d740fce314d67b51ff4f9d80b34bd37d3fd84 -r 6390e1f3a72300974c113f927b80eec98b32fe94 templates/admin/tool_shed_repository/browse_tool_dependency.mako --- a/templates/admin/tool_shed_repository/browse_tool_dependency.mako +++ b/templates/admin/tool_shed_repository/browse_tool_dependency.mako @@ -21,9 +21,12 @@ <div popupmenu="tool_dependency-${tool_dependency.id}-popup"><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a> - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get repository updates</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or uninstall repository</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', tool_dependency_ids=tool_dependency_ids )}">Manage tool dependencies</a> + %if can_uninstall: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='uninstall_tool_dependencies', tool_dependency_ids=trans.security.encode_id( tool_dependency.id ) )}">Uninstall this tool dependency</a> + %endif </div></ul> @@ -45,6 +48,18 @@ <div style="clear: both"></div></div><div class="form-row" > + <label>Tool dependency status:</label> + ${tool_dependency.status} + <div style="clear: both"></div> + </div> + %if in_error_state: + <div class="form-row" > + <label>Tool dependency installation error:</label> + ${tool_dependency.error_message} + <div style="clear: both"></div> + </div> + %endif + <div class="form-row" ><label>Tool dependency installation directory:</label> ${tool_dependency.installation_directory( trans.app )} <div style="clear: both"></div> diff -r da9d740fce314d67b51ff4f9d80b34bd37d3fd84 -r 6390e1f3a72300974c113f927b80eec98b32fe94 templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako --- a/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako +++ b/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako @@ -8,7 +8,7 @@ <div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a> - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get repository updates</a> %if repository.tool_dependencies: <% tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in repository.tool_dependencies ] %><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', tool_dependency_ids=tool_dependency_ids )}">Manage tool dependencies</a> diff -r da9d740fce314d67b51ff4f9d80b34bd37d3fd84 -r 6390e1f3a72300974c113f927b80eec98b32fe94 templates/admin/tool_shed_repository/manage_repository.mako --- a/templates/admin/tool_shed_repository/manage_repository.mako +++ b/templates/admin/tool_shed_repository/manage_repository.mako @@ -6,16 +6,22 @@ <ul class="manage-table-actions"><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a> - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> - %if repository.includes_tools: - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='set_tool_versions', id=trans.security.encode_id( repository.id ) )}">Set tool versions</a> + %if in_error_state: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='reset_to_install', id=trans.security.encode_id( repository.id ), reset_repository=True )}">Reset to install</a> + %elif can_install: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ), operation='install' )}">Install</a> + %else: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get repository updates</a> + %if repository.includes_tools: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='set_tool_versions', id=trans.security.encode_id( repository.id ) )}">Set tool versions</a> + %endif + %if repository.tool_dependencies: + <% tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in repository.tool_dependencies ] %> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', tool_dependency_ids=tool_dependency_ids )}">Manage tool dependencies</a> + %endif + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or uninstall repository</a> %endif - %if repository.tool_dependencies: - <% tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in repository.tool_dependencies ] %> - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', tool_dependency_ids=tool_dependency_ids )}">Manage tool dependencies</a> - %endif - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or uninstall repository</a></div></ul> @@ -39,7 +45,11 @@ </div><div class="form-row"><label>Description:</label> - <input name="description" type="textfield" value="${description}" size="80"/> + %if in_error_state: + ${description} + %else: + <input name="description" type="textfield" value="${description}" size="80"/> + %endif <div style="clear: both"></div></div><div class="form-row"> @@ -50,17 +60,26 @@ <label>Owner:</label> ${repository.owner} </div> - <div class="form-row"> - <label>Location:</label> - ${repo_files_dir} - </div> + %if in_error_state: + <div class="form-row"> + <label>Repository installation error:</label> + ${repository.error_message} + </div> + %else: + <div class="form-row"> + <label>Location:</label> + ${repo_files_dir} + </div> + %endif <div class="form-row"><label>Deleted:</label> ${repository.deleted} </div> - <div class="form-row"> - <input type="submit" name="edit_repository_button" value="Save"/> - </div> + %if not in_error_state: + <div class="form-row"> + <input type="submit" name="edit_repository_button" value="Save"/> + </div> + %endif </form></div></div> diff -r da9d740fce314d67b51ff4f9d80b34bd37d3fd84 -r 6390e1f3a72300974c113f927b80eec98b32fe94 templates/admin/tool_shed_repository/manage_tool_dependencies.mako --- a/templates/admin/tool_shed_repository/manage_tool_dependencies.mako +++ b/templates/admin/tool_shed_repository/manage_tool_dependencies.mako @@ -9,7 +9,7 @@ <div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a> - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get repository updates</a> %if repository.includes_tools: <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='set_tool_versions', id=trans.security.encode_id( repository.id ) )}">Set tool versions</a> %endif diff -r da9d740fce314d67b51ff4f9d80b34bd37d3fd84 -r 6390e1f3a72300974c113f927b80eec98b32fe94 templates/admin/tool_shed_repository/view_tool_metadata.mako --- a/templates/admin/tool_shed_repository/view_tool_metadata.mako +++ b/templates/admin/tool_shed_repository/view_tool_metadata.mako @@ -7,7 +7,7 @@ <div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a> - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get repository updates</a> %if repository.tool_dependencies: <% tool_dependency_ids = [ trans.security.encode_id( td.id ) for td in repository.tool_dependencies ] %><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', tool_dependency_ids=tool_dependency_ids )}">Manage tool dependencies</a> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Revert previous change to message.mako for now -- we do use html in the message box elsewhere (links, etc) and this breaks them.
by Bitbucket 19 Sep '12

19 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/da9d740fce31/ changeset: da9d740fce31 user: dannon date: 2012-09-19 19:20:45 summary: Revert previous change to message.mako for now -- we do use html in the message box elsewhere (links, etc) and this breaks them. affected #: 1 file diff -r 96871214fe2f962004decde001de94d1ba827e94 -r da9d740fce314d67b51ff4f9d80b34bd37d3fd84 templates/message.mako --- a/templates/message.mako +++ b/templates/message.mako @@ -82,12 +82,12 @@ ## Render large message. <%def name="render_large_message( message, status )"> - <div class="${status}messagelarge" style="margin: 1em">${_(message) | h}</div> + <div class="${status}messagelarge" style="margin: 1em">${_(message)}</div></%def> ## Render a message <%def name="render_msg( msg, status='done' )"> - <div class="${status}message">${_(msg) | h}</div> + <div class="${status}message">${_(msg)}</div><br/></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Prevent reflective XSS through message display.
by Bitbucket 19 Sep '12

19 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/96871214fe2f/ changeset: 96871214fe2f user: dannon date: 2012-09-19 16:32:19 summary: Prevent reflective XSS through message display. affected #: 1 file diff -r 70b60fd07d6a0ab6889c79a9518fd894e13f9c8d -r 96871214fe2f962004decde001de94d1ba827e94 templates/message.mako --- a/templates/message.mako +++ b/templates/message.mako @@ -82,12 +82,12 @@ ## Render large message. <%def name="render_large_message( message, status )"> - <div class="${status}messagelarge" style="margin: 1em">${_(message)}</div> + <div class="${status}messagelarge" style="margin: 1em">${_(message) | h}</div></%def> ## Render a message <%def name="render_msg( msg, status='done' )"> - <div class="${status}message">${_(msg)}</div> + <div class="${status}message">${_(msg) | h}</div><br/></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Cloud Launch - Fix for rare instance udpate() that happens when (rarely) Amazon doesn't have the instance fully registered before update() is called.
by Bitbucket 19 Sep '12

19 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/70b60fd07d6a/ changeset: 70b60fd07d6a user: dannon date: 2012-09-19 06:10:47 summary: Cloud Launch - Fix for rare instance udpate() that happens when (rarely) Amazon doesn't have the instance fully registered before update() is called. affected #: 1 file diff -r 572f0d4ed0ae934e1b2975a6a2940589fc593204 -r 70b60fd07d6a0ab6889c79a9518fd894e13f9c8d lib/galaxy/web/controllers/cloudlaunch.py --- a/lib/galaxy/web/controllers/cloudlaunch.py +++ b/lib/galaxy/web/controllers/cloudlaunch.py @@ -22,7 +22,6 @@ from boto.exception import EC2ResponseError from boto.s3.connection import OrdinaryCallingFormat, S3Connection - log = logging.getLogger(__name__) PKEY_PREFIX = 'gxy_pkey' @@ -98,7 +97,12 @@ while not instance.public_dns_name: # Can take a second to have public dns name registered. # DBTODO, push this into a page update, this is not ideal. - instance.update() + try: + instance.update() + except EC2ResponseError: + #This can happen when update is invoked before the instance is fully registered. Prevent + #failure, wait it out. + pass ct +=1 time.sleep(1) if kp_material: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix bug in setting dbkey for new track browser.
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/572f0d4ed0ae/ changeset: 572f0d4ed0ae user: jgoecks date: 2012-09-19 04:33:49 summary: Fix bug in setting dbkey for new track browser. affected #: 1 file diff -r 8153e8d25009d71a523e0f2df24ed12922825d8f -r 572f0d4ed0ae934e1b2975a6a2940589fc593204 lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -696,11 +696,11 @@ Display browser for the visualization denoted by id and add the datasets listed in `dataset_ids`. """ - # Display new browser if no id provided. + # Set up new browser if no id provided. if not id: return trans.fill_template( "tracks/browser.mako", config={}, add_dataset=kwargs.get("dataset_id", None), - default_dbkey=kwargs.get("default_dbkey", None) ) + default_dbkey=kwargs.get("dbkey", None) ) # Display saved visualization. vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Fix create_all_fasta_loc to work when inspect_dir is not set.
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8153e8d25009/ changeset: 8153e8d25009 user: dannon date: 2012-09-19 02:49:29 summary: Fix create_all_fasta_loc to work when inspect_dir is not set. affected #: 1 file diff -r 05a1728683032985f7feccc007b25c083d263c9b -r 8153e8d25009d71a523e0f2df24ed12922825d8f scripts/loc_files/create_all_fasta_loc.py --- a/scripts/loc_files/create_all_fasta_loc.py +++ b/scripts/loc_files/create_all_fasta_loc.py @@ -195,7 +195,7 @@ if options.inspect_dir: paths_to_look_in = [ os.path.join( options.genome_dir, '%s', id ) for id in options.inspect_dir.split( ',' ) ] else: - paths_to_look_in = os.path.join( options.genome_dir, '%s' ) + paths_to_look_in = [os.path.join( options.genome_dir, '%s' )] # say what we're looking in print '\nLooking in:\n\t%s' % '\n\t'.join( [ p % '<build_name>' for p in paths_to_look_in ] ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Tophat2 wrapper fixes. Thanks to Jim Johnson and Lance Parsons.
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/05a172868303/ changeset: 05a172868303 user: jgoecks date: 2012-09-18 23:11:18 summary: Tophat2 wrapper fixes. Thanks to Jim Johnson and Lance Parsons. affected #: 1 file diff -r 0cf3b64e80777c45425a57f4f69d806df839fcf4 -r 05a1728683032985f7feccc007b25c083d263c9b tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -3,6 +3,8 @@ <description>Gapped-read mapper for RNA-seq data</description><version_command>tophat2 --version</version_command><requirements> + <requirement type="package">samtools</requirement> + <requirement type="package">bowtie2</requirement><requirement type="package">tophat2</requirement></requirements><command interpreter="python"> @@ -297,7 +299,7 @@ <outputs><data format="tabular" name="fusions" label="${tool.name} on ${on_string}: fusions" from_work_dir="tophat_out/fusions.out"> - <filter>(params['fusion_search']['do_search'] == 'Yes')</filter> + <filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter></data><data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed"><actions> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Wrap Sweepster in a requireJS module and add needed module qualifications. Pack scripts.
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0cf3b64e8077/ changeset: 0cf3b64e8077 user: jgoecks date: 2012-09-18 22:50:45 summary: Wrap Sweepster in a requireJS module and add needed module qualifications. Pack scripts. affected #: 9 files diff -r 3f12146d6d81e08f662ada2011a6973e4230512d -r 0cf3b64e80777c45425a57f4f69d806df839fcf4 static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -5,6 +5,40 @@ * changes; this is advantageous because multiple views can use the same object * 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() { + $.ajax(ajax_settings).success(function(result) { + if (success_fn(result)) { + // Result is good, so resolve. + deferred.resolve(result); + } + else { + // Result not good, try again. + setTimeout(_go, interval); + } + }); + }; + _go(); + return deferred; + } +}); /** * Simple base model for any visible element. Includes useful attributes and ability diff -r 3f12146d6d81e08f662ada2011a6973e4230512d -r 0cf3b64e80777c45425a57f4f69d806df839fcf4 static/scripts/packed/mvc/tools.js --- a/static/scripts/packed/mvc/tools.js +++ b/static/scripts/packed/mvc/tools.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,inputs:[]},relations:[{type:Backbone.HasMany,key:"inputs",relatedModel:"ToolInput",reverseRelation:{key:"tool",includeInJSON:false}}],urlRoot:galaxy_paths.get("tool_url"),copy:function(b){var c=new Tool(this.toJSON());if(b){var a=new Backbone.Collection();c.get("inputs").each(function(d){if(d.get_samples()){a.push(d)}});c.set("inputs",a)}return c},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(a,b){this.get("inputs").find(function(c){return c.get("name")===a}).set("value",b)},set_input_values:function(b){var a=this;_.each(_.keys(b),function(c){a.set_input_value(c,b[c])})},run:function(){return this._run()},rerun:function(b,a){return this._run({action:"rerun",target_dataset_id:b.id,regions:a})},get_inputs_dict:function(){var a={};this.get("inputs").each(function(b){a[b.get("name")]=b.get("value")});return a},_run:function(c){var d=_.extend({tool_id:this.id,inputs:this.get_inputs_dict()},c);var b=$.Deferred(),a=new ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(d),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(e){return e!=="pending"}});$.when(a.go()).then(function(e){b.resolve(new DatasetCollection().reset(e))});return b}});var ToolInput=Backbone.RelationalModel.extend({defaults:{name:null,label:null,type:null,value:null,num_samples:5},initialize:function(){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new ToolInput(this.toJSON())},get_samples:function(){var b=this.get("type"),a=null;if(b==="number"){a=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(b==="select"){a=_.map(this.get("options"),function(c){return c[0]})}}return a}});var ToolCollection=Backbone.Collection.extend({model:Tool});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<this.attributes.min_chars_for_search){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",tools:new ToolCollection(),parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this);this.on("reset",this.populate_tools,this)},populate_tools:function(){var a=this;a.tools=new ToolCollection();this.each(function(b){if(b instanceof ToolPanelSection){_.each(b.attributes.elems,function(c){if(c instanceof Tool){a.tools.push(c)}})}else{if(b instanceof Tool){a.tools.push(b)}}})},clear_search_results:function(){this.each(function(a){if(a instanceof ToolPanelSection){a.clear_search_results()}else{a.show()}})},apply_search_results:function(){var b=this.tool_search.attributes.results;if(b===null){this.clear_search_results();return}var a=null;this.each(function(c){if(c instanceof ToolPanelLabel){a=c;a.hide()}else{if(c instanceof Tool){if(c.apply_search_results(b)){if(a){a.show()}}}else{a=null;c.apply_search_results(b)}}})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.name));return this}});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(a){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===a.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var a=this;var b=new ToolSearchView({model:this.collection.tool_search});b.render();a.$el.append(b.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();a.$el.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();a.$el.append(e.$el)}else{if(d instanceof ToolPanelLabel){var f=new ToolPanelLabelView({model:d});f.render();a.$el.append(f.$el)}}}});a.$el.find("a.tool-link").click(function(f){var d=$(this).attr("class").split(/\s+/)[0],c=a.collection.tools.get(d);a.trigger("tool_link_click",f,c)});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var ToolFormView=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var IntegratedToolMenuAndView=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new ToolPanelView({collection:this.collection});this.tool_form_view=new ToolFormView()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var a=this;this.tool_panel_view.on("tool_link_click",function(c,b){c.preventDefault();a.show_tool(b)})},show_tool:function(b){var a=this;b.fetch().done(function(){a.tool_form_view.model=b;a.tool_form_view.render();a.tool_form_view.$el.show();$("#left").width("650px")})}}); \ No newline at end of file +var ServerStateDeferred=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(a){return true}},go:function(){var d=$.Deferred(),c=this,f=c.get("ajax_settings"),e=c.get("success_fn"),b=c.get("interval"),a=function(){$.ajax(f).success(function(g){if(e(g)){d.resolve(g)}else{setTimeout(a,b)}})};a();return d}});var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var Tool=BaseModel.extend({defaults:{description:null,target:null,inputs:[]},relations:[{type:Backbone.HasMany,key:"inputs",relatedModel:"ToolInput",reverseRelation:{key:"tool",includeInJSON:false}}],urlRoot:galaxy_paths.get("tool_url"),copy:function(b){var c=new Tool(this.toJSON());if(b){var a=new Backbone.Collection();c.get("inputs").each(function(d){if(d.get_samples()){a.push(d)}});c.set("inputs",a)}return c},apply_search_results:function(a){(_.indexOf(a,this.attributes.id)!==-1?this.show():this.hide());return this.is_visible()},set_input_value:function(a,b){this.get("inputs").find(function(c){return c.get("name")===a}).set("value",b)},set_input_values:function(b){var a=this;_.each(_.keys(b),function(c){a.set_input_value(c,b[c])})},run:function(){return this._run()},rerun:function(b,a){return this._run({action:"rerun",target_dataset_id:b.id,regions:a})},get_inputs_dict:function(){var a={};this.get("inputs").each(function(b){a[b.get("name")]=b.get("value")});return a},_run:function(c){var d=_.extend({tool_id:this.id,inputs:this.get_inputs_dict()},c);var b=$.Deferred(),a=new ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(d),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(e){return e!=="pending"}});$.when(a.go()).then(function(e){b.resolve(new DatasetCollection().reset(e))});return b}});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())},get_samples:function(){var b=this.get("type"),a=null;if(b==="number"){a=d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}else{if(b==="select"){a=_.map(this.get("options"),function(c){return c[0]})}}return a}});var ToolCollection=Backbone.Collection.extend({model:Tool});var ToolPanelLabel=BaseModel.extend({});var ToolPanelSection=BaseModel.extend({defaults:{elems:[],open:false},clear_search_results:function(){_.each(this.attributes.elems,function(a){a.show()});this.show();this.set("open",false)},apply_search_results:function(b){var c=true,a;_.each(this.attributes.elems,function(d){if(d instanceof ToolPanelLabel){a=d;a.hide()}else{if(d instanceof Tool){if(d.apply_search_results(b)){c=false;if(a){a.show()}}}}});if(c){this.hide()}else{this.show();this.set("open",true)}}});var ToolSearch=BaseModel.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:true,query:"",results:null,clear_key:27},initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var c=this.attributes.query;if(c.length<this.attributes.min_chars_for_search){this.set("results",null);return}var b=c+"*";if(this.timer){clearTimeout(this.timer)}$("#search-clear-btn").hide();$("#search-spinner").show();var a=this;this.timer=setTimeout(function(){$.get(a.attributes.search_url,{query:b},function(d){a.set("results",d);$("#search-spinner").hide();$("#search-clear-btn").show()},"json")},200)},clear_search:function(){this.set("query","");this.set("results",null)}});var ToolPanel=Backbone.Collection.extend({url:"/tools",tools:new ToolCollection(),parse:function(a){var b=function(e){var d=e.type;if(d==="tool"){return new Tool(e)}else{if(d==="section"){var c=_.map(e.elems,b);e.elems=c;return new ToolPanelSection(e)}else{if(d==="label"){return new ToolPanelLabel(e)}}}};return _.map(a,b)},initialize:function(a){this.tool_search=a.tool_search;this.tool_search.on("change:results",this.apply_search_results,this);this.on("reset",this.populate_tools,this)},populate_tools:function(){var a=this;a.tools=new ToolCollection();this.each(function(b){if(b instanceof ToolPanelSection){_.each(b.attributes.elems,function(c){if(c instanceof Tool){a.tools.push(c)}})}else{if(b instanceof Tool){a.tools.push(b)}}})},clear_search_results:function(){this.each(function(a){if(a instanceof ToolPanelSection){a.clear_search_results()}else{a.show()}})},apply_search_results:function(){var b=this.tool_search.attributes.results;if(b===null){this.clear_search_results();return}var a=null;this.each(function(c){if(c instanceof ToolPanelLabel){a=c;a.hide()}else{if(c instanceof Tool){if(c.apply_search_results(b)){if(a){a.show()}}}else{a=null;c.apply_search_results(b)}}})}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){(this.model.attributes.hidden?this.$el.hide():this.$el.show())}});var ToolLinkView=BaseView.extend({tagName:"div",template:Handlebars.templates.tool_link,render:function(){this.$el.append(this.template(this.model.toJSON()));return this}});var ToolPanelLabelView=BaseView.extend({tagName:"div",className:"toolPanelLabel",render:function(){this.$el.append($("<span/>").text(this.model.attributes.name));return this}});var ToolPanelSectionView=BaseView.extend({tagName:"div",className:"toolSectionWrapper",template:Handlebars.templates.panel_section,initialize:function(){BaseView.prototype.initialize.call(this);this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(this.template(this.model.toJSON()));var a=this.$el.find(".toolSectionBody");_.each(this.model.attributes.elems,function(b){if(b instanceof Tool){var c=new ToolLinkView({model:b,className:"toolTitle"});c.render();a.append(c.$el)}else{if(b instanceof ToolPanelLabel){var d=new ToolPanelLabelView({model:b});d.render();a.append(d.$el)}else{}}});return this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){(this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast"))}});var ToolSearchView=Backbone.View.extend({tagName:"div",id:"tool-search",className:"bar",template:Handlebars.templates.tool_search,events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){this.$el.append(this.template(this.model.toJSON()));if(!this.model.is_visible()){this.$el.hide()}return this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){this.model.clear_search();this.$el.find(":input").val(this.model.attributes.search_hint_string);this.focus_and_select();return false},query_changed:function(a){if((this.model.attributes.clear_key)&&(this.model.attributes.clear_key===a.which)){this.clear();return false}this.model.set("query",this.$el.find(":input").val())}});var ToolPanelView=Backbone.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.collection.tool_search.on("change:results",this.handle_search_results,this)},render:function(){var a=this;var b=new ToolSearchView({model:this.collection.tool_search});b.render();a.$el.append(b.$el);this.collection.each(function(d){if(d instanceof ToolPanelSection){var c=new ToolPanelSectionView({model:d});c.render();a.$el.append(c.$el)}else{if(d instanceof Tool){var e=new ToolLinkView({model:d,className:"toolTitleNoSection"});e.render();a.$el.append(e.$el)}else{if(d instanceof ToolPanelLabel){var f=new ToolPanelLabelView({model:d});f.render();a.$el.append(f.$el)}}}});a.$el.find("a.tool-link").click(function(f){var d=$(this).attr("class").split(/\s+/)[0],c=a.collection.tools.get(d);a.trigger("tool_link_click",f,c)});return this},handle_search_results:function(){var a=this.collection.tool_search.attributes.results;if(a&&a.length===0){$("#search-no-results").show()}else{$("#search-no-results").hide()}}});var ToolFormView=Backbone.View.extend({className:"toolForm",template:Handlebars.templates.tool_form,render:function(){this.$el.children().remove();this.$el.append(this.template(this.model.toJSON()))}});var IntegratedToolMenuAndView=Backbone.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new ToolPanelView({collection:this.collection});this.tool_form_view=new ToolFormView()},render:function(){this.tool_panel_view.render();this.tool_panel_view.$el.css("float","left");this.$el.append(this.tool_panel_view.$el);this.tool_form_view.$el.hide();this.$el.append(this.tool_form_view.$el);var a=this;this.tool_panel_view.on("tool_link_click",function(c,b){c.preventDefault();a.show_tool(b)})},show_tool:function(b){var a=this;b.fetch().done(function(){a.tool_form_view.model=b;a.tool_form_view.render();a.tool_form_view.$el.show();$("#left").width("650px")})}}); \ No newline at end of file diff -r 3f12146d6d81e08f662ada2011a6973e4230512d -r 0cf3b64e80777c45425a57f4f69d806df839fcf4 static/scripts/packed/viz/sweepster.js --- a/static/scripts/packed/viz/sweepster.js +++ b/static/scripts/packed/viz/sweepster.js @@ -1,1 +1,1 @@ -var ToolInputsSettings=Backbone.Model.extend({defaults:{inputs:null,values:null}});var ToolParameterTree=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(b){var a=this;this.get("tool").get("inputs").each(function(c){if(!c.get_samples()){return}c.on("change:min change:max change:num_samples",function(d){if(d.get("in_ptree")){a.set_tree_data()}},a);c.on("change:in_ptree",function(d){if(d.get("in_ptree")){a.add_param(d)}else{a.remove_param(d)}a.set_tree_data()},a)});if(b.config){_.each(b.config,function(d){var c=a.get("tool").get("inputs").find(function(e){return e.get("name")===d.name});a.add_param(c);c.set(d)})}},add_param:function(a){if(a.get("ptree_index")){return}a.set("in_ptree",true);a.set("ptree_index",this.get_tree_params().length)},remove_param:function(a){a.set("in_ptree",false);a.set("ptree_index",null);_(this.get_tree_params()).each(function(b,c){b.set("ptree_index",c+1)})},set_tree_data:function(){var b=_.map(this.get_tree_params(),function(d){return{param:d,samples:d.get_samples()}});var a=0,c=function(g,d){var i=g[d],h=i.param,f=h.get("label"),e=i.samples;if(g.length-1===d){return _.map(e,function(j){return{id:a++,name:j,param:h,value:j}})}return _.map(e,function(j){return{id:a++,name:j,param:h,value:j,children:c(g,d+1)}})};this.set("tree_data",{name:"Root",id:a++,children:(b.length!==0?c(b,0):null)})},get_tree_params:function(){return _(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(a){return a.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(a,b){return a*b.get_samples().length},1)},get_node_settings:function(e){var c=this.get("tool").get_inputs_dict();var f=e.parent;if(f){while(f.depth!==0){c[f.param.get("name")]=f.value;f=f.parent}}var a=this,b=function(h,g){if(h.param){g[h.param.get("name")]=h.value}if(!h.children){return new ToolInputsSettings({inputs:a.get("tool").get("inputs"),values:g})}else{return _.flatten(_.map(h.children,function(i){return b(i,_.clone(g))}))}},d=b(e,c);if(!_.isArray(d)){d=[d]}return d},get_connected_nodes:function(c){var d=function(e){if(!e.children){return e}else{return _.flatten([e,_.map(e.children,function(f){return d(f)})])}};var b=[],a=c.parent;while(a){b.push(a);a=a.parent}return _.flatten([b,d(c)])},get_leaf:function(b){var c=this.get("tree_data"),a=function(d){return _.find(d,function(e){return b[e.param.get("name")]===e.value})};while(c.children){c=a(c.children)}return c},toJSON:function(){return this.get_tree_params().map(function(a){return{name:a.get("name"),min:a.get("min"),max:a.get("max"),num_samples:a.get("num_samples")}})}});var SweepsterTrack=Backbone.RelationalModel.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:"GenomeRegion"}],initialize:function(a){if(a.track){var b=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},a.track);this.set("track",object_from_template(b,{},null))}},same_settings:function(a){var b=this.get("settings"),c=a.get("settings");for(var d in b){if(!c[d]||b[d]!==c[d]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var TrackCollection=Backbone.Collection.extend({model:SweepsterTrack});var SweepsterVisualization=Visualization.extend({defaults:_.extend({},Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:"Dataset"},{type:Backbone.HasOne,key:"tool",relatedModel:"Tool"},{type:Backbone.HasMany,key:"regions",relatedModel:"GenomeRegion"},{type:Backbone.HasMany,key:"tracks",relatedModel:"SweepsterTrack"}],initialize:function(a){var b=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",b);this.set("parameter_tree",new ToolParameterTree({tool:b,config:a.tree_config}))},add_track:function(a){this.get("tracks").add(a)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var SweepsterTrackView=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(a){this.canvas_manager=a.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var f=this.model.get("settings"),b=f.get("values"),d=$("<td/>").addClass("settings").appendTo(this.$el),c=$("<div/>").addClass("track-info").hide().appendTo(d);c.append($("<div/>").css("font-weight","bold").text("Track Settings"));f.get("inputs").each(function(h){c.append(h.get("label")+": "+b[h.get("name")]+"<br/>")});var a=this,g=$("<button/>").appendTo(c).text("Run on complete dataset").click(function(){c.toggle();a.trigger("run_on_dataset",f)});var e=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){c.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){a.$el.remove();$(".bs-tooltip").remove()}}]);d.prepend(e.$el);this.model.get("regions").each(function(){a.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_paths.get("image_path")+"/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var b=this,a=this.model.get("track"),d=this.model.get("regions"),c=this.$el.find("td.tile");if(!a){return}$.when(a.data_manager.data_is_ready()).then(function(e){d.each(function(h,g){var f=h.length()/b.TILE_LEN,j=1/f,i=b.model.get("mode");$.when(a.data_manager.get_data(h,i,f,{})).then(function(l){var k=b.canvas_manager.new_canvas();k.width=b.TILE_LEN;k.height=a.get_canvas_height(l,i,j,k.width);a.draw_tile(l,k.getContext("2d"),i,f,h,j);$(c[g]).empty().append(k)})})})}});var ToolInputValOrSweepView=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(a){this.$el=a.tool_row;this.render()},render:function(){var b=this.model,f=b.get("type"),h=this.$el.find(".form-row-input"),d=null;h.find(":input").change(function(){b.set("value",$(this).val())});if(f==="number"){d=$(_.template(this.number_input_template,this.model.toJSON()))}else{if(f==="select"){var c=_.map(this.$el.find("select option"),function(i){return $(i).val()}),e=c.join(", ");d=$(_.template(this.select_input_template,{options:e}))}}d.insertAfter(h);var a=this,g=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){b.set("in_ptree",true);h.hide();d.show();$(this).hide();a.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){b.set("in_ptree",false);d.hide();h.show();$(this).hide();a.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(g.$el);if(b.get("in_ptree")){h.hide();a.$el.find(".icon-button.plus-button").hide()}else{a.$el.find(".icon-button.toggle").hide();d.hide()}_.each(["min","max","num_samples"],function(i){d.find("."+i).change(function(){b.set(i,parseFloat($(this).val()))})})}});var ToolParameterTreeDesignView=Backbone.View.extend({className:"tree-design",initialize:function(a){this.render()},render:function(){var c=new ToolFormView({model:this.model.get("tool")});c.render();this.$el.append(c.$el);var b=this,a=b.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(d){var e=new ToolInputValOrSweepView({model:a.at(d),tool_row:$(this)})})}});var ToolParameterTreeView=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(a){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var i=this.model.get_tree_params();if(!i.length){return}this.width=100*(2+i.length);this.height=15*this.model.get_num_leaves();var h=this;var g=d3.layout.cluster().size([this.height,this.width-160]);var c=d3.svg.diagonal().projection(function(j){return[j.y,j.x]});var a=g.nodes(this.model.get("tree_data"));var d=_.uniq(_.pluck(a,"y"));_.each(i,function(l,k){var j=d[k+1],m=$("#center").position().left;h.$el.append($("<div>").addClass("label").text(l.get("label")).css("left",j+m))});var b=d3.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var f=b.selectAll("path.link").data(g.links(a)).enter().append("path").attr("class","link").attr("d",c);var e=b.selectAll("g.node").data(a).enter().append("g").attr("class","node").attr("transform",function(j){return"translate("+j.y+","+j.x+")"}).on("mouseover",function(k){var j=_.pluck(h.model.get_connected_nodes(k),"id");e.filter(function(l){return _.find(j,function(m){return m===l.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){e.style("fill","#000")});e.append("circle").attr("r",9);e.append("text").attr("dx",function(j){return j.children?-12:12}).attr("dy",3).attr("text-anchor",function(j){return j.children?"end":"start"}).text(function(j){return j.name})}});var SweepsterVisualizationView=Backbone.View.extend({className:"Sweepster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(b){this.canvas_manager=new CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new ToolParameterTreeView({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var a=this;this.model.get("tracks").each(function(c){c.get("track").view=a});this.block_color=get_random_color();this.reverse_strand_color=get_random_color([this.block_color,"#ffffff"])},render:function(){var g=new ToolParameterTreeDesignView({model:this.model.get("parameter_tree")});$("#left").append(g.$el);var j=this,d=j.model.get("regions"),h=$("<tr/>").appendTo(this.track_collection_container);d.each(function(k){h.append($("<th>").text(k.toString()))});h.children().first().attr("colspan",2);var e=$("<div>").addClass("tiles");$("#right").append(e.append(this.track_collection_container));j.model.get("tracks").each(function(k){j.add_track(k)});var i=$(this.helpText).addClass("help"),f=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".bs-tooltip").remove();i.remove()}}]);i.prepend(f.$el.css("float","right"));$("#center").append(i);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var c=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var b=["Squish","Pack"],a={};_.each(b,function(k){a[k]=function(){j.model.set("default_mode",k);j.model.get("tracks").each(function(l){l.set("mode",k)})}});make_popupmenu(c.$el.find(".chevron-expand"),a);c.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(c.$el)},run_tool_on_dataset:function(b){var a=this.model.get("tool"),d=a.get("name"),c=this.model.get("dataset");a.set_input_values(b.get("values"));$.when(a.rerun(c)).then(function(e){});show_modal("Running "+d+" on complete dataset",d+" is running on dataset '"+c.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(d){var b=this,c=this.model.get("parameter_tree");b.model.add_track(d);var a=new SweepsterTrackView({model:d,canvas_manager:b.canvas_manager});a.on("run_on_dataset",b.run_tool_on_dataset,b);b.track_collection_container.append(a.$el);a.$el.hover(function(){var f=c.get_leaf(d.get("settings").get("values"));var e=_.pluck(c.get_connected_nodes(f),"id");d3.select(b.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(g){return _.find(e,function(h){return h===g.id})!==undefined}).style("fill","#f00")},function(){d3.select(b.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return d},handle_node_clicks:function(){var a=this,b=this.model.get("parameter_tree"),d=this.model.get("regions"),c=d3.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");c.on("click",function(k,g){var f=a.model.get("tool"),j=a.model.get("dataset"),h=b.get_node_settings(k),e=$.Deferred();if(h.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+a.model.get("tool").get("name")+" with "+h.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();e.resolve(false)}})}else{e.resolve(true)}$.when(e).then(function(i){if(!i){return}var l=_.map(h,function(m){var n=new SweepsterTrack({settings:m,regions:d,mode:a.model.get("default_mode")});a.add_track(n);return n});_.each(l,function(n,m){setTimeout(function(){f.set_input_values(n.get("settings").get("values"));$.when(f.rerun(j,d)).then(function(p){var q=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},p.first().get("track_config")),o=object_from_template(q,a,null);o.data_manager.set("data_type","raw_data");o.prefs.block_color=a.block_color;o.prefs.reverse_strand_color=a.reverse_strand_color;n.set("track",o)})},m*10000)})})})}}); \ No newline at end of file +define(["libs/d3","viz/trackster/util","viz/visualization","viz/trackster/tracks"],function(m,e,l,f){var k=Backbone.Model.extend({defaults:{inputs:null,values:null}});var n=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(p){var o=this;this.get("tool").get("inputs").each(function(q){if(!q.get_samples()){return}q.on("change:min change:max change:num_samples",function(r){if(r.get("in_ptree")){o.set_tree_data()}},o);q.on("change:in_ptree",function(r){if(r.get("in_ptree")){o.add_param(r)}else{o.remove_param(r)}o.set_tree_data()},o)});if(p.config){_.each(p.config,function(r){var q=o.get("tool").get("inputs").find(function(s){return s.get("name")===r.name});o.add_param(q);q.set(r)})}},add_param:function(o){if(o.get("ptree_index")){return}o.set("in_ptree",true);o.set("ptree_index",this.get_tree_params().length)},remove_param:function(o){o.set("in_ptree",false);o.set("ptree_index",null);_(this.get_tree_params()).each(function(p,q){p.set("ptree_index",q+1)})},set_tree_data:function(){var p=_.map(this.get_tree_params(),function(r){return{param:r,samples:r.get_samples()}});var o=0,q=function(u,r){var w=u[r],v=w.param,t=v.get("label"),s=w.samples;if(u.length-1===r){return _.map(s,function(x){return{id:o++,name:x,param:v,value:x}})}return _.map(s,function(x){return{id:o++,name:x,param:v,value:x,children:q(u,r+1)}})};this.set("tree_data",{name:"Root",id:o++,children:(p.length!==0?q(p,0):null)})},get_tree_params:function(){return _(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(o){return o.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(o,p){return o*p.get_samples().length},1)},get_node_settings:function(s){var q=this.get("tool").get_inputs_dict();var t=s.parent;if(t){while(t.depth!==0){q[t.param.get("name")]=t.value;t=t.parent}}var o=this,p=function(v,u){if(v.param){u[v.param.get("name")]=v.value}if(!v.children){return new k({inputs:o.get("tool").get("inputs"),values:u})}else{return _.flatten(_.map(v.children,function(w){return p(w,_.clone(u))}))}},r=p(s,q);if(!_.isArray(r)){r=[r]}return r},get_connected_nodes:function(q){var r=function(s){if(!s.children){return s}else{return _.flatten([s,_.map(s.children,function(t){return r(t)})])}};var p=[],o=q.parent;while(o){p.push(o);o=o.parent}return _.flatten([p,r(q)])},get_leaf:function(p){var q=this.get("tree_data"),o=function(r){return _.find(r,function(s){return p[s.param.get("name")]===s.value})};while(q.children){q=o(q.children)}return q},toJSON:function(){return this.get_tree_params().map(function(o){return{name:o.get("name"),min:o.get("min"),max:o.get("max"),num_samples:o.get("num_samples")}})}});var c=Backbone.RelationalModel.extend({defaults:{track:null,mode:"Pack",settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:l.GenomeRegion}],initialize:function(o){if(o.track){var p=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},o.track);this.set("track",f.object_from_template(p,{},null))}},same_settings:function(o){var p=this.get("settings"),q=o.get("settings");for(var r in p){if(!q[r]||p[r]!==q[r]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var a=Backbone.Collection.extend({model:c});var g=l.Visualization.extend({defaults:_.extend({},l.Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null,default_mode:"Pack"}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:Dataset},{type:Backbone.HasOne,key:"tool",relatedModel:Tool},{type:Backbone.HasMany,key:"regions",relatedModel:l.GenomeRegion},{type:Backbone.HasMany,key:"tracks",relatedModel:c}],initialize:function(o){var p=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",p);this.set("parameter_tree",new n({tool:p,config:o.tree_config}))},add_track:function(o){this.get("tracks").add(o)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"sweepster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var j=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(o){this.canvas_manager=o.canvas_manager;this.render();this.model.on("change:track change:mode",this.draw_tiles,this)},render:function(){var t=this.model.get("settings"),p=t.get("values"),r=$("<td/>").addClass("settings").appendTo(this.$el),q=$("<div/>").addClass("track-info").hide().appendTo(r);q.append($("<div/>").css("font-weight","bold").text("Track Settings"));t.get("inputs").each(function(v){q.append(v.get("label")+": "+p[v.get("name")]+"<br/>")});var o=this,u=$("<button/>").appendTo(q).text("Run on complete dataset").click(function(){q.toggle();o.trigger("run_on_dataset",t)});var s=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){q.toggle()}},{title:"Remove",icon_class:"cross-circle",on_click:function(){o.$el.remove();$(".bs-tooltip").remove()}}]);r.prepend(s.$el);this.model.get("regions").each(function(){o.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_paths.get("image_path")+"/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var p=this,o=this.model.get("track"),r=this.model.get("regions"),q=this.$el.find("td.tile");if(!o){return}$.when(o.data_manager.data_is_ready()).then(function(s){r.each(function(v,u){var t=v.length()/p.TILE_LEN,x=1/t,w=p.model.get("mode");$.when(o.data_manager.get_data(v,w,t,{})).then(function(z){var y=p.canvas_manager.new_canvas();y.width=p.TILE_LEN;y.height=o.get_canvas_height(z,w,x,y.width);o.draw_tile(z,y.getContext("2d"),w,t,v,x);$(q[u]).empty().append(y)})})})}});var b=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(o){this.$el=o.tool_row;this.render()},render:function(){var p=this.model,t=p.get("type"),v=this.$el.find(".form-row-input"),r=null;v.find(":input").change(function(){p.set("value",$(this).val())});if(t==="number"){r=$(_.template(this.number_input_template,this.model.toJSON()))}else{if(t==="select"){var q=_.map(this.$el.find("select option"),function(w){return $(w).val()}),s=q.join(", ");r=$(_.template(this.select_input_template,{options:s}))}}r.insertAfter(v);var o=this,u=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){p.set("in_ptree",true);v.hide();r.show();$(this).hide();o.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){p.set("in_ptree",false);r.hide();v.show();$(this).hide();o.$el.find(".icon-button.plus-button").show()}}],{});this.$el.prepend(u.$el);if(p.get("in_ptree")){v.hide();o.$el.find(".icon-button.plus-button").hide()}else{o.$el.find(".icon-button.toggle").hide();r.hide()}_.each(["min","max","num_samples"],function(w){r.find("."+w).change(function(){p.set(w,parseFloat($(this).val()))})})}});var i=Backbone.View.extend({className:"tree-design",initialize:function(o){this.render()},render:function(){var q=new ToolFormView({model:this.model.get("tool")});q.render();this.$el.append(q.$el);var p=this,o=p.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(r){var s=new b({model:o.at(r),tool_row:$(this)})})}});var h=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(o){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var w=this.model.get_tree_params();if(!w.length){return}this.width=100*(2+w.length);this.height=15*this.model.get_num_leaves();var v=this;var u=m.layout.cluster().size([this.height,this.width-160]);var q=m.svg.diagonal().projection(function(x){return[x.y,x.x]});var o=u.nodes(this.model.get("tree_data"));var r=_.uniq(_.pluck(o,"y"));_.each(w,function(A,z){var y=r[z+1],B=$("#center").position().left;v.$el.append($("<div>").addClass("label").text(A.get("label")).css("left",y+B))});var p=m.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+30).append("g").attr("transform","translate(40, 20)");var t=p.selectAll("path.link").data(u.links(o)).enter().append("path").attr("class","link").attr("d",q);var s=p.selectAll("g.node").data(o).enter().append("g").attr("class","node").attr("transform",function(x){return"translate("+x.y+","+x.x+")"}).on("mouseover",function(y){var x=_.pluck(v.model.get_connected_nodes(y),"id");s.filter(function(z){return _.find(x,function(A){return A===z.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){s.style("fill","#000")});s.append("circle").attr("r",9);s.append("text").attr("dx",function(x){return x.children?-12:12}).attr("dy",3).attr("text-anchor",function(x){return x.children?"end":"start"}).text(function(x){return x.name})}});var d=Backbone.View.extend({className:"Sweepster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(p){this.canvas_manager=new l.CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new h({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var o=this;this.model.get("tracks").each(function(q){q.get("track").view=o});this.block_color=e.get_random_color();this.reverse_strand_color=e.get_random_color([this.block_color,"#ffffff"])},render:function(){var u=new i({model:this.model.get("parameter_tree")});$("#left").append(u.$el);var x=this,r=x.model.get("regions"),v=$("<tr/>").appendTo(this.track_collection_container);r.each(function(y){v.append($("<th>").text(y.toString()))});v.children().first().attr("colspan",2);var s=$("<div>").addClass("tiles");$("#right").append(s.append(this.track_collection_container));x.model.get("tracks").each(function(y){x.add_track(y)});var w=$(this.helpText).addClass("help"),t=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".bs-tooltip").remove();w.remove()}}]);w.prepend(t.$el.css("float","right"));$("#center").append(w);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks();var q=create_icon_buttons_menu([{icon_class:"chevron-expand",title:"Set display mode"},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});var p=["Squish","Pack"],o={};_.each(p,function(y){o[y]=function(){x.model.set("default_mode",y);x.model.get("tracks").each(function(z){z.set("mode",y)})}});make_popupmenu(q.$el.find(".chevron-expand"),o);q.$el.attr("style","float: right");$("#right .unified-panel-header-inner").append(q.$el)},run_tool_on_dataset:function(p){var o=this.model.get("tool"),r=o.get("name"),q=this.model.get("dataset");o.set_input_values(p.get("values"));$.when(o.rerun(q)).then(function(s){});show_modal("Running "+r+" on complete dataset",r+" is running on dataset '"+q.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(r){var p=this,q=this.model.get("parameter_tree");p.model.add_track(r);var o=new j({model:r,canvas_manager:p.canvas_manager});o.on("run_on_dataset",p.run_tool_on_dataset,p);p.track_collection_container.append(o.$el);o.$el.hover(function(){var t=q.get_leaf(r.get("settings").get("values"));var s=_.pluck(q.get_connected_nodes(t),"id");m.select(p.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(u){return _.find(s,function(v){return v===u.id})!==undefined}).style("fill","#f00")},function(){m.select(p.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return r},handle_node_clicks:function(){var o=this,p=this.model.get("parameter_tree"),r=this.model.get("regions"),q=m.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");q.on("click",function(x,u){var t=o.model.get("tool"),w=o.model.get("dataset"),v=p.get_node_settings(x),s=$.Deferred();if(v.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+o.model.get("tool").get("name")+" with "+v.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();s.resolve(false)}})}else{s.resolve(true)}$.when(s).then(function(y){if(!y){return}var z=_.map(v,function(A){var B=new c({settings:A,regions:r,mode:o.model.get("default_mode")});o.add_track(B);return B});_.each(z,function(B,A){setTimeout(function(){t.set_input_values(B.get("settings").get("values"));$.when(t.rerun(w,r)).then(function(D){var E=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},D.first().get("track_config")),C=f.object_from_template(E,o,null);C.data_manager.set("data_type","raw_data");C.prefs.block_color=o.block_color;C.prefs.reverse_strand_color=o.reverse_strand_color;B.set("track",C)})},A*10000)})})})}});return{SweepsterVisualization:g,SweepsterVisualizationView:d}}); \ No newline at end of file diff -r 3f12146d6d81e08f662ada2011a6973e4230512d -r 0cf3b64e80777c45425a57f4f69d806df839fcf4 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters"],function(ad,m,v,L){var r=ad.extend;var Q=m.get_random_color;var X=function(ae){return("isResolved" in ae)};var o={};var l=function(ae,af){o[ae.attr("id")]=af};var n=function(ae,ag,ai,ah){ai=".group";var af={};o[ae.attr("id")]=ah;ae.bind("drag",{handle:"."+ag,relative:true},function(aq,ar){var ap=$(this),av=$(this).parent(),am=av.children(),ao=o[$(this).attr("id")],al,ak,at,aj,an;ak=$(this).parents(ai);if(ak.length!==0){at=ak.position().top;aj=at+ak.outerHeight();if(ar.offsetY<at){$(this).insertBefore(ak);var au=o[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable_before(ao,au);return}else{if(ar.offsetY>aj){$(this).insertAfter(ak);var au=o[ak.attr("id")];au.remove_drawable(ao);au.container.add_drawable(ao);return}}}ak=null;for(an=0;an<am.length;an++){al=$(am.get(an));at=al.position().top;aj=at+al.outerHeight();if(al.is(ai)&&this!==al.get(0)&&ar.offsetY>=at&&ar.offsetY<=aj){if(ar.offsetY-at<aj-ar.offsetY){al.find(".content-div").prepend(this)}else{al.find(".content-div").append(this)}if(ao.container){ao.container.remove_drawable(ao)}o[al.attr("id")].add_drawable(ao);return}}for(an=0;an<am.length;an++){al=$(am.get(an));if(ar.offsetY<al.position().top&&!(al.hasClass("reference-track")||al.hasClass("intro"))){break}}if(an===am.length){if(this!==am.get(an-1)){av.append(this);o[av.attr("id")].move_drawable(ao,an)}}else{if(this!==am.get(an)){$(this).insertBefore(am.get(an));o[av.attr("id")].move_drawable(ao,(ar.deltaY>0?an-1:an))}}}).bind("dragstart",function(){af["border-top"]=ae.css("border-top");af["border-bottom"]=ae.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(af)})};exports.moveable=n;var ac=16,G=9,D=20,A=100,I=12000,T=400,K=5000,x=100,p="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",W="Ready for display",R=10,H=20;function Y(af,ae){if(!ae){ae=0}var ag=Math.pow(10,ae);return Math.round(af*ag)/ag}var s=function(af,ae,ah){if(!s.id_counter){s.id_counter=0}this.id=s.id_counter++;this.name=ah.name;this.view=af;this.container=ae;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ah.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ai){ai.stopPropagation()});var ag=this;this.container_div.hover(function(){ag.icons_div.show()},function(){ag.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};s.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ae){if(ae.content_visible){ae.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ae.hide_contents();ae.content_visible=false}else{ae.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ae.content_visible=true;ae.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(af){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){af.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure",af.config.build_form(),{Cancel:ah,OK:ae})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.remove()}}];r(s.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ae){this.old_name=this.name;this.name=ae;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ae=this.view;this.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(af,ak,aj,ai,ae,ah){var ag=this;this.action_icons[af]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tooltip().click(function(){ai(ag)}).appendTo(this.icons_div);if(ah){this.action_icons[af].hide()}},build_action_icons:function(ae){var ag;for(var af=0;af<ae.length;af++){ag=ae[af];this.add_action_icon(ag.name,ag.title,ag.css_class,ag.on_click_fn,ag.prepend,ag.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(af,ae,ag){s.call(this,af,ae,ag);this.obj_type=ag.obj_type;this.drawables=[]};r(z.prototype,s.prototype,{unpack_drawables:function(ag){this.drawables=[];var af;for(var ae=0;ae<ag.length;ae++){af=q(ag[ae],this.view,this);this.add_drawable(af)}},init:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].init()}},_draw:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw()}},to_dict:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:af}},add_drawable:function(ae){this.drawables.push(ae);ae.container=this;this.changed()},add_drawable_before:function(ag,ae){this.changed();var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables.splice(af,0,ag);return true}return false},replace_drawable:function(ag,ae,af){var ah=this.drawables.indexOf(ag);if(ah!==-1){this.drawables[ah]=ae;if(af){ag.container_div.replaceWith(ae.container_div)}this.changed()}return ah},remove_drawable:function(af){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);af.container=null;this.changed();return true}return false},move_drawable:function(af,ag){var ae=this.drawables.indexOf(af);if(ae!==-1){this.drawables.splice(ae,1);this.drawables.splice(ag,0,af);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(af,ae,ah){r(ah,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,af,ae,ah);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new Z(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ah){this.unpack_drawables(ah.drawables)}if("filters" in ah){var ag=this.filters_manager;this.filters_manager=new Z(this,ah.filters);ag.parent_div.replaceWith(this.filters_manager.parent_div);if(ah.filters.visible){this.setup_multitrack_filtering()}}};r(P.prototype,s.prototype,z.prototype,{action_icons_def:[s.prototype.action_icons_def[0],s.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters();ae._restore_filter_managers()}else{ae.setup_multitrack_filtering();ae.request_draw(true)}ae.filters_manager.toggle()}},s.prototype.action_icons_def[2]],build_container_div:function(){var ae=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ae)}return ae},build_header_div:function(){var ae=$("<div/>").addClass("track-header");ae.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ae);return ae},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ag=this.drawables.length;if(ag===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ag===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var an,am,ak,aq=true,ai=this.drawables[0].get_type(),ae=0;for(an=0;an<ag;an++){ak=this.drawables[an];if(ak.get_type()!==ai){can_composite=false;break}if(ak instanceof d){ae++}}if(aq||ae===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ae>1&&ae===this.drawables.length){var ar={},af;ak=this.drawables[0];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];ar[af.name]=[af]}for(an=1;an<this.drawables.length;an++){ak=this.drawables[an];for(am=0;am<ak.filters_manager.filters.length;am++){af=ak.filters_manager.filters[am];if(af.name in ar){ar[af.name].push(af)}}}this.filters_manager.remove_all();var ah,aj,al,ao;for(var ap in ar){ah=ar[ap];if(ah.length===ae){aj=new U({name:ah[0].name,index:ah[0].index});this.filters_manager.add_filter(aj)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].filters_manager=this.saved_filters_managers[ae]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ae=0;ae<this.drawables.length;ae++){drawable=this.drawables[ae];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ai=[];for(var af=0;af<this.drawables.length;af++){ai.push(this.drawables[af].name)}var ag="Composite Track of "+this.drawables.length+" tracks ("+ai.join(", ")+")";var ah=new h(this.view,this.view,{name:ag,drawables:this.drawables});var ae=this.container.replace_drawable(this,ah,true);ah.request_draw()},add_drawable:function(ae){z.prototype.add_drawable.call(this,ae);this.update_icons()},remove_drawable:function(ae){z.prototype.remove_drawable.call(this,ae);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ae=r(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ae},request_draw:function(ae,ag){for(var af=0;af<this.drawables.length;af++){this.drawables[af].request_draw(ae,ag)}}});var ab=function(ae){r(ae,{obj_type:"View"});z.call(this,"View",ae.container,ae);this.chrom=null;this.vis_id=ae.vis_id;this.dbkey=ae.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new CanvasManager(this.container.get(0).ownerDocument);this.reset()};ad.extend(ab.prototype,Backbone.Events);r(ab.prototype,z.prototype,{init:function(){this.requested_redraw=false;var ag=this.container,ae=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ag);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ag);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ag);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ae);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ah=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_datasets(add_datasets_url,add_track_async_url,function(ai){ad.each(ai,function(aj){ae.add_drawable(q(aj,ae,ae))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var af=function(ai){if(ai.type==="focusout"||(ai.keyCode||ai.which)===13||(ai.keyCode||ai.which)===27){if((ai.keyCode||ai.which)!==27){ae.go_to($(this).val())}$(this).hide();$(this).val("");ae.location_span.show();ae.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",af).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ae.location_span.hide();ae.chrom_select.hide();ae.nav_input.val(ae.chrom+":"+ae.low+"-"+ae.high);ae.nav_input.css("display","inline-block");ae.nav_input.select();ae.nav_input.focus();ae.nav_input.autocomplete({source:function(ak,ai){var al=[],aj=$.map(ae.get_drawables(),function(am){return am.data_manager.search_features(ak.term).success(function(an){al=al.concat(an)})});$.when.apply($,aj).done(function(){ai($.map(al,function(am){return{label:am[0],value:am[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ae.zoom_out();ae.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ae.zoom_in();ae.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ae.change_chrom(ae.chrom_select.val())});this.browser_content_div.click(function(ai){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ai){ae.zoom_in(ai.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ai,aj){this.current_x=aj.offsetX}).bind("drag",function(ai,ak){var al=ak.offsetX-this.current_x;this.current_x=ak.offsetX;var aj=Math.round(al/ae.viewport_container.width()*(ae.max_high-ae.max_low));ae.move_delta(-aj)});this.overview_close.click(function(){ae.reset_overview()});this.viewport_container.bind("draginit",function(ai,aj){if(ai.clientX>ae.viewport_container.width()-16){return false}}).bind("dragstart",function(ai,aj){aj.original_low=ae.low;aj.current_height=ai.clientY;aj.current_x=aj.offsetX}).bind("drag",function(ak,am){var ai=$(this);var an=am.offsetX-am.current_x;var aj=ai.scrollTop()-(ak.clientY-am.current_height);ai.scrollTop(aj);am.current_height=ak.clientY;am.current_x=am.offsetX;var al=Math.round(an/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}).bind("mousewheel",function(ak,am,aj,ai){if(aj){aj*=50;var al=Math.round(-aj/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}});this.top_labeltrack.bind("dragstart",function(ai,aj){return $("<div />").css({height:ae.browser_content_div.height()+ae.top_labeltrack.height()+ae.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(am,an){$(an.proxy).css({left:Math.min(am.pageX,an.startX)-ae.container.offset().left,width:Math.abs(am.pageX-an.startX)});var aj=Math.min(am.pageX,an.startX)-ae.container.offset().left,ai=Math.max(am.pageX,an.startX)-ae.container.offset().left,al=(ae.high-ae.low),ak=ae.viewport_container.width();ae.update_location(Math.round(aj/ak*al)+ae.low,Math.round(ai/ak*al)+ae.low)}).bind("dragend",function(an,ao){var aj=Math.min(an.pageX,ao.startX),ai=Math.max(an.pageX,ao.startX),al=(ae.high-ae.low),ak=ae.viewport_container.width(),am=ae.low;ae.low=Math.round(aj/ak*al)+am;ae.high=Math.round(ai/ak*al)+am;$(ao.proxy).remove();ae.request_redraw()});this.add_label_track(new aa(this,{content_div:this.top_labeltrack}));this.add_label_track(new aa(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ae.resize_window()},500)});$(document).bind("redraw",function(){ae.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(af,ah,ae,ai){if(this.timer){clearTimeout(this.timer)}if(ai){var ag=this;this.timer=setTimeout(function(){ag.trigger("navigate",af+":"+ah+"-"+ae)},500)}else{view.trigger("navigate",af+":"+ah+"-"+ae)}},update_location:function(ae,ag){this.location_span.text(commatize(ae)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(ae)+"-"+commatize(ag));var af=view.chrom_select.val();if(af!==""){this.trigger_navigate(af,view.low,view.high,true)}},load_chroms:function(ag){ag.num=x;var ae=this,af=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ag,dataType:"json",success:function(ai){if(ai.chrom_info.length===0){return}if(ai.reference){ae.add_label_track(new B(ae))}ae.chrom_data=ai.chrom_info;var al='<option value="">Select Chrom/Contig</option>';for(var ak=0,ah=ae.chrom_data.length;ak<ah;ak++){var aj=ae.chrom_data[ak].chrom;al+='<option value="'+aj+'">'+aj+"</option>"}if(ai.prev_chroms){al+='<option value="previous">Previous '+x+"</option>"}if(ai.next_chroms){al+='<option value="next">Next '+x+"</option>"}ae.chrom_select.html(al);ae.chrom_start_index=ai.start_index;af.resolve(ai)},error:function(){alert("Could not load chroms for this dbkey:",ae.dbkey)}});return af},change_chrom:function(aj,af,al){var ag=this;if(!ag.chrom_data){ag.load_chroms_deferred.then(function(){ag.change_chrom(aj,af,al)});return}if(!aj||aj==="None"){return}if(aj==="previous"){ag.load_chroms({low:this.chrom_start_index-x});return}if(aj==="next"){ag.load_chroms({low:this.chrom_start_index+x});return}var ak=$.grep(ag.chrom_data,function(am,an){return am.chrom===aj})[0];if(ak===undefined){ag.load_chroms({chrom:aj},function(){ag.change_chrom(aj,af,al)});return}else{if(aj!==ag.chrom){ag.chrom=aj;ag.chrom_select.val(ag.chrom);ag.max_high=ak.len-1;ag.reset();ag.request_redraw(true);for(var ai=0,ae=ag.drawables.length;ai<ae;ai++){var ah=ag.drawables[ai];if(ah.init){ah.init()}}if(ag.reference_track){ag.reference_track.init()}}if(af!==undefined&&al!==undefined){ag.low=Math.max(af,0);ag.high=Math.min(al,ag.max_high)}else{ag.low=0;ag.high=ag.max_high}ag.reset_overview();ag.request_redraw()}},go_to:function(ai){ai=ai.replace(/ |,/g,"");var am=this,ae,ah,af=ai.split(":"),ak=af[0],al=af[1];if(al!==undefined){try{var aj=al.split("-");ae=parseInt(aj[0],10);ah=parseInt(aj[1],10)}catch(ag){return false}}am.change_chrom(ak,ae,ah)},move_fraction:function(ag){var ae=this;var af=ae.high-ae.low;this.move_delta(ag*af)},move_delta:function(ah){var ae=this;var ag=ae.high-ae.low;if(ae.low-ah<ae.max_low){ae.low=ae.max_low;ae.high=ae.max_low+ag}else{if(ae.high-ah>ae.max_high){ae.high=ae.max_high;ae.low=ae.max_high-ag}else{ae.high-=ah;ae.low-=ah}}ae.request_redraw();var af=ae.chrom_select.val();this.trigger_navigate(af,ae.low,ae.high,true)},add_drawable:function(ae){z.prototype.add_drawable.call(this,ae);ae.init();this.changed();this.update_intro_div()},add_label_track:function(ae){ae.view=this;ae.init();this.label_tracks.push(ae)},remove_drawable:function(ag,af){z.prototype.remove_drawable.call(this,ag);if(af){var ae=this;ag.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(am,ae,al,an){var ak=this,aj=(an?[an]:ak.drawables),ag;var af;for(var ai=0;ai<aj.length;ai++){af=aj[ai];ag=-1;for(var ah=0;ah<ak.tracks_to_be_redrawn.length;ah++){if(ak.tracks_to_be_redrawn[ah][0]===af){ag=ah;break}}if(ag<0){ak.tracks_to_be_redrawn.push([af,ae,al])}else{ak.tracks_to_be_redrawn[ai][1]=ae;ak.tracks_to_be_redrawn[ai][2]=al}}if(!this.requested_redraw){requestAnimationFrame(function(){ak._redraw(am)});this.requested_redraw=true}},_redraw:function(ao){this.requested_redraw=false;var al=this.low,ah=this.high;if(al<this.max_low){al=this.max_low}if(ah>this.max_high){ah=this.max_high}var an=this.high-this.low;if(this.high!==0&&an<this.min_separation){ah=al+this.min_separation}this.low=Math.floor(al);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ap=13;this.overview_box.css({left:ae,width:Math.max(ap,ak)}).show();if(ak<ap){this.overview_box.css("left",ae-(ap-ak)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ak})}if(!ao){var ag,af,am;for(var ai=0,aj=this.tracks_to_be_redrawn.length;ai<aj;ai++){ag=this.tracks_to_be_redrawn[ai][0];af=this.tracks_to_be_redrawn[ai][1];am=this.tracks_to_be_redrawn[ai][2];if(ag){ag._draw(af,am)}}this.tracks_to_be_redrawn=[];for(ai=0,aj=this.label_tracks.length;ai<aj;ai++){this.label_tracks[ai]._draw()}}},zoom_in:function(af,ag){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ah=this.high-this.low,ai=ah/2+this.low,ae=(ah/this.zoom_factor)/2;if(af){ai=af/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ai-ae);this.high=Math.round(ai+ae);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var af=this.high-this.low,ag=af/2+this.low,ae=(af*this.zoom_factor)/2;this.low=Math.round(ag-ae);this.high=Math.round(ag+ae);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ag){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ag.dataset_id){return}this.overview_viewport.find(".track").remove()}var af=ag.copy({content_div:this.overview_viewport}),ae=this;af.header_div.hide();af.is_overview=true;ae.overview_drawable=af;this.overview_drawable.postdraw_actions=function(){ae.overview_highlight.show().height(ae.overview_drawable.content_div.height());ae.overview_viewport.height(ae.overview_drawable.content_div.height()+ae.overview_box.outerHeight());ae.overview_close.show();ae.resize_window()};ae.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var t=function(ag,al,ah){this.track=ag;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],af=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params.push(new f(af,ar,aj,(af in ah?ah[af]:au),an.min,an.max))}else{if(ap==="select"){this.params.push(new N(af,ar,aj,(af in ah?ah[af]:au)))}else{console.log("WARNING: unrecognized tool parameter type:",af,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("param-input").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var ae=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);ae.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()});if("visible" in ah&&ah.visible){this.parent_div.show()}};r(t.prototype,{update_params:function(){for(var ae=0;ae<this.params.length;ae++){this.params[ae].update_value()}},state_dict:function(){var af={};for(var ae=0;ae<this.params.length;ae++){af[this.params[ae].name]=this.params[ae].value}af.visible=this.parent_div.is(":visible");return af},get_param_values_dict:function(){var ae={};this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();ae[af]=ag});return ae},get_param_values:function(){var ae=[];this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();if(af){ae[ae.length]=ag}});return ae},run_on_dataset:function(){var ae=this;ae.run({target_dataset_id:this.track.original_dataset_id,tool_id:ae.name},null,function(af){show_modal(ae.name+" is Running",ae.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var af={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},aj=this.track,ag=af.tool_id+aj.tool_region_and_parameters_str(af.chrom,af.low,af.high),ae;if(aj.container===view){var ai=new P(view,view,{name:this.name});var ah=aj.container.replace_drawable(aj,ai,false);ai.container_div.insertBefore(aj.view.content_div.children()[ah]);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);ae=ai}else{ae=aj.container}var ak=new aj.constructor(view,ae,{name:ag,hda_ldda:"hda"});ak.init_for_tool_data();ak.change_mode(aj.mode);ak.set_filters_manager(aj.filters_manager.copy(ak));ak.update_icons();ae.add_drawable(ak);ak.tiles_div.text("Starting job.");this.update_params();this.run(af,ak,function(al){ak.set_dataset(new Dataset(al));ak.tiles_div.text("Running job.");ak.init()})},run:function(ae,ag,ah){ae.inputs=this.get_param_values_dict();var af=new ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ae),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ai){return ai!=="pending"}});$.when(af.go()).then(function(ai){if(ai==="no converter"){ag.container_div.addClass("error");ag.content_div.text(J)}else{if(ai.error){ag.container_div.addClass("error");ag.content_div.text(y+ai.message)}else{ah(ai)}}})}});var N=function(af,ae,ag,ah){this.name=af;this.label=ae;this.html=$(ag);this.value=ah};r(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ag,af,ai,aj,ah,ae){N.call(this,ag,af,ai,aj);this.min=ah;this.max=ae};r(f.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(ae){this.manager=null;this.name=ae.name;this.index=ae.index;this.tool_id=ae.tool_id;this.tool_exp_name=ae.tool_exp_name};r(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var c=function(ag,af,ae){return $("<a/>").attr("href","javascript:void(0);").attr("title",ag).addClass("icon-button").addClass(af).tooltip().click(ae)};var U=function(am){g.call(this,am);this.low=("low" in am?am.low:-Number.MAX_VALUE);this.high=("high" in am?am.high:Number.MAX_VALUE);this.min=("min" in am?am.min:Number.MAX_VALUE);this.max=("max" in am?am.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ai=function(an,ao,ap){an.click(function(){var av=ao.text(),at=parseFloat(ap.slider("option","max")),ar=(at<=1?4:at<=1000000?at.toString().length:6),au=false,aq=$(this).parents(".slider-row");aq.addClass("input");if(ap.slider("option","values")){ar=2*ar+1;au=true}ao.text("");$("<input type='text'/>").attr("size",ar).attr("maxlength",ar).attr("value",av).appendTo(ao).focus().select().click(function(aw){aw.stopPropagation()}).blur(function(){$(this).remove();ao.text(av);aq.removeClass("input")}).keyup(function(aA){if(aA.keyCode===27){$(this).trigger("blur")}else{if(aA.keyCode===13){var ay=ap.slider("option","min"),aw=ap.slider("option","max"),az=function(aB){return(isNaN(aB)||aB>aw||aB<ay)},ax=$(this).val();if(!au){ax=parseFloat(ax);if(az(ax)){alert("Parameter value must be in the range ["+ay+"-"+aw+"]");return $(this)}}else{ax=ax.split("-");ax=[parseFloat(ax[0]),parseFloat(ax[1])];if(az(ax[0])||az(ax[1])){alert("Parameter value must be in the range ["+ay+"-"+aw+"]");return $(this)}}ap.slider((au?"values":"value"),ax);aq.removeClass("input")}}})})};var af=this;af.parent_div=$("<div/>").addClass("filter-row slider-row");var ae=$("<div/>").addClass("elt-label").appendTo(af.parent_div),ak=$("<span/>").addClass("slider-name").text(af.name+" ").appendTo(ae),ag=$("<span/>").text(this.low+"-"+this.high),ah=$("<span/>").addClass("slider-value").appendTo(ae).append("[").append(ag).append("]");af.values_span=ag;var aj=$("<div/>").addClass("slider").appendTo(af.parent_div);af.control_element=$("<div/>").attr("id",af.name+"-filter-control").appendTo(aj);af.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(an,ao){af.slide(an,ao)},change:function(an,ao){af.control_element.slider("option","slide").call(af.control_element,an,ao)}});af.slider=af.control_element;af.slider_label=ag;ai(ah,ag,af.control_element);var al=$("<div/>").addClass("display-controls").appendTo(af.parent_div);this.transparency_icon=c("Use filter for data transparency","layer-transparent",function(){if(af.manager.alpha_filter!==af){af.manager.alpha_filter=af;af.manager.parent_div.find(".layer-transparent").removeClass("active").hide();af.transparency_icon.addClass("active").show()}else{af.manager.alpha_filter=null;af.transparency_icon.removeClass("active")}af.manager.track.request_draw(true,true)}).appendTo(al).hide();this.height_icon=c("Use filter for data height","arrow-resize-090",function(){if(af.manager.height_filter!==af){af.manager.height_filter=af;af.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();af.height_icon.addClass("active").show()}else{af.manager.height_filter=null;af.height_icon.removeClass("active")}af.manager.track.request_draw(true,true)}).appendTo(al).hide();af.parent_div.hover(function(){af.transparency_icon.show();af.height_icon.show()},function(){if(af.manager.alpha_filter!==af){af.transparency_icon.hide()}if(af.manager.height_filter!==af){af.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(af.parent_div)};r(U.prototype,{to_dict:function(){var ae=g.prototype.to_dict.call(this);return r(ae,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new U({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ag,ae){var af=ae-ag;return(af<=2?0.01:1)},slide:function(ag,ah){var af=ah.values;this.values_span.text(af[0]+"-"+af[1]);this.low=af[0];this.high=af[1];var ae=this;setTimeout(function(){if(af[0]===ae.low&&af[1]===ae.high){ae.manager.track.request_draw(true,true)}},25)},applies_to:function(ae){if(ae.length>this.index){return true}return false},_keep_val:function(ae){return(isNaN(ae)||(ae>=this.low&&ae<=this.high))},keep:function(af){if(!this.applies_to(af)){return true}var ah=this;var ai=af[this.index];if(ai instanceof Array){var ag=true;for(var ae=0;ae<ai.length;ae++){if(!this._keep_val(ai[ae])){ag=false;break}}return ag}else{return this._keep_val(af[this.index])}},update_attrs:function(ah){var ae=false;if(!this.applies_to(ah)){return ae}var af=ah[this.index];if(!(af instanceof Array)){af=[af]}for(var ag=0;ag<af.length;ag++){var ai=af[ag];if(ai<this.min){this.min=Math.floor(ai);ae=true}if(ai>this.max){this.max=Math.ceil(ai);ae=true}}return ae},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var af=this.slider.slider("option","min"),ae=this.slider.slider("option","max");if(this.min<af||this.max>ae){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var Z=function(ag,am){this.track=ag;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(ao){ao.stopPropagation()}).click(function(ao){ao.stopPropagation()}).bind("dblclick",function(ao){ao.stopPropagation()}).bind("keydown",function(ao){ao.stopPropagation()});if(am&&"filters" in am){var ae=("alpha_filter" in am?am.alpha_filter:null),ah=("height_filter" in am?am.height_filter:null),aj=am.filters,af;for(var ak=0;ak<aj.length;ak++){if(aj[ak].type==="number"){af=new U(aj[ak]);this.add_filter(af);if(af.name===ae){this.alpha_filter=af;af.transparency_icon.addClass("active").show()}if(af.name===ah){this.height_filter=af;af.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in am&&am.visible){this.parent_div.show()}}if(this.filters.length!==0){var an=$("<div/>").addClass("param-row").appendTo(this.parent_div);var al=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(an);var ai=this;al.click(function(){ai.run_on_dataset()})}};r(Z.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var ah={},ag=[],af;for(var ae=0;ae<this.filters.length;ae++){af=this.filters[ae];ag.push(af.to_dict())}ah.filters=ag;ah.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);ah.height_filter=(this.height_filter?this.height_filter.name:null);ah.visible=this.parent_div.is(":visible");return ah},copy:function(af){var ag=new Z(af);for(var ae=0;ae<this.filters.length;ae++){ag.add_filter(this.filters[ae].copy())}return ag},add_filter:function(ae){ae.manager=this;this.parent_div.append(ae.parent_div);this.filters.push(ae)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ae=0;ae<this.filters.length;ae++){var af=this.filters[ae];af.update_ui_elt()}},clear_filters:function(){for(var ae=0;ae<this.filters.length;ae++){var af=this.filters[ae];af.slider.slider("option","values",[af.min,af.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var aj={},al,ae;for(var ai=0;ai<this.filters.length;ai++){al=this.filters[ai];if(al.tool_id){if(al.min!==al.low){ae=ak(aj,al.tool_id,[]);ae[ae.length]=al.tool_exp_name+" >= "+al.low}if(al.max!==al.high){ae=ak(aj,al.tool_id,[]);ae[ae.length]=al.tool_exp_name+" <= "+al.high}}}var af=[];for(var ah in aj){af[af.length]=[ah,aj[ah]]}(function ag(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ag(au.dataset_id,ap)}}})})(this.track.dataset_id,af)}});var C=function(ae,af){L.Scaler.call(this,af);this.filter=ae};C.prototype.gen_val=function(ae){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ae[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ae){this.track=ae.track;this.params=ae.params;this.values={};this.restore_values((ae.saved_values?ae.saved_values:{}));this.onchange=ae.onchange};r(F.prototype,{restore_values:function(ae){var af=this;$.each(this.params,function(ag,ah){if(ae[ah.key]!==undefined){af.values[ah.key]=ae[ah.key]}else{af.values[ah.key]=ah.default_value}})},build_form:function(){var ah=this;var ae=$("<div />");var ag;function af(am,ai){for(var aq=0;aq<am.length;aq++){ag=am[aq];if(ag.hidden){continue}var ak="param_"+aq;var av=ah.values[ag.key];var ax=$("<div class='form-row' />").appendTo(ai);ax.append($("<label />").attr("for",ak).text(ag.label+":"));if(ag.type==="bool"){ax.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",av))}else{if(ag.type==="text"){ax.append($('<input type="text"/>').attr("id",ak).val(av).click(function(){$(this).select()}))}else{if(ag.type==="select"){var at=$("<select />").attr("id",ak);for(var ao=0;ao<ag.options.length;ao++){$("<option/>").text(ag.options[ao].label).attr("value",ag.options[ao].value).appendTo(at)}at.val(av);ax.append(at)}else{if(ag.type==="color"){var aw=$("<div/>").appendTo(ax),ar=$("<input />").attr("id",ak).attr("name",ak).val(av).css("float","left").appendTo(aw).click(function(az){$(".bs-tooltip").removeClass("in");var ay=$(this).siblings(".bs-tooltip").addClass("in");ay.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ay).height()/2)+($(this).height()/2)}).show();ay.click(function(aA){aA.stopPropagation()});$(document).bind("click.color-picker",function(){ay.hide();$(document).unbind("click.color-picker")});az.stopPropagation()}),ap=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(aw).attr("title","Set new random color").tooltip(),au=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(aw).hide(),al=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(au),aj=$("<div class='tooltip-arrow'></div>").appendTo(au),an=$.farbtastic(al,{width:100,height:100,callback:ar,color:av});aw.append($("<div/>").css("clear","both"));(function(ay){ap.click(function(){ay.setColor(Q())})})(an)}else{ax.append($("<input />").attr("id",ak).attr("name",ak).val(av))}}}}if(ag.help){ax.append($("<div class='help'/>").text(ag.help))}}}af(this.params,ae);return ae},update_from_form:function(ae){var ag=this;var af=false;$.each(this.params,function(ah,aj){if(!aj.hidden){var ak="param_"+ah;var ai=ae.find("#"+ak).val();if(aj.type==="float"){ai=parseFloat(ai)}else{if(aj.type==="int"){ai=parseInt(ai)}else{if(aj.type==="bool"){ai=ae.find("#"+ak).is(":checked")}}}if(ai!==ag.values[aj.key]){ag.values[aj.key]=ai;af=true}}});if(af){this.onchange();this.track.changed()}}});var b=function(ae,ai,ag,af,ah){this.track=ae;this.region=ai;this.low=ai.get("start");this.high=ai.get("end");this.resolution=ag;this.html_elt=$("<div class='track-tile'/>").append(af).height($(af).attr("height"));this.data=ah;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ae,aj,ag,af,ah,ai){b.call(this,ae,aj,ag,af,ah);this.max_val=ai};r(k.prototype,b.prototype);var O=function(ah,ap,ai,ag,ak,ar,al,at,af,ao){b.call(this,ah,ap,ai,ag,ak);this.mode=al;this.all_slotted=af;this.feature_mapper=ao;this.has_icons=false;if(at){this.has_icons=true;var am=this;ag=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ag.width}).prependTo(this.html_elt);var an=new GenomeRegion({chrom:ah.view.chrom,start:this.low,end:this.high}),aq=ak.length,aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);aj.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()});ae.click(function(){am.stale=true;ah.data_manager.get_more_data(an,ah.mode,am.resolution,{},ah.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ah.request_draw(true)}).dblclick(function(au){au.stopPropagation()})}};r(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var af=this,ae={};if(af.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(aq){if(!this.hovered){return}var al=$(this).offset(),ap=aq.pageX-al.left,ao=aq.pageY-al.top,av=af.feature_mapper.get_feature_data(ap,ao),am=(av?av[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!am||$(this).attr("id")!==am.toString()){$(this).remove()}});if(av){var ah=ae[am];if(!ah){var am=av[0],ar={name:av[3],start:av[1],end:av[2],strand:av[4]},ak=af.track.filters_manager.filters,aj;for(var an=0;an<ak.length;an++){aj=ak[an];ar[aj.name]=av[aj.index]}var ah=$("<div/>").attr("id",am).addClass("feature-popup"),aw=$("<table/>"),au,at,ax;for(au in ar){at=ar[au];ax=$("<tr/>").appendTo(aw);$("<th/>").appendTo(ax).text(au);$("<td/>").attr("align","left").appendTo(ax).text(typeof(at)==="number"?Y(at,2):at)}ah.append($("<div class='feature-popup-inner'>").append(aw));ae[am]=ah}ah.appendTo($(this).parents(".track-content").children(".overlay"));var ai=ap+parseInt(af.html_elt.css("left"))-ah.width()/2,ag=ao+parseInt(af.html_elt.css("top"))+7;ah.css("left",ai+"px").css("top",ag+"px")}else{if(!aq.isPropagationStopped()){aq.stopPropagation();$(this).siblings().each(function(){$(this).trigger(aq)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var i=function(af,ae,ag){r(ag,{drag_handle_class:"draghandle"});s.call(this,af,ae,ag);this.dataset=new Dataset({id:ag.dataset_id,hda_ldda:ag.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ag?ag.data_query_wait:K);this.data_manager=("data_manager" in ag?ag.data_manager:new GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ag)||ag.resize){this.add_resize_handle()}}};r(i.prototype,s.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},s.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ae){ae.view.set_overview(ae)}},s.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){if(ae.filters_manager.visible()){ae.filters_manager.clear_filters()}else{ae.filters_manager.init_filters()}ae.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ae){ae.dynamic_tool_div.toggle();if(ae.dynamic_tool_div.is(":visible")){ae.set_name(ae.name+ae.tool_region_and_parameters_str())}else{ae.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ae){var ah='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ag=ad.template(ah,{track:ae});var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){var al=$('select[name="regions"] option:selected').val(),an,ak=new GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),am=ad.map($(".bookmark"),function(ao){return new GenomeRegion({from_str:$(ao).children(".position").text()})});if(al==="cur"){an=[ak]}else{if(al==="bookmarks"){an=am}else{an=[ak].concat(am)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ae.dataset_id,hda_ldda:ae.hda_ldda,regions:JSON.stringify(new Backbone.Collection(an).toJSON())})},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){af()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ag,{No:aj,Yes:af})}},s.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&s.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ae=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ae)}this.name_div=$("<div/>").addClass("track-name").appendTo(ae).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ae},on_resize:function(){},add_resize_handle:function(){var ae=this;var ah=false;var ag=false;var af=$("<div class='track-resize'>");$(ae.container_div).hover(function(){if(ae.content_visible){ah=true;af.show()}},function(){ah=false;if(!ag){af.hide()}});af.hide().bind("dragstart",function(ai,aj){ag=true;aj.original_height=$(ae.content_div).height()}).bind("drag",function(aj,ak){var ai=Math.min(Math.max(ak.original_height+ak.deltaY,ae.min_height_px),ae.max_height_px);$(ae.tiles_div).css("height",ai);ae.visible_height_px=(ae.max_height_px===ai?0:ai);ae.on_resize()}).bind("dragend",function(ai,aj){ae.tile_cache.clear();ag=false;if(!ah){af.hide()}ae.config.values.height=ae.visible_height_px;ae.changed()}).appendTo(ae.container_div)},set_display_modes:function(ah,ak){this.display_modes=ah;this.mode=(ak?ak:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var af=this,ai={};for(var ag=0,ae=af.display_modes.length;ag<ae;ag++){var aj=af.display_modes[ag];ai[aj]=function(al){return function(){af.change_mode(al);af.icons_div.show();af.container_div.mouseleave(function(){af.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)},build_action_icons:function(){s.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof aa){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof V){return"ReadTrack"}else{if(this instanceof S){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.tiles_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}var ae=$.Deferred(),ag={hda_ldda:af.hda_ldda,data_type:this.dataset_check_type,chrom:af.view.chrom};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){af.container_div.addClass("error");af.tiles_div.text(p);if(ah.message){var ai=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})});af.tiles_div.append(ai)}}else{if(ah==="no converter"){af.container_div.addClass("error");af.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){af.container_div.addClass("nodata");af.tiles_div.text(E)}else{if(ah==="pending"){af.container_div.addClass("pending");af.tiles_div.html(w);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){af.valid_chroms=ah.valid_chroms;af.update_icons()}af.tiles_div.text(W);if(af.view.chrom){af.tiles_div.text("");af.tiles_div.css("height",af.visible_height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){ae.resolve();af.container_div.removeClass("nodata error pending");af.request_draw()})}else{ae.resolve()}}}}}}});this.update_icons();return ae},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ag,af,ah){i.call(this,ag,af,ah);var ae=this;n(ae.container_div,ae.drag_handle_class,".group",ae);this.filters_manager=new Z(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ah&&ah.tool?new t(this,ah.tool,ah.tool_state):null);this.tile_cache=new Cache(R);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};r(M.prototype,s.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.slotters[ae.view.resolution_px_b].max_rows*=2;ae.request_draw(true)},hide:true}]),copy:function(ae){var af=this.to_dict();r(af,{data_manager:this.data_manager});var ag=new this.constructor(this.view,ae,af);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},set_filters_manager:function(ae){this.filters_manager=ae;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(af){var ae=this;ae.mode=af;ae.config.values.mode=af;ae.tile_cache.clear();ae.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ae.mode+")");return ae},update_icons:function(){var ae=this;if(ae.filters_available){ae.action_icons.filters_icon.show()}else{ae.action_icons.filters_icon.hide()}if(ae.tool){ae.action_icons.tools_icon.show();ae.action_icons.param_space_viz_icon.show()}else{ae.action_icons.tools_icon.hide();ae.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(af,ag,ae){return af+"_"+ag+"_"+ae},request_draw:function(af,ae){this.view.request_redraw(false,af,ae,this)},before_draw:function(){},_draw:function(af,ap){if(!this.can_draw()){return}var an=this.view.low,aj=this.view.high,al=aj-an,ag=this.view.container.width(),ar=this.view.resolution_px_b,ai=this.view.resolution_b_px;if(this.is_overview){an=this.view.max_low;aj=this.view.max_high;ai=(view.max_high-view.max_low)/ag;ar=1/ai}this.before_draw();this.tiles_div.children().addClass("remove");var ae=Math.floor(an/(ai*T)),am=true,aq=[],ak=function(at){return(at&&"track" in at)};while((ae*T*ai)<aj){var ao=this.draw_helper(af,ag,ae,ai,this.tiles_div,ar);if(ak(ao)){aq.push(ao)}else{am=false}ae+=1}if(!ap){this.tiles_div.children(".remove").removeClass("remove").remove()}var ah=this;if(am){this.tiles_div.children(".remove").remove();ah.postdraw_actions(aq,ag,ar,ap)}},postdraw_actions:function(ag,ah,aj,ae){var ai=false;for(var af=0;af<ag.length;af++){if(ag[af].has_icons){ai=true;break}}if(ai){for(var af=0;af<ag.length;af++){tile=ag[af];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}}}},draw_helper:function(ae,aq,aw,au,aj,ak,ar){var ap=this,az=this._gen_tile_cache_key(aq,ak,aw),ah=this._get_tile_bounds(aw,au);if(!ar){ar={}}var ay=(ae?undefined:ap.tile_cache.get_elt(az));if(ay){ap.show_tile(ay,aj,ak);return ay}var an=true;var av=ap.data_manager.get_data(ah,ap.mode,au,ap.data_url_extra_params);if(X(av)){an=false}var al;if(view.reference_track&&ak>view.canvas_manager.char_width_px){al=view.reference_track.data_manager.get_data(ah,ap.mode,au,view.reference_track.data_url_extra_params);if(X(al)){an=false}}if(an){r(av,ar.more_tile_data);var am=ap.mode;if(am==="Auto"){am=ap.get_mode(av);ap.update_auto_mode(am)}var ag=ap.view.canvas_manager.new_canvas(),ax=ah.get("start"),af=ah.get("end"),aq=Math.ceil((af-ax)*ak)+ap.left_offset,ao=ap.get_canvas_height(av,am,ak,aq);ag.width=aq;ag.height=ao;var at=ag.getContext("2d");at.translate(this.left_offset,0);var ay=ap.draw_tile(av,at,am,au,ah,ak,al);if(ay!==undefined){ap.tile_cache.set_elt(az,ay);ap.show_tile(ay,aj,ak)}return ay}var ai=$.Deferred();$.when(av,al).then(function(){view.request_redraw(false,false,false,ap);ai.resolve()});return ai},get_canvas_height:function(ae,ag,ah,af){return this.visible_height_px},draw_tile:function(ae,af,aj,ah,ai,ak,ag){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ag,ai,aj){var af=this,ae=ag.html_elt;ag.predisplay_actions();var ah=(ag.low-(this.is_overview?this.view.max_low:this.view.low))*aj;if(this.left_offset){ah-=this.left_offset}ae.css({position:"absolute",top:0,left:ah});if(ae.hasClass("remove")){ae.removeClass("remove")}else{ai.append(ae)}af.after_show_tile(ag)},after_show_tile:function(ae){this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ae,af){var ah=Math.floor(ae*T*af),ai=Math.ceil(T*af),ag=(ah+ai<=this.view.max_high?ah+ai:this.view.max_high);return new GenomeRegion({chrom:this.view.chrom,start:ah,end:ag})},tool_region_and_parameters_str:function(ag,ae,ah){var af=this,ai=(ag!==undefined&&ae!==undefined&&ah!==undefined?ag+":"+ae+"-"+ah:"all");return" - region=["+ai+"], parameters=["+af.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ae,af){return true},can_subset:function(ae){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ag,ah,aj,ae){var af=this;af.normal_postdraw_actions(ag,ah,aj,ae);af.dataset_check_type="converted_datasets_state";af.data_query_wait=K;var ai=new ServerStateDeferred({url:af.dataset_state_url,url_params:{dataset_id:af.dataset_id,hda_ldda:af.hda_ldda},interval:af.data_query_wait,success_fn:function(ak){return ak!=="pending"}});$.when(ai.go()).then(function(){af.data_manager.set("data_type","data")});af.postdraw_actions=af.normal_postdraw_actions}}});var aa=function(af,ae){var ag={resize:false};i.call(this,af,ae,ag);this.container_div.addClass("label-track")};r(aa.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ag=this.view,ah=ag.high-ag.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ah)/Math.log(10)))),ae=Math.floor(ag.low/ak)*ak,ai=this.view.container.width(),af=$("<div style='position: relative; height: 1.3em;'></div>");while(ae<ag.high){var aj=(ae-ag.low)/ah*ai;af.append($("<div class='label'>"+commatize(ae)+"</div>").css({position:"absolute",left:aj-1}));ae+=ak}this.content_div.children(":first").remove();this.content_div.append(af)}});var h=function(af,ae,ai){M.call(this,af,ae,ai);this.drawables=[];this.left_offset=0;if("drawables" in ai){var ah;for(var ag=0;ag<ai.drawables.length;ag++){ah=ai.drawables[ag];this.drawables[ag]=q(ah,af,null);if(ah.left_offset>this.left_offset){this.left_offset=ah.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};r(h.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ae){$(".bs-tooltip").remove();ae.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ae){M.prototype.change_mode.call(this,ae);for(var af=0;af<this.drawables.length;af++){this.drawables[af].change_mode(ae)}},init:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].init())}var ae=this;$.when.apply($,ag).then(function(){ae.enabled=true;ae.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:s.prototype.can_draw,draw_helper:function(af,av,aB,ay,am,ao,aw){var au=this,aF=this._gen_tile_cache_key(av,ao,aB),aj=this._get_tile_bounds(aB,ay);if(!aw){aw={}}var aE=(af?undefined:au.tile_cache.get_elt(aF));if(aE){au.show_tile(aE,am,ao);return aE}var an=[],au,ar=true,az,ap;for(var aA=0;aA<this.drawables.length;aA++){au=this.drawables[aA];az=au.data_manager.get_data(aj,au.mode,ay,au.data_url_extra_params);if(X(az)){ar=false}an.push(az);ap=null;if(view.reference_track&&ao>view.canvas_manager.char_width_px){ap=view.reference_track.data_manager.get_data(aj,au.mode,ay,view.reference_track.data_url_extra_params);if(X(ap)){ar=false}}an.push(ap)}if(ar){r(az,aw.more_tile_data);this.tile_predraw_init();var ai=au.view.canvas_manager.new_canvas(),ak=au._get_tile_bounds(aB,ay),aC=aj.get("start"),ag=aj.get("end"),aD=0,av=Math.ceil((ag-aC)*ao)+this.left_offset,at=0,ah=[],aA;var ae=0;for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];var aq=au.mode;if(aq==="Auto"){aq=au.get_mode(az);au.update_auto_mode(aq)}ah.push(aq);ae=au.get_canvas_height(az,aq,ao,av);if(ae>at){at=ae}}ai.width=av;ai.height=(aw.height?aw.height:at);aD=0;var ax=ai.getContext("2d");ax.translate(this.left_offset,0);ax.globalAlpha=0.5;ax.globalCompositeOperation="source-over";for(aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];ap=an[aD+1];aE=au.draw_tile(az,ax,ah[aA],ay,aj,ao,ap)}this.tile_cache.set_elt(aF,aE);this.show_tile(aE,am,ao);return aE}var al=$.Deferred(),au=this;$.when.apply($,an).then(function(){view.request_redraw(false,false,false,au);al.resolve()});return al},show_group:function(){var ah=new P(this.view,this.container,{name:this.name}),ae;for(var ag=0;ag<this.drawables.length;ag++){ae=this.drawables[ag];ae.update_icons();ah.add_drawable(ae);ae.container=ah;ah.content_div.append(ae.container_div)}var af=this.container.replace_drawable(this,ah,true);ah.request_draw()},tile_predraw_init:function(){var ah=Number.MAX_VALUE,ae=-ah,af;for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];if(af instanceof j){if(af.prefs.min_value<ah){ah=af.prefs.min_value}if(af.prefs.max_value>ae){ae=af.prefs.max_value}}}for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];af.prefs.min_value=ah;af.prefs.max_value=ae}},postdraw_actions:function(ag,aj,al,af){M.prototype.postdraw_actions.call(this,ag,aj,al,af);var ai=-1;for(var ah=0;ah<ag.length;ah++){var ae=ag[ah].html_elt.find("canvas").height();if(ae>ai){ai=ae}}for(var ah=0;ah<ag.length;ah++){var ak=ag[ah];if(ak.html_elt.find("canvas").height()!==ai){this.draw_helper(true,aj,ak.index,ak.resolution,ak.html_elt.parent(),al,{height:ai});ak.html_elt.remove()}}}});var B=function(ae){M.call(this,ae,{content_div:ae.top_labeltrack},{resize:false});ae.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};r(B.prototype,s.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:s.prototype.can_draw,draw_helper:function(ai,ag,ae,af,aj,ak,ah){if(ak>this.view.canvas_manager.char_width_px){return M.prototype.draw_helper.call(this,ai,ag,ae,af,aj,ak,ah)}else{this.hide_contents();return null}},draw_tile:function(am,an,ai,ah,ak,ao){var ag=this;if(ao>this.view.canvas_manager.char_width_px){if(am.data===null){this.hide_contents();return}var af=an.canvas;an.font=an.canvas.manager.default_font;an.textAlign="center";am=am.data;for(var aj=0,al=am.length;aj<al;aj++){var ae=Math.floor(aj*ao);an.fillText(am[aj],ae,10)}this.show_contents();return new b(ag,ak,ah,af,am)}this.hide_contents()}});var j=function(ag,af,ah){var ae=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:Q()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};r(j.prototype,s.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ae=this;ae.vertical_range=undefined;return $.getJSON(ae.dataset.url(),{data_type:"data",stats:true,chrom:ae.view.chrom,low:0,high:ae.view.max_high,hda_ldda:ae.hda_ldda,dataset_id:ae.dataset_id},function(af){ae.container_div.addClass("line-track");var ai=af.data;if(isNaN(parseFloat(ae.prefs.min_value))||isNaN(parseFloat(ae.prefs.max_value))){var ag=ai.min,ak=ai.max;ag=Math.floor(Math.min(0,Math.max(ag,ai.mean-2*ai.sd)));ak=Math.ceil(Math.max(0,Math.min(ak,ai.mean+2*ai.sd)));ae.prefs.min_value=ag;ae.prefs.max_value=ak;$("#track_"+ae.dataset_id+"_minval").val(ae.prefs.min_value);$("#track_"+ae.dataset_id+"_maxval").val(ae.prefs.max_value)}ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.total_frequency=ai.total_frequency;ae.container_div.find(".yaxislabel").remove();var aj=$("<div/>").text(Y(ae.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_min_value(al)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ae.dataset_id+"_minval").prependTo(ae.container_div),ah=$("<div/>").text(Y(ae.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(al){$(".bs-tooltip").remove();var al=parseFloat(al);if(!isNaN(al)){ae.set_max_value(al)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ae.dataset_id+"_maxval").prependTo(ae.container_div)})},draw_tile:function(an,al,ag,af,ai,am){var ae=al.canvas,ah=ai.get("start"),ak=ai.get("end"),aj=new L.LinePainter(an.data,ah,ak,this.prefs,ag);aj.draw(al,ae.width,ae.height,am);return new b(this,ai,af,ae,an.data)},can_subset:function(ae){return false}});var u=function(ag,af,ah){var ae=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ag,af,ah);this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ah.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.set_min_value(ae.prefs.min_value);ae.set_max_value(ae.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};r(u.prototype,s.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ae){this.prefs.min_value=ae;this.tile_cache.clear();this.request_draw()},set_max_value:function(ae){this.prefs.max_value=ae;this.tile_cache.clear();this.request_draw()},draw_tile:function(ao,am,aj,ah,af,an){var ag=am.canvas,ae=this._get_tile_bounds(af,ah),ai=ae[0],al=ae[1],ak=new L.DiagonalHeatmapPainter(ao.data,ai,al,this.prefs,aj);ak.draw(am,ag.width,ag.height,an);return new b(this,af,ah,ag,ao.data)}});var d=function(ah,ag,aj){var af=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,ah,ag,aj);var ai=Q(),ae=Q([ai,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:aj.prefs,onchange:function(){af.set_name(af.prefs.name);af.tile_cache.clear();af.set_painter_from_config();af.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=aj.hda_ldda;this.dataset_id=aj.dataset_id;this.original_dataset_id=aj.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};r(d.prototype,s.prototype,M.prototype,{set_dataset:function(ae){this.dataset_id=ae.get("id");this.hda_ldda=ae.get("hda_ldda");this.dataset=ae;this.data_manager.set("dataset",ae)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(au,ao,aj,ai){M.prototype.postdraw_actions.call(this,au,ai);var an=this,aq;if(an.mode==="Coverage"){var af=-1;for(aq=0;aq<au.length;aq++){var ap=au[aq].max_val;if(ap>af){af=ap}}for(aq=0;aq<au.length;aq++){var aw=au[aq];if(aw.max_val!==af){aw.html_elt.remove();an.draw_helper(true,ao,aw.index,aw.resolution,aw.html_elt.parent(),aj,{more_tile_data:{max:af}})}}}if(an.filters_manager){var ak=an.filters_manager.filters;for(var at=0;at<ak.length;at++){ak[at].update_ui_elt()}var av=false,ae,al;for(aq=0;aq<au.length;aq++){if(au[aq].data.length){ae=au[aq].data[0];for(var at=0;at<ak.length;at++){al=ak[at];if(al.applies_to(ae)&&al.min!==al.max){av=true;break}}}}if(an.filters_available!==av){an.filters_available=av;if(!an.filters_available){an.filters_manager.hide()}an.update_icons()}}this.container_div.find(".yaxislabel").remove();var ah=au[0];if(ah instanceof k){var am=(this.prefs.histogram_max?this.prefs.histogram_max:ah.max_val),ag=$("<div/>").text(am).make_text_editable({num_cols:12,on_finish:function(ax){$(".bs-tooltip").remove();var ax=parseFloat(ax);an.prefs.histogram_max=(!isNaN(ax)?ax:null);an.tile_cache.clear();an.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ag)}if(ah instanceof O){var ar=true;for(aq=0;aq<au.length;aq++){if(!au[aq].all_slotted){ar=false;break}}if(!ar){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ae){var ae;if(this.mode==="Auto"){if(ae==="no_detail"){ae="feature spans"}else{if(ae==="summary_tree"){ae="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ae+")")}},incremental_slots:function(ai,ae,ah){var af=this.view.canvas_manager.dummy_context,ag=this.slotters[ai];if(!ag||(ag.mode!==ah)){ag=new (v.FeatureSlotter)(ai,ah,A,function(aj){return af.measureText(aj)});this.slotters[ai]=ag}return ag.slot_features(ae)},get_mode:function(ae){if(ae.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ae.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ae,ai,aj,af){if(ai==="summary_tree"||ai==="Coverage"){return this.summary_draw_height}else{var ah=this.incremental_slots(aj,ae.data,ai);var ag=new (this.painter)(null,null,null,this.prefs,ai);return Math.max(ac,ag.get_required_height(ah,af))}},draw_tile:function(ao,at,aq,au,ah,al,ag){var ar=this,af=at.canvas,aA=ah.get("start"),ae=ah.get("end"),ai=this.left_offset;if(aq==="summary_tree"||aq==="Coverage"){var aC=new L.SummaryTreePainter(ao,aA,ae,this.prefs);aC.draw(at,af.width,af.height,al);return new k(ar,ah,au,af,ao.data,ao.max)}var ak=[],ap=this.slotters[al].slots;all_slotted=true;if(ao.data){var am=this.filters_manager.filters;for(var av=0,ax=ao.data.length;av<ax;av++){var aj=ao.data[av];var aw=false;var an;for(var az=0,aE=am.length;az<aE;az++){an=am[az];an.update_attrs(aj);if(!an.keep(aj)){aw=true;break}}if(!aw){ak.push(aj);if(!(aj[0] in ap)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null);var aC=new (this.painter)(ak,aA,ae,this.prefs,aq,aD,aB,ag);var ay=null;at.fillStyle=this.prefs.block_color;at.font=at.canvas.manager.default_font;at.textAlign="right";if(ao.data){ay=aC.draw(at,af.width,af.height,al,ap);ay.translation=-ai}return new O(ar,ah,au,af,ao.data,al,aq,ao.message,all_slotted,ay)},data_and_mode_compatible:function(ae,af){if(af==="Auto"){return true}else{if(af==="Coverage"){return ae.dataset_type==="summary_tree"}else{if(ae.extra_info==="no_detail"||ae.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ae){if(ae.dataset_type==="summary_tree"||ae.message||ae.extra_info==="no_detail"){return false}return true}});var S=function(af,ae,ag){d.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:Q()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};r(S.prototype,s.prototype,M.prototype,d.prototype);var V=function(ag,af,ai){d.call(this,ag,af,ai);var ah=Q(),ae=Q([ah,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ae},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{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:ai.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};r(V.prototype,s.prototype,M.prototype,d.prototype);var e={LineTrack:j,FeatureTrack:d,VcfTrack:S,ReadTrack:V,CompositeTrack:h,DrawableGroup:P};var q=function(ag,af,ae){if("copy" in ag){return ag.copy(ae)}else{var ah=ag.obj_type;if(!ah){ah=ag.track_type}return new e[ah](af,ae,ag)}};return{View:ab,DrawableGroup:P,LineTrack:j,FeatureTrack:d,DiagonalHeatmapTrack:u,ReadTrack:V,VcfTrack:S,CompositeTrack:h,object_from_template:q}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters"],function(ae,y,m,v,M){var r=ae.extend;var R=m.get_random_color;var Y=function(af){return("isResolved" in af)};var o={};var l=function(af,ag){o[af.attr("id")]=ag};var n=function(af,ah,aj,ai){aj=".group";var ag={};o[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this),aw=$(this).parent(),an=aw.children(),ap=o[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=o[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=o[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}o[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){am=$(an.get(ao));if(at.offsetY<am.position().top&&!(am.hasClass("reference-track")||am.hasClass("intro"))){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);o[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));o[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};exports.moveable=n;var ad=16,H=9,E=20,B=100,J=12000,U=400,L=5000,x=100,p="There was an error in indexing this dataset. ",K="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",F="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",a="Loading data...",X="Ready for display",S=10,I=20;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var s=function(ag,af,ai){if(!s.id_counter){s.id_counter=0}this.id=s.id_counter++;this.name=ai.name;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ai.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ai.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(aj){aj.stopPropagation()});var ah=this;this.container_div.hover(function(){ah.icons_div.show()},function(){ah.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};s.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(af){if(af.content_visible){af.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");af.hide_contents();af.content_visible=false}else{af.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");af.content_visible=true;af.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ag){var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ah);show_modal("Configure",ag.config.build_form(),{Cancel:ai,OK:af})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(af){$(".bs-tooltip").remove();af.remove()}}];r(s.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var af=this.view;this.container_div.hide(0,function(){$(this).remove();af.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ag,al,ak,aj,af,ai){var ah=this;this.action_icons[ag]=$("<a/>").attr("href","javascript:void(0);").attr("title",al).addClass("icon-button").addClass(ak).tooltip().click(function(){aj(ah)}).appendTo(this.icons_div);if(ai){this.action_icons[ag].hide()}},build_action_icons:function(af){var ah;for(var ag=0;ag<af.length;ag++){ah=af[ag];this.add_action_icon(ah.name,ah.title,ah.css_class,ah.on_click_fn,ah.prepend,ah.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var A=function(ag,af,ah){s.call(this,ag,af,ah);this.obj_type=ah.obj_type;this.drawables=[]};r(A.prototype,s.prototype,{unpack_drawables:function(ah){this.drawables=[];var ag;for(var af=0;af<ah.length;af++){ag=q(ah[af],this.view,this);this.add_drawable(ag)}},init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_dict:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this;this.changed()},add_drawable_before:function(ah,af){this.changed();var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables.splice(ag,0,ah);return true}return false},replace_drawable:function(ah,af,ag){var ai=this.drawables.indexOf(ah);if(ai!==-1){this.drawables[ai]=af;if(ag){ah.container_div.replaceWith(af.container_div)}this.changed()}return ai},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!==-1){this.drawables.splice(af,1);ag.container=null;this.changed();return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!==-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var Q=function(ag,af,ai){r(ai,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});A.call(this,ag,af,ai);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);n(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new aa(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ai){this.unpack_drawables(ai.drawables)}if("filters" in ai){var ah=this.filters_manager;this.filters_manager=new aa(this,ai.filters);ah.parent_div.replaceWith(this.filters_manager.parent_div);if(ai.filters.visible){this.setup_multitrack_filtering()}}};r(Q.prototype,s.prototype,A.prototype,{action_icons_def:[s.prototype.action_icons_def[0],s.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(af){$(".bs-tooltip").remove();af.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){if(af.filters_manager.visible()){af.filters_manager.clear_filters();af._restore_filter_managers()}else{af.setup_multitrack_filtering();af.request_draw(true)}af.filters_manager.toggle()}},s.prototype.action_icons_def[2]],build_container_div:function(){var af=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(af)}return af},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ah=this.drawables.length;if(ah===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ah===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ao,an,al,ar=true,aj=this.drawables[0].get_type(),af=0;for(ao=0;ao<ah;ao++){al=this.drawables[ao];if(al.get_type()!==aj){can_composite=false;break}if(al instanceof d){af++}}if(ar||af===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(af>1&&af===this.drawables.length){var at={},ag;al=this.drawables[0];for(an=0;an<al.filters_manager.filters.length;an++){ag=al.filters_manager.filters[an];at[ag.name]=[ag]}for(ao=1;ao<this.drawables.length;ao++){al=this.drawables[ao];for(an=0;an<al.filters_manager.filters.length;an++){ag=al.filters_manager.filters[an];if(ag.name in at){at[ag.name].push(ag)}}}this.filters_manager.remove_all();var ai,ak,am,ap;for(var aq in at){ai=at[aq];if(ai.length===af){ak=new V({name:ai[0].name,index:ai[0].index});this.filters_manager.add_filter(ak)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].filters_manager=this.saved_filters_managers[af]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var af=0;af<this.drawables.length;af++){drawable=this.drawables[af];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var aj=[];for(var ag=0;ag<this.drawables.length;ag++){aj.push(this.drawables[ag].name)}var ah="Composite Track of "+this.drawables.length+" tracks ("+aj.join(", ")+")";var ai=new h(this.view,this.view,{name:ah,drawables:this.drawables});var af=this.container.replace_drawable(this,ai,true);ai.request_draw()},add_drawable:function(af){A.prototype.add_drawable.call(this,af);this.update_icons()},remove_drawable:function(af){A.prototype.remove_drawable.call(this,af);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var af=r(A.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return af},request_draw:function(af,ah){for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].request_draw(af,ah)}}});var ac=function(af){r(af,{obj_type:"View"});A.call(this,"View",af.container,af);this.chrom=null;this.vis_id=af.vis_id;this.dbkey=af.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new CanvasManager(this.container.get(0).ownerDocument);this.reset()};ae.extend(ac.prototype,Backbone.Events);r(ac.prototype,A.prototype,{init:function(){this.requested_redraw=false;var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_datasets(add_datasets_url,add_track_async_url,function(aj){ae.each(aj,function(ak){af.add_drawable(q(ak,af,af))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus();af.nav_input.autocomplete({source:function(al,aj){var am=[],ak=$.map(af.get_drawables(),function(an){return an.data_manager.search_features(al.term).success(function(ao){am=am.concat(ao)})});$.when.apply($,ak).done(function(){aj($.map(am,function(an){return{label:an[0],value:an[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX)-af.container.offset().left,width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){af.resize_window()},500)});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ag,ai,af,aj){if(this.timer){clearTimeout(this.timer)}if(aj){var ah=this;this.timer=setTimeout(function(){ah.trigger("navigate",ag+":"+ai+"-"+af)},500)}else{view.trigger("navigate",ag+":"+ai+"-"+af)}},update_location:function(af,ah){this.location_span.text(commatize(af)+" - "+commatize(ah));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ah));var ag=view.chrom_select.val();if(ag!==""){this.trigger_navigate(ag,view.low,view.high,true)}},load_chroms:function(ah){ah.num=x;var af=this,ag=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){return}if(aj.reference){af.add_label_track(new C(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+x+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+x+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){var ah=this;if(!ah.chrom_data){ah.load_chroms_deferred.then(function(){ah.change_chrom(ak,ag,am)});return}if(!ak||ak==="None"){return}if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-x});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+x});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}if(ah.reference_track){ah.reference_track.init()}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}else{ah.low=0;ah.high=ah.max_high}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ai){var af=this;var ah=af.high-af.low;if(af.low-ai<af.max_low){af.low=af.max_low;af.high=af.max_low+ah}else{if(af.high-ai>af.max_high){af.high=af.max_high;af.low=af.max_high-ah}else{af.high-=ai;af.low-=ai}}af.request_redraw();var ag=af.chrom_select.val();this.trigger_navigate(ag,af.low,af.high,true)},add_drawable:function(af){A.prototype.add_drawable.call(this,af);af.init();this.changed();this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){A.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ao){var al=this,ak=(ao?[ao]:al.drawables),ah;var ag;for(var aj=0;aj<ak.length;aj++){ag=ak[aj];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[aj][1]=af;al.tracks_to_be_redrawn[aj][2]=am}}if(!this.requested_redraw){requestAnimationFrame(function(){al._redraw(an)});this.requested_redraw=true}},_redraw:function(ap){this.requested_redraw=false;var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};af.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var t=function(ah,am,ai){this.track=ah;this.name=am.name;this.params=[];var au=am.params;for(var aj=0;aj<au.length;aj++){var ao=au[aj],ag=ao.name,at=ao.label,ak=unescape(ao.html),av=ao.value,aq=ao.type;if(aq==="number"){this.params.push(new f(ag,at,ak,(ag in ai?ai[ag]:av),ao.min,ao.max))}else{if(aq==="select"){this.params.push(new O(ag,at,ak,(ag in ai?ai[ag]:av)))}else{console.log("WARNING: unrecognized tool parameter type:",ag,aq)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ax){ax.stopPropagation()}).click(function(ax){ax.stopPropagation()}).bind("dblclick",function(ax){ax.stopPropagation()});var ar=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ap=this.params;var an=this;$.each(this.params,function(ay,aB){var aA=$("<div>").addClass("param-row").appendTo(an.parent_div);var ax=$("<div>").addClass("param-label").text(aB.label).appendTo(aA);var az=$("<div/>").addClass("param-input").html(aB.html).appendTo(aA);az.find(":input").val(aB.value);$("<div style='clear: both;'/>").appendTo(aA)});this.parent_div.find("input").click(function(){$(this).select()});var aw=$("<div>").addClass("param-row").appendTo(this.parent_div);var al=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(aw);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(aw);af.click(function(){an.run_on_region()});al.click(function(){an.run_on_dataset()});if("visible" in ai&&ai.visible){this.parent_div.show()}};r(t.prototype,{update_params:function(){for(var af=0;af<this.params.length;af++){this.params[af].update_value()}},state_dict:function(){var ag={};for(var af=0;af<this.params.length;af++){ag[this.params[af].name]=this.params[af].value}ag.visible=this.parent_div.is(":visible");return ag},get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=ah});return af},get_param_values:function(){var af=[];this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();if(ag){af[af.length]=ah}});return af},run_on_dataset:function(){var af=this;af.run({target_dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[{chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}]},ak=this.track,ah=ag.tool_id+ak.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(ak.container===view){var aj=new Q(view,view,{name:this.name});var ai=ak.container.replace_drawable(ak,aj,false);aj.container_div.insertBefore(ak.view.content_div.children()[ai]);aj.add_drawable(ak);ak.container_div.appendTo(aj.content_div);af=aj}else{af=ak.container}var al=new ak.constructor(view,af,{name:ah,hda_ldda:"hda"});al.init_for_tool_data();al.change_mode(ak.mode);al.set_filters_manager(ak.filters_manager.copy(al));al.update_icons();af.add_drawable(al);al.tiles_div.text("Starting job.");this.update_params();this.run(ag,al,function(am){al.set_dataset(new Dataset(am));al.tiles_div.text("Running job.");al.init()})},run:function(af,ah,ai){af.inputs=this.get_param_values_dict();var ag=new ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(af),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(aj){return aj!=="pending"}});$.when(ag.go()).then(function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(z+aj.message)}else{ai(aj)}}})}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=$(ah);this.value=ai};r(O.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};r(f.prototype,O.prototype,{update_value:function(){O.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(af){this.manager=null;this.name=af.name;this.index=af.index;this.tool_id=af.tool_id;this.tool_exp_name=af.tool_exp_name};r(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var c=function(ah,ag,af){return $("<a/>").attr("href","javascript:void(0);").attr("title",ah).addClass("icon-button").addClass(ag).tooltip().click(af)};var V=function(an){g.call(this,an);this.low=("low" in an?an.low:-Number.MAX_VALUE);this.high=("high" in an?an.high:Number.MAX_VALUE);this.min=("min" in an?an.min:Number.MAX_VALUE);this.max=("max" in an?an.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var aj=function(ao,ap,aq){ao.click(function(){var aw=ap.text(),au=parseFloat(aq.slider("option","max")),at=(au<=1?4:au<=1000000?au.toString().length:6),av=false,ar=$(this).parents(".slider-row");ar.addClass("input");if(aq.slider("option","values")){at=2*at+1;av=true}ap.text("");$("<input type='text'/>").attr("size",at).attr("maxlength",at).attr("value",aw).appendTo(ap).focus().select().click(function(ax){ax.stopPropagation()}).blur(function(){$(this).remove();ap.text(aw);ar.removeClass("input")}).keyup(function(aB){if(aB.keyCode===27){$(this).trigger("blur")}else{if(aB.keyCode===13){var az=aq.slider("option","min"),ax=aq.slider("option","max"),aA=function(aC){return(isNaN(aC)||aC>ax||aC<az)},ay=$(this).val();if(!av){ay=parseFloat(ay);if(aA(ay)){alert("Parameter value must be in the range ["+az+"-"+ax+"]");return $(this)}}else{ay=ay.split("-");ay=[parseFloat(ay[0]),parseFloat(ay[1])];if(aA(ay[0])||aA(ay[1])){alert("Parameter value must be in the range ["+az+"-"+ax+"]");return $(this)}}aq.slider((av?"values":"value"),ay);ar.removeClass("input")}}})})};var ag=this;ag.parent_div=$("<div/>").addClass("filter-row slider-row");var af=$("<div/>").addClass("elt-label").appendTo(ag.parent_div),al=$("<span/>").addClass("slider-name").text(ag.name+" ").appendTo(af),ah=$("<span/>").text(this.low+"-"+this.high),ai=$("<span/>").addClass("slider-value").appendTo(af).append("[").append(ah).append("]");ag.values_span=ah;var ak=$("<div/>").addClass("slider").appendTo(ag.parent_div);ag.control_element=$("<div/>").attr("id",ag.name+"-filter-control").appendTo(ak);ag.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(ao,ap){ag.slide(ao,ap)},change:function(ao,ap){ag.control_element.slider("option","slide").call(ag.control_element,ao,ap)}});ag.slider=ag.control_element;ag.slider_label=ah;aj(ai,ah,ag.control_element);var am=$("<div/>").addClass("display-controls").appendTo(ag.parent_div);this.transparency_icon=c("Use filter for data transparency","layer-transparent",function(){if(ag.manager.alpha_filter!==ag){ag.manager.alpha_filter=ag;ag.manager.parent_div.find(".layer-transparent").removeClass("active").hide();ag.transparency_icon.addClass("active").show()}else{ag.manager.alpha_filter=null;ag.transparency_icon.removeClass("active")}ag.manager.track.request_draw(true,true)}).appendTo(am).hide();this.height_icon=c("Use filter for data height","arrow-resize-090",function(){if(ag.manager.height_filter!==ag){ag.manager.height_filter=ag;ag.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ag.height_icon.addClass("active").show()}else{ag.manager.height_filter=null;ag.height_icon.removeClass("active")}ag.manager.track.request_draw(true,true)}).appendTo(am).hide();ag.parent_div.hover(function(){ag.transparency_icon.show();ag.height_icon.show()},function(){if(ag.manager.alpha_filter!==ag){ag.transparency_icon.hide()}if(ag.manager.height_filter!==ag){ag.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(ag.parent_div)};r(V.prototype,{to_dict:function(){var af=g.prototype.to_dict.call(this);return r(af,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new V({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ah,af){var ag=af-ah;return(ag<=2?0.01:1)},slide:function(ah,ai){var ag=ai.values;this.values_span.text(ag[0]+"-"+ag[1]);this.low=ag[0];this.high=ag[1];var af=this;setTimeout(function(){if(ag[0]===af.low&&ag[1]===af.high){af.manager.track.request_draw(true,true)}},25)},applies_to:function(af){if(af.length>this.index){return true}return false},_keep_val:function(af){return(isNaN(af)||(af>=this.low&&af<=this.high))},keep:function(ag){if(!this.applies_to(ag)){return true}var ai=this;var aj=ag[this.index];if(aj instanceof Array){var ah=true;for(var af=0;af<aj.length;af++){if(!this._keep_val(aj[af])){ah=false;break}}return ah}else{return this._keep_val(ag[this.index])}},update_attrs:function(ai){var af=false;if(!this.applies_to(ai)){return af}var ag=ai[this.index];if(!(ag instanceof Array)){ag=[ag]}for(var ah=0;ah<ag.length;ah++){var aj=ag[ah];if(aj<this.min){this.min=Math.floor(aj);af=true}if(aj>this.max){this.max=Math.ceil(aj);af=true}}return af},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(ah,an){this.track=ah;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(ap){ap.stopPropagation()}).click(function(ap){ap.stopPropagation()}).bind("dblclick",function(ap){ap.stopPropagation()}).bind("keydown",function(ap){ap.stopPropagation()});if(an&&"filters" in an){var af=("alpha_filter" in an?an.alpha_filter:null),ai=("height_filter" in an?an.height_filter:null),ak=an.filters,ag;for(var al=0;al<ak.length;al++){if(ak[al].type==="number"){ag=new V(ak[al]);this.add_filter(ag);if(ag.name===af){this.alpha_filter=ag;ag.transparency_icon.addClass("active").show()}if(ag.name===ai){this.height_filter=ag;ag.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in an&&an.visible){this.parent_div.show()}}if(this.filters.length!==0){var ao=$("<div/>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ao);var aj=this;am.click(function(){aj.run_on_dataset()})}};r(aa.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var ai={},ah=[],ag;for(var af=0;af<this.filters.length;af++){ag=this.filters[af];ah.push(ag.to_dict())}ai.filters=ah;ai.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);ai.height_filter=(this.height_filter?this.height_filter.name:null);ai.visible=this.parent_div.is(":visible");return ai},copy:function(ag){var ah=new aa(ag);for(var af=0;af<this.filters.length;af++){ah.add_filter(this.filters[af].copy())}return ah},add_filter:function(af){af.manager=this;this.parent_div.append(af.parent_div);this.filters.push(af)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var af=0;af<this.filters.length;af++){var ag=this.filters[af];ag.update_ui_elt()}},clear_filters:function(){for(var af=0;af<this.filters.length;af++){var ag=this.filters[af];ag.slider.slider("option","values",[ag.min,ag.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var al=function(ap,an,ao){if(!(an in ap)){ap[an]=ao}return ap[an]};var ak={},am,af;for(var aj=0;aj<this.filters.length;aj++){am=this.filters[aj];if(am.tool_id){if(am.min!==am.low){af=al(ak,am.tool_id,[]);af[af.length]=am.tool_exp_name+" >= "+am.low}if(am.max!==am.high){af=al(ak,am.tool_id,[]);af[af.length]=am.tool_exp_name+" <= "+am.high}}}var ag=[];for(var ai in ak){ag[ag.length]=[ai,ak[ai]]}(function ah(au,aq){var ao=aq[0],ap=ao[0],at=ao[1],ar="("+at.join(") and (")+")",an={cond:ar,input:au,target_dataset_id:au,tool_id:ap},aq=aq.slice(1);$.getJSON(run_tool_url,an,function(av){if(av.error){show_modal("Filter Dataset","Error running tool "+ap,{Close:hide_modal})}else{if(aq.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(av.dataset_id,aq)}}})})(this.track.dataset_id,ag)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};r(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(an,aj){for(var ar=0;ar<an.length;ar++){ah=an[ar];if(ah.hidden){continue}var al="param_"+ar;var aw=ai.values[ah.key];var ay=$("<div class='form-row' />").appendTo(aj);ay.append($("<label />").attr("for",al).text(ah.label+":"));if(ah.type==="bool"){ay.append($('<input type="checkbox" />').attr("id",al).attr("name",al).attr("checked",aw))}else{if(ah.type==="text"){ay.append($('<input type="text"/>').attr("id",al).val(aw).click(function(){$(this).select()}))}else{if(ah.type==="select"){var au=$("<select />").attr("id",al);for(var ap=0;ap<ah.options.length;ap++){$("<option/>").text(ah.options[ap].label).attr("value",ah.options[ap].value).appendTo(au)}au.val(aw);ay.append(au)}else{if(ah.type==="color"){var ax=$("<div/>").appendTo(ay),at=$("<input />").attr("id",al).attr("name",al).val(aw).css("float","left").appendTo(ax).click(function(aA){$(".bs-tooltip").removeClass("in");var az=$(this).siblings(".bs-tooltip").addClass("in");az.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(az).height()/2)+($(this).height()/2)}).show();az.click(function(aB){aB.stopPropagation()});$(document).bind("click.color-picker",function(){az.hide();$(document).unbind("click.color-picker")});aA.stopPropagation()}),aq=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(ax).attr("title","Set new random color").tooltip(),av=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(ax).hide(),am=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(av),ak=$("<div class='tooltip-arrow'></div>").appendTo(av),ao=$.farbtastic(am,{width:100,height:100,callback:at,color:aw});ax.append($("<div/>").css("clear","both"));(function(az){aq.click(function(){az.setColor(R())})})(ao)}else{ay.append($("<input />").attr("id",al).attr("name",al).val(aw))}}}}if(ah.help){ay.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange();this.track.changed()}}});var b=function(af,aj,ah,ag,ai){this.track=af;this.region=aj;this.low=aj.get("start");this.high=aj.get("end");this.resolution=ah;this.html_elt=$("<div class='track-tile'/>").append(ag).height($(ag).attr("height"));this.data=ai;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ak,ah,ag,ai,aj){b.call(this,af,ak,ah,ag,ai);this.max_val=aj};r(k.prototype,b.prototype);var P=function(ai,aq,aj,ah,al,at,am,au,ag,ap){b.call(this,ai,aq,aj,ah,al);this.mode=am;this.all_slotted=ag;this.feature_mapper=ap;this.has_icons=false;if(au){this.has_icons=true;var an=this;ah=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:E-1,width:ah.width}).prependTo(this.html_elt);var ao=new GenomeRegion({chrom:ai.view.chrom,start:this.low,end:this.high}),ar=al.length,ak=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ak.click(function(){an.stale=true;ai.data_manager.get_more_data(ao,ai.mode,an.resolution,{},ai.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();ai.request_draw(true)}).dblclick(function(av){av.stopPropagation()});af.click(function(){an.stale=true;ai.data_manager.get_more_data(ao,ai.mode,an.resolution,{},ai.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();ai.request_draw(true)}).dblclick(function(av){av.stopPropagation()})}};r(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)==="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(this).parents(".track-content").children(".overlay"));var aj=aq+parseInt(ag.html_elt.css("left"))-ai.width()/2,ah=ap+parseInt(ag.html_elt.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var i=function(ag,af,ah){r(ah,{drag_handle_class:"draghandle"});s.call(this,ag,af,ah);this.dataset=new Dataset({id:ah.dataset_id,hda_ldda:ah.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ah?ah.data_query_wait:L);this.data_manager=("data_manager" in ah?ah.data_manager:new y.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ah)||ah.resize){this.add_resize_handle()}}};r(i.prototype,s.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},s.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(af){af.view.set_overview(af)}},s.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){if(af.filters_manager.visible()){af.filters_manager.clear_filters()}else{af.filters_manager.init_filters()}af.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(af){af.dynamic_tool_div.toggle();if(af.dynamic_tool_div.is(":visible")){af.set_name(af.name+af.tool_region_and_parameters_str())}else{af.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(af){var ai='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ah=ae.template(ai,{track:af});var ak=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(){var am=$('select[name="regions"] option:selected').val(),ao,al=new GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),an=ae.map($(".bookmark"),function(ap){return new GenomeRegion({from_str:$(ap).children(".position").text()})});if(am==="cur"){ao=[al]}else{if(am==="bookmarks"){ao=an}else{ao=[al].concat(an)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:af.dataset_id,hda_ldda:af.hda_ldda,regions:JSON.stringify(new Backbone.Collection(ao).toJSON())})},aj=function(al){if((al.keyCode||al.which)===27){ak()}else{if((al.keyCode||al.which)===13){ag()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ah,{No:ak,Yes:ag})}},s.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&s.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},on_resize:function(){},add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.tiles_div).css("height",aj);af.visible_height_px=(af.max_height_px===aj?0:aj);af.on_resize()}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.visible_height_px;af.changed()}).appendTo(af.container_div)},set_display_modes:function(ai,al){this.display_modes=ai;this.mode=(al?al:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ag=this,aj={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var ak=ag.display_modes[ah];aj[ak]=function(am){return function(){ag.change_mode(am);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(ak)}make_popupmenu(this.action_icons.mode_icon,aj)},build_action_icons:function(){s.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof T){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ag=this;ag.enabled=false;ag.tile_cache.clear();ag.data_manager.clear();ag.content_div.css("height","auto");ag.tiles_div.children().remove();ag.container_div.removeClass("nodata error pending");if(!ag.dataset_id){return}var af=$.Deferred(),ah={hda_ldda:ag.hda_ldda,data_type:this.dataset_check_type,chrom:ag.view.chrom};$.getJSON(this.dataset.url(),ah,function(ai){if(!ai||ai==="error"||ai.kind==="error"){ag.container_div.addClass("error");ag.tiles_div.text(p);if(ai.message){var aj=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ai.message+"</pre>",{Close:hide_modal})});ag.tiles_div.append(aj)}}else{if(ai==="no converter"){ag.container_div.addClass("error");ag.tiles_div.text(K)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ag.container_div.addClass("nodata");ag.tiles_div.text(F)}else{if(ai==="pending"){ag.container_div.addClass("pending");ag.tiles_div.html(w);setTimeout(function(){ag.init()},ag.data_query_wait)}else{if(ai==="data"||ai.status==="data"){if(ai.valid_chroms){ag.valid_chroms=ai.valid_chroms;ag.update_icons()}ag.tiles_div.text(X);if(ag.view.chrom){ag.tiles_div.text("");ag.tiles_div.css("height",ag.visible_height_px+"px");ag.enabled=true;$.when(ag.predraw_init()).done(function(){af.resolve();ag.container_div.removeClass("nodata error pending");ag.request_draw()})}else{af.resolve()}}}}}}});this.update_icons();return af},predraw_init:function(){},get_drawables:function(){return this}});var N=function(ah,ag,ai){i.call(this,ah,ag,ai);var af=this;n(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,("filters" in ai?ai.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in ai&&ai.tool?new t(this,ai.tool,ai.tool_state):null);this.tile_cache=new y.Cache(S);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ai.mode){this.change_mode(ai.mode)}};r(N.prototype,s.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(af){$(".bs-tooltip").remove();af.slotters[af.view.resolution_px_b].max_rows*=2;af.request_draw(true)},hide:true}]),copy:function(af){var ag=this.to_dict();r(ag,{data_manager:this.data_manager});var ah=new this.constructor(this.view,af,ag);ah.change_mode(this.mode);ah.enabled=this.enabled;return ah},set_filters_manager:function(af){this.filters_manager=af;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available){af.action_icons.filters_icon.show()}else{af.action_icons.filters_icon.hide()}if(af.tool){af.action_icons.tools_icon.show();af.action_icons.param_space_viz_icon.show()}else{af.action_icons.tools_icon.hide();af.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},before_draw:function(){},_draw:function(ag,aq){if(!this.can_draw()){return}var ao=this.view.low,ak=this.view.high,am=ak-ao,ah=this.view.container.width(),at=this.view.resolution_px_b,aj=this.view.resolution_b_px;if(this.is_overview){ao=this.view.max_low;ak=this.view.max_high;aj=(view.max_high-view.max_low)/ah;at=1/aj}this.before_draw();this.tiles_div.children().addClass("remove");var af=Math.floor(ao/(aj*U)),an=true,ar=[],al=function(au){return(au&&"track" in au)};while((af*U*aj)<ak){var ap=this.draw_helper(ag,ah,af,aj,this.tiles_div,at);if(al(ap)){ar.push(ap)}else{an=false}af+=1}if(!aq){this.tiles_div.children(".remove").removeClass("remove").remove()}var ai=this;if(an){this.tiles_div.children(".remove").remove();ai.postdraw_actions(ar,ah,at,aq)}},postdraw_actions:function(ah,ai,ak,af){var aj=false;for(var ag=0;ag<ah.length;ag++){if(ah[ag].has_icons){aj=true;break}}if(aj){for(var ag=0;ag<ah.length;ag++){tile=ah[ag];if(!tile.has_icons){tile.html_elt.css("padding-top",E)}}}},draw_helper:function(af,ar,ax,av,ak,al,at){var aq=this,aA=this._gen_tile_cache_key(ar,al,ax),ai=this._get_tile_bounds(ax,av);if(!at){at={}}var az=(af?undefined:aq.tile_cache.get_elt(aA));if(az){aq.show_tile(az,ak,al);return az}var ao=true;var aw=aq.data_manager.get_data(ai,aq.mode,av,aq.data_url_extra_params);if(Y(aw)){ao=false}var am;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ai,aq.mode,av,view.reference_track.data_url_extra_params);if(Y(am)){ao=false}}if(ao){r(aw,at.more_tile_data);var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}var ah=aq.view.canvas_manager.new_canvas(),ay=ai.get("start"),ag=ai.get("end"),ar=Math.ceil((ag-ay)*al)+aq.left_offset,ap=aq.get_canvas_height(aw,an,al,ar);ah.width=ar;ah.height=ap;var au=ah.getContext("2d");au.translate(this.left_offset,0);var az=aq.draw_tile(aw,au,an,av,ai,al,am);if(az!==undefined){aq.tile_cache.set_elt(aA,az);aq.show_tile(az,ak,al)}return az}var aj=$.Deferred();$.when(aw,am).then(function(){view.request_redraw(false,false,false,aq);aj.resolve()});return aj},get_canvas_height:function(af,ah,ai,ag){return this.visible_height_px},draw_tile:function(af,ag,ak,ai,aj,al,ah){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ah,aj,ak){var ag=this,af=ah.html_elt;ah.predisplay_actions();var ai=(ah.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}af.css({position:"absolute",top:0,left:ai});if(af.hasClass("remove")){af.removeClass("remove")}else{aj.append(af)}ag.after_show_tile(ah)},after_show_tile:function(af){this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},_get_tile_bounds:function(af,ag){var ai=Math.floor(af*U*ag),aj=Math.ceil(U*ag),ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return new GenomeRegion({chrom:this.view.chrom,start:ai,end:ah})},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(af,ag){return true},can_subset:function(af){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ah,ai,ak,af){var ag=this;ag.normal_postdraw_actions(ah,ai,ak,af);ag.dataset_check_type="converted_datasets_state";ag.data_query_wait=L;var aj=new ServerStateDeferred({url:ag.dataset_state_url,url_params:{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},interval:ag.data_query_wait,success_fn:function(al){return al!=="pending"}});$.when(aj.go()).then(function(){ag.data_manager.set("data_type","data")});ag.postdraw_actions=ag.normal_postdraw_actions}}});var ab=function(ag,af){var ah={resize:false};i.call(this,ag,af,ah);this.container_div.addClass("label-track")};r(ab.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var h=function(ag,af,aj){N.call(this,ag,af,aj);this.drawables=[];this.left_offset=0;if("drawables" in aj){var ai;for(var ah=0;ah<aj.drawables.length;ah++){ai=aj.drawables[ah];this.drawables[ah]=q(ai,ag,null);if(ai.left_offset>this.left_offset){this.left_offset=ai.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};r(h.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(af){$(".bs-tooltip").remove();af.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(af){N.prototype.change_mode.call(this,af);for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].change_mode(af)}},init:function(){var ah=[];for(var ag=0;ag<this.drawables.length;ag++){ah.push(this.drawables[ag].init())}var af=this;$.when.apply($,ah).then(function(){af.enabled=true;af.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:s.prototype.can_draw,draw_helper:function(ag,aw,aC,az,an,ap,ax){var av=this,aG=this._gen_tile_cache_key(aw,ap,aC),ak=this._get_tile_bounds(aC,az);if(!ax){ax={}}var aF=(ag?undefined:av.tile_cache.get_elt(aG));if(aF){av.show_tile(aF,an,ap);return aF}var ao=[],av,at=true,aA,aq;for(var aB=0;aB<this.drawables.length;aB++){av=this.drawables[aB];aA=av.data_manager.get_data(ak,av.mode,az,av.data_url_extra_params);if(Y(aA)){at=false}ao.push(aA);aq=null;if(view.reference_track&&ap>view.canvas_manager.char_width_px){aq=view.reference_track.data_manager.get_data(ak,av.mode,az,view.reference_track.data_url_extra_params);if(Y(aq)){at=false}}ao.push(aq)}if(at){r(aA,ax.more_tile_data);this.tile_predraw_init();var aj=av.view.canvas_manager.new_canvas(),al=av._get_tile_bounds(aC,az),aD=ak.get("start"),ah=ak.get("end"),aE=0,aw=Math.ceil((ah-aD)*ap)+this.left_offset,au=0,ai=[],aB;var af=0;for(aB=0;aB<this.drawables.length;aB++,aE+=2){av=this.drawables[aB];aA=ao[aE];var ar=av.mode;if(ar==="Auto"){ar=av.get_mode(aA);av.update_auto_mode(ar)}ai.push(ar);af=av.get_canvas_height(aA,ar,ap,aw);if(af>au){au=af}}aj.width=aw;aj.height=(ax.height?ax.height:au);aE=0;var ay=aj.getContext("2d");ay.translate(this.left_offset,0);ay.globalAlpha=0.5;ay.globalCompositeOperation="source-over";for(aB=0;aB<this.drawables.length;aB++,aE+=2){av=this.drawables[aB];aA=ao[aE];aq=ao[aE+1];aF=av.draw_tile(aA,ay,ai[aB],az,ak,ap,aq)}this.tile_cache.set_elt(aG,aF);this.show_tile(aF,an,ap);return aF}var am=$.Deferred(),av=this;$.when.apply($,ao).then(function(){view.request_redraw(false,false,false,av);am.resolve()});return am},show_group:function(){var ai=new Q(this.view,this.container,{name:this.name}),af;for(var ah=0;ah<this.drawables.length;ah++){af=this.drawables[ah];af.update_icons();ai.add_drawable(af);af.container=ai;ai.content_div.append(af.container_div)}var ag=this.container.replace_drawable(this,ai,true);ai.request_draw()},tile_predraw_init:function(){var ai=Number.MAX_VALUE,af=-ai,ag;for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];if(ag instanceof j){if(ag.prefs.min_value<ai){ai=ag.prefs.min_value}if(ag.prefs.max_value>af){af=ag.prefs.max_value}}}for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];ag.prefs.min_value=ai;ag.prefs.max_value=af}},postdraw_actions:function(ah,ak,am,ag){N.prototype.postdraw_actions.call(this,ah,ak,am,ag);var aj=-1;for(var ai=0;ai<ah.length;ai++){var af=ah[ai].html_elt.find("canvas").height();if(af>aj){aj=af}}for(var ai=0;ai<ah.length;ai++){var al=ah[ai];if(al.html_elt.find("canvas").height()!==aj){this.draw_helper(true,ak,al.index,al.resolution,al.html_elt.parent(),am,{height:aj});al.html_elt.remove()}}}});var C=function(af){N.call(this,af,{content_div:af.top_labeltrack},{resize:false});af.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};r(C.prototype,s.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:s.prototype.can_draw,draw_helper:function(aj,ah,af,ag,ak,al,ai){if(al>this.view.canvas_manager.char_width_px){return N.prototype.draw_helper.call(this,aj,ah,af,ag,ak,al,ai)}else{this.hide_contents();return null}},draw_tile:function(an,ao,aj,ai,al,ap){var ah=this;if(ap>this.view.canvas_manager.char_width_px){if(an.data===null){this.hide_contents();return}var ag=ao.canvas;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";an=an.data;for(var ak=0,am=an.length;ak<am;ak++){var af=Math.floor(ak*ap);ao.fillText(an[ak],af,10)}this.show_contents();return new b(ah,al,ai,ag,an)}this.hide_contents()}});var j=function(ah,ag,ai){var af=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ah,ag,ai);this.hda_ldda=ai.hda_ldda;this.dataset_id=ai.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:R()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ai.prefs,onchange:function(){af.set_name(af.prefs.name);af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.set_min_value(af.prefs.min_value);af.set_max_value(af.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};r(j.prototype,s.prototype,N.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(af){this.prefs.min_value=af;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(af){this.prefs.max_value=af;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.dataset.url(),{data_type:"data",stats:true,chrom:af.view.chrom,low:0,high:af.view.max_high,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min,al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div/>").text(Z(af.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(am){$(".bs-tooltip").remove();var am=parseFloat(am);if(!isNaN(am)){af.set_min_value(am)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+af.dataset_id+"_minval").prependTo(af.container_div),ai=$("<div/>").text(Z(af.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(am){$(".bs-tooltip").remove();var am=parseFloat(am);if(!isNaN(am)){af.set_max_value(am)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+af.dataset_id+"_maxval").prependTo(af.container_div)})},draw_tile:function(ao,am,ah,ag,aj,an){var af=am.canvas,ai=aj.get("start"),al=aj.get("end"),ak=new M.LinePainter(ao.data,ai,al,this.prefs,ah);ak.draw(am,af.width,af.height,an);return new b(this,aj,ag,af,ao.data)},can_subset:function(af){return false}});var u=function(ah,ag,ai){var af=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,ah,ag,ai);this.hda_ldda=ai.hda_ldda;this.dataset_id=ai.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"4169E1"},{key:"negative_color",label:"Negative Color",type:"color",default_value:"FF8C00"},{key:"min_value",label:"Min Value",type:"float",default_value:0},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ai.prefs,onchange:function(){af.set_name(af.prefs.name);af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.set_min_value(af.prefs.min_value);af.set_max_value(af.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};r(u.prototype,s.prototype,N.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(af){this.prefs.min_value=af;this.tile_cache.clear();this.request_draw()},set_max_value:function(af){this.prefs.max_value=af;this.tile_cache.clear();this.request_draw()},draw_tile:function(ap,an,ak,ai,ag,ao){var ah=an.canvas,af=this._get_tile_bounds(ag,ai),aj=af[0],am=af[1],al=new M.DiagonalHeatmapPainter(ap.data,aj,am,this.prefs,ak);al.draw(an,ah.width,ah.height,ao);return new b(this,ag,ai,ah,ap.data)}});var d=function(ai,ah,ak){var ag=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ai,ah,ak);var aj=R(),af=R([aj,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:aj},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:af},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ak.prefs,onchange:function(){ag.set_name(ag.prefs.name);ag.tile_cache.clear();ag.set_painter_from_config();ag.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ak.hda_ldda;this.dataset_id=ak.dataset_id;this.original_dataset_id=ak.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};r(d.prototype,s.prototype,N.prototype,{set_dataset:function(af){this.dataset_id=af.get("id");this.hda_ldda=af.get("hda_ldda");this.dataset=af;this.data_manager.set("dataset",af)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=M.ArcLinkedFeaturePainter}else{this.painter=M.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(av,ap,ak,aj){N.prototype.postdraw_actions.call(this,av,aj);var ao=this,ar;if(ao.mode==="Coverage"){var ag=-1;for(ar=0;ar<av.length;ar++){var aq=av[ar].max_val;if(aq>ag){ag=aq}}for(ar=0;ar<av.length;ar++){var ax=av[ar];if(ax.max_val!==ag){ax.html_elt.remove();ao.draw_helper(true,ap,ax.index,ax.resolution,ax.html_elt.parent(),ak,{more_tile_data:{max:ag}})}}}if(ao.filters_manager){var al=ao.filters_manager.filters;for(var au=0;au<al.length;au++){al[au].update_ui_elt()}var aw=false,af,am;for(ar=0;ar<av.length;ar++){if(av[ar].data.length){af=av[ar].data[0];for(var au=0;au<al.length;au++){am=al[au];if(am.applies_to(af)&&am.min!==am.max){aw=true;break}}}}if(ao.filters_available!==aw){ao.filters_available=aw;if(!ao.filters_available){ao.filters_manager.hide()}ao.update_icons()}}this.container_div.find(".yaxislabel").remove();var ai=av[0];if(ai instanceof k){var an=(this.prefs.histogram_max?this.prefs.histogram_max:ai.max_val),ah=$("<div/>").text(an).make_text_editable({num_cols:12,on_finish:function(ay){$(".bs-tooltip").remove();var ay=parseFloat(ay);ao.prefs.histogram_max=(!isNaN(ay)?ay:null);ao.tile_cache.clear();ao.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ah)}if(ai instanceof P){var at=true;for(ar=0;ar<av.length;ar++){if(!av[ar].all_slotted){at=false;break}}if(!at){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(af){var af;if(this.mode==="Auto"){if(af==="no_detail"){af="feature spans"}else{if(af==="summary_tree"){af="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,af,ai){var ag=this.view.canvas_manager.dummy_context,ah=this.slotters[aj];if(!ah||(ah.mode!==ai)){ah=new (v.FeatureSlotter)(aj,ai,B,function(ak){return ag.measureText(ak)});this.slotters[aj]=ah}return ah.slot_features(af)},get_mode:function(af){if(af.dataset_type==="summary_tree"){mode="summary_tree"}else{if(af.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>J){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(af,aj,ak,ag){if(aj==="summary_tree"||aj==="Coverage"){return this.summary_draw_height}else{var ai=this.incremental_slots(ak,af.data,aj);var ah=new (this.painter)(null,null,null,this.prefs,aj);return Math.max(ad,ah.get_required_height(ai,ag))}},draw_tile:function(ap,au,ar,av,ai,am,ah){var at=this,ag=au.canvas,aB=ai.get("start"),af=ai.get("end"),aj=this.left_offset;if(ar==="summary_tree"||ar==="Coverage"){var aD=new M.SummaryTreePainter(ap,aB,af,this.prefs);aD.draw(au,ag.width,ag.height,am);return new k(at,ai,av,ag,ap.data,ap.max)}var al=[],aq=this.slotters[am].slots;all_slotted=true;if(ap.data){var an=this.filters_manager.filters;for(var aw=0,ay=ap.data.length;aw<ay;aw++){var ak=ap.data[aw];var ax=false;var ao;for(var aA=0,aF=an.length;aA<aF;aA++){ao=an[aA];ao.update_attrs(ak);if(!ao.keep(ak)){ax=true;break}}if(!ax){al.push(ak);if(!(ak[0] in aq)){all_slotted=false}}}}var aE=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aC=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aD=new (this.painter)(al,aB,af,this.prefs,ar,aE,aC,ah);var az=null;au.fillStyle=this.prefs.block_color;au.font=au.canvas.manager.default_font;au.textAlign="right";if(ap.data){az=aD.draw(au,ag.width,ag.height,am,aq);az.translation=-aj}return new P(at,ai,av,ag,ap.data,am,ar,ap.message,all_slotted,az)},data_and_mode_compatible:function(af,ag){if(ag==="Auto"){return true}else{if(ag==="Coverage"){return af.dataset_type==="summary_tree"}else{if(af.extra_info==="no_detail"||af.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(af){if(af.dataset_type==="summary_tree"||af.message||af.extra_info==="no_detail"){return false}return true}});var T=function(ag,af,ah){d.call(this,ag,af,ah);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:R()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};r(T.prototype,s.prototype,N.prototype,d.prototype);var W=function(ah,ag,aj){d.call(this,ah,ag,aj);var ai=R(),af=R([ai,"#ffffff"]);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:af},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{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:aj.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_icons()};r(W.prototype,s.prototype,N.prototype,d.prototype);var e={LineTrack:j,FeatureTrack:d,VcfTrack:T,ReadTrack:W,CompositeTrack:h,DrawableGroup:Q};var q=function(ah,ag,af){if("copy" in ah){return ah.copy(af)}else{var ai=ah.obj_type;if(!ai){ai=ah.track_type}return new e[ai](ag,af,ah)}};return{View:ac,DrawableGroup:Q,LineTrack:j,FeatureTrack:d,DiagonalHeatmapTrack:u,ReadTrack:W,VcfTrack:T,CompositeTrack:h,object_from_template:q}}); \ No newline at end of file diff -r 3f12146d6d81e08f662ada2011a6973e4230512d -r 0cf3b64e80777c45425a57f4f69d806df839fcf4 static/scripts/packed/viz/trackster_ui.js --- a/static/scripts/packed/viz/trackster_ui.js +++ b/static/scripts/packed/viz/trackster_ui.js @@ -1,1 +1,1 @@ -define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks"],function(f,c,g,d,b){var a=b.object_from_template;var e=f.Base.extend({initialize:function(h){this.baseURL=h},createButtonMenu:function(){var h=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){add_datasets(add_datasets_url,add_track_async_url,function(j){c.each(j,function(k){view.add_drawable(trackster_ui.object_from_template(k,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new b.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){parent.force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location="${h.url_for( controller='visualization', action='circster' )}?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){show_modal("Saving...","progress");var j=[];$(".bookmark").each(function(){j.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var k=(view.overview_drawable?view.overview_drawable.name:null),l={id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",datasets:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:k},bookmarks:j};$.ajax({url:galaxy_paths.get("visualization_url"),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(l)}}).success(function(m){hide_modal();view.vis_id=m.vis_id;view.has_changes=false;window.history.pushState({},"",m.url+window.location.hash)}).error(function(){show_modal("Could Not Save","Could not save visualization. Please try again later.",{Close:hide_modal})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location="${h.url_for( controller='visualization', action='list' )}"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=h;return h},add_bookmarks:function(){var h=this.baseURL;show_modal("Select dataset for new bookmarks","progress");$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(j){show_modal("Select dataset for new bookmarks",j,{Cancel:function(){hide_modal()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var k,l=$(this).val();if($(this).attr("name")==="id"){k={hda_id:l}}else{k={ldda_id:l}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:k,dataType:"json",}).then(function(m){for(i=0;i<m.data.length;i++){var n=m.data[i];add_bookmark(n[0],n[1])}})});hide_modal()}})}})},add_bookmark:function(m,k,h){var o=$("#bookmarks-container"),q=$("<div/>").addClass("bookmark").appendTo(o);var r=$("<div/>").addClass("position").appendTo(q),n=$("<a href=''/>").text(m).appendTo(r).click(function(){view.go_to(m);return false}),l=$("<div/>").text(k).appendTo(q);if(h){var p=$("<div/>").addClass("delete-icon-container").prependTo(q).click(function(){q.slideUp("fast");q.remove();view.has_changes=true;return false}),j=$("<a href=''/>").addClass("icon-button delete").appendTo(p);l.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return q},create_visualization:function(l,h,k,m,j){view=new b.View(l);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(h){var v=h.chrom,n=h.start,s=h.end,p=h.overview;if(v&&(n!==undefined)&&s){view.change_chrom(v,n,s)}}if(k){var q,o,r;for(var t=0;t<k.length;t++){view.add_drawable(a(k[t],view,view))}}view.update_intro_div();var w;for(var t=0;t<view.drawables.length;t++){if(view.drawables[t].name===p){view.set_overview(view.drawables[t]);break}}if(m){var u;for(var t=0;t<m.length;t++){u=m[t];add_bookmark(u.position,u.annotation,j)}}view.has_changes=false});return view},init_keyboard_nav:function(h){$(document).keydown(function(j){if($(j.srcElement).is(":input")){return}switch(j.which){case 37:h.move_fraction(0.25);break;case 38:var k=Math.round(h.viewport_container.height()/15);h.viewport_container.scrollTop(h.viewport_container.scrollTop()-20);break;case 39:h.move_fraction(-0.25);break;case 40:var k=Math.round(h.viewport_container.height()/15);h.viewport_container.scrollTop(h.viewport_container.scrollTop()+20);break}})}});return{object_from_template:a,TracksterUI:e}}); \ No newline at end of file +define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks"],function(f,c,g,d,b){var a=b.object_from_template;var e=f.Base.extend({initialize:function(h){this.baseURL=h},createButtonMenu:function(){var h=this,j=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){add_datasets(add_datasets_url,add_track_async_url,function(k){c.each(k,function(l){view.add_drawable(trackster_ui.object_from_template(l,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new b.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){parent.force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=h.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){show_modal("Saving...","progress");var k=[];$(".bookmark").each(function(){k.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var l=(view.overview_drawable?view.overview_drawable.name:null),m={id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",datasets:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:l},bookmarks:k};$.ajax({url:galaxy_paths.get("visualization_url"),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(m)}}).success(function(n){hide_modal();view.vis_id=n.vis_id;view.has_changes=false;window.history.pushState({},"",n.url+window.location.hash)}).error(function(){show_modal("Could Not Save","Could not save visualization. Please try again later.",{Close:hide_modal})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=h.baseURL+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=j;return j},add_bookmarks:function(){var h=this.baseURL;show_modal("Select dataset for new bookmarks","progress");$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(j){show_modal("Select dataset for new bookmarks",j,{Cancel:function(){hide_modal()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var k,l=$(this).val();if($(this).attr("name")==="id"){k={hda_id:l}}else{k={ldda_id:l}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:k,dataType:"json"}).then(function(m){for(i=0;i<m.data.length;i++){var n=m.data[i];add_bookmark(n[0],n[1])}})});hide_modal()}})}})},add_bookmark:function(m,k,h){var o=$("#bookmarks-container"),q=$("<div/>").addClass("bookmark").appendTo(o);var r=$("<div/>").addClass("position").appendTo(q),n=$("<a href=''/>").text(m).appendTo(r).click(function(){view.go_to(m);return false}),l=$("<div/>").text(k).appendTo(q);if(h){var p=$("<div/>").addClass("delete-icon-container").prependTo(q).click(function(){q.slideUp("fast");q.remove();view.has_changes=true;return false}),j=$("<a href=''/>").addClass("icon-button delete").appendTo(p);l.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return q},create_visualization:function(l,h,k,m,j){view=new b.View(l);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(h){var v=h.chrom,n=h.start,s=h.end,p=h.overview;if(v&&(n!==undefined)&&s){view.change_chrom(v,n,s)}}if(k){var q,o,r;for(var t=0;t<k.length;t++){view.add_drawable(a(k[t],view,view))}}view.update_intro_div();var w;for(var t=0;t<view.drawables.length;t++){if(view.drawables[t].name===p){view.set_overview(view.drawables[t]);break}}if(m){var u;for(var t=0;t<m.length;t++){u=m[t];add_bookmark(u.position,u.annotation,j)}}view.has_changes=false});return view},init_keyboard_nav:function(h){$(document).keydown(function(j){if($(j.srcElement).is(":input")){return}switch(j.which){case 37:h.move_fraction(0.25);break;case 38:var k=Math.round(h.viewport_container.height()/15);h.viewport_container.scrollTop(h.viewport_container.scrollTop()-20);break;case 39:h.move_fraction(-0.25);break;case 40:var k=Math.round(h.viewport_container.height()/15);h.viewport_container.scrollTop(h.viewport_container.scrollTop()+20);break}})}});return{object_from_template:a,TracksterUI:e}}); \ No newline at end of file diff -r 3f12146d6d81e08f662ada2011a6973e4230512d -r 0cf3b64e80777c45425a57f4f69d806df839fcf4 static/scripts/viz/sweepster.js --- a/static/scripts/viz/sweepster.js +++ b/static/scripts/viz/sweepster.js @@ -3,6 +3,8 @@ * genomic visualization. */ +define( ["libs/d3", "viz/trackster/util", "viz/visualization", "viz/trackster/tracks"], function( d3, util, visualization, tracks ) { + /** * A collection of tool input settings. Object is useful for keeping a list of settings * for future use without changing the input's value and for preserving inputs order. @@ -259,7 +261,7 @@ { type: Backbone.HasMany, key: 'regions', - relatedModel: 'GenomeRegion' + relatedModel: visualization.GenomeRegion } ], @@ -270,7 +272,7 @@ data_url: galaxy_paths.get('raw_data_url'), converted_datasets_state_url: galaxy_paths.get('dataset_state_url') }, options.track); - this.set('track', object_from_template(track_config, {}, null)); + this.set('track', tracks.object_from_template(track_config, {}, null)); } }, @@ -302,8 +304,8 @@ /** * Sweepster visualization model. */ -var SweepsterVisualization = Visualization.extend({ - defaults: _.extend({}, Visualization.prototype.defaults, { +var SweepsterVisualization = visualization.Visualization.extend({ + defaults: _.extend({}, visualization.Visualization.prototype.defaults, { dataset: null, tool: null, parameter_tree: null, @@ -316,22 +318,22 @@ { type: Backbone.HasOne, key: 'dataset', - relatedModel: 'Dataset' + relatedModel: Dataset }, { type: Backbone.HasOne, key: 'tool', - relatedModel: 'Tool' + relatedModel: Tool }, { type: Backbone.HasMany, key: 'regions', - relatedModel: 'GenomeRegion' + relatedModel: visualization.GenomeRegion }, { type: Backbone.HasMany, key: 'tracks', - relatedModel: 'SweepsterTrack' + relatedModel: SweepsterTrack } // NOTE: cannot use relationship for parameter tree because creating tree is complex. ], @@ -690,7 +692,7 @@ '</ol></div>', initialize: function(options) { - this.canvas_manager = new CanvasManager(this.$el.parents('body')); + this.canvas_manager = new visualization.CanvasManager(this.$el.parents('body')); this.tool_param_tree_view = new ToolParameterTreeView({ model: this.model.get('parameter_tree') }); this.track_collection_container = $('<table/>').addClass('tracks'); @@ -704,8 +706,8 @@ }); // Set block, reverse strand block colors; these colors will be used for all tracks. - this.block_color = get_random_color(); - this.reverse_strand_color = get_random_color( [ this.block_color, "#ffffff" ] ); + this.block_color = util.get_random_color(); + this.reverse_strand_color = util.get_random_color( [ this.block_color, "#ffffff" ] ); }, render: function() { @@ -901,7 +903,7 @@ if (!run_jobs) { return; } // Create and add tracks for each settings group. - var tracks = _.map(all_settings, function(settings) { + var new_tracks = _.map(all_settings, function(settings) { var pm_track = new SweepsterTrack({ settings: settings, regions: regions, @@ -912,7 +914,7 @@ }); // For each track, run tool using track's settings and update track. - _.each(tracks, function(pm_track, index) { + _.each(new_tracks, function(pm_track, index) { setTimeout(function() { // Set inputs and run tool. // console.log('running with settings', pm_track.get('settings')); @@ -923,7 +925,7 @@ data_url: galaxy_paths.get('raw_data_url'), converted_datasets_state_url: galaxy_paths.get('dataset_state_url') }, output.first().get('track_config')), - track_obj = object_from_template(track_config, self, null); + track_obj = tracks.object_from_template(track_config, self, null); // Track uses only raw data. track_obj.data_manager.set('data_type', 'raw_data'); @@ -939,4 +941,11 @@ }); }); } +}); + +return { + SweepsterVisualization: SweepsterVisualization, + SweepsterVisualizationView: SweepsterVisualizationView +}; + }); \ No newline at end of file diff -r 3f12146d6d81e08f662ada2011a6973e4230512d -r 0cf3b64e80777c45425a57f4f69d806df839fcf4 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1,4 +1,4 @@ -define( ["libs/underscore", "viz/trackster/util", "viz/trackster/slotting", "viz/trackster/painters" ], function( _, util, slotting, painters ) { +define( ["libs/underscore", "viz/visualization", "viz/trackster/util", "viz/trackster/slotting", "viz/trackster/painters" ], function( _, visualization, util, slotting, painters ) { var extend = _.extend; var get_random_color = util.get_random_color; @@ -2827,7 +2827,7 @@ // A little ugly creating data manager right now due to transition to Backbone-based objects. this.data_manager = ('data_manager' in obj_dict ? obj_dict.data_manager : - new GenomeDataManager({ + new visualization.GenomeDataManager({ dataset: this.dataset, data_mode_compatible: this.data_and_mode_compatible, can_subset: this.can_subset @@ -3228,7 +3228,7 @@ this.data_manager.set('filters_manager', this.filters_manager); this.filters_available = false; this.tool = ('tool' in obj_dict && obj_dict.tool ? new Tool(this, obj_dict.tool, obj_dict.tool_state) : null); - this.tile_cache = new Cache(TILE_CACHE_SIZE); + this.tile_cache = new visualization.Cache(TILE_CACHE_SIZE); if (this.header_div) { // diff -r 3f12146d6d81e08f662ada2011a6973e4230512d -r 0cf3b64e80777c45425a57f4f69d806df839fcf4 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -232,8 +232,8 @@ visualizations = data.get_visualizations() ## HACK: if there are visualizations, only provide trackster for now since others ## are not ready. - #if visualizations: - # visualizations = [ 'trackster' ] + if visualizations: + visualizations = [ 'trackster' ] %> %if visualizations: <a href="${h.url_for( controller='visualization' )}" diff -r 3f12146d6d81e08f662ada2011a6973e4230512d -r 0cf3b64e80777c45425a57f4f69d806df839fcf4 templates/visualization/sweepster.mako --- a/templates/visualization/sweepster.mako +++ b/templates/visualization/sweepster.mako @@ -107,18 +107,30 @@ ${parent.javascripts()} ${h.templates( "tool_link", "panel_section", "tool_search", "tool_form" )} - ${h.js( "libs/d3", "mvc/data", "mvc/tools", "viz/visualization", "viz/sweepster", - "viz/trackster", "viz/trackster_ui", "libs/jquery/jquery-ui-1.8.23.custom.min" )} + ${h.js( "libs/require", "libs/jquery/jquery-ui-1.8.23.custom.min" )} + ${h.js( "mvc/data", "mvc/tools" )} <script type="text/javascript"> - var viz; - $(function() { - // -- Viz set up. -- - var viz = new SweepsterVisualization( - ${ h.to_json_string( config ).replace('\\', '\\\\' )} - ); - var viz_view = new SweepsterVisualizationView({ model: viz }); - viz_view.render(); + require.config({ + baseUrl: "${h.url_for('/static/scripts')}", + shim: { + "libs/underscore": { exports: "_" }, + "libs/d3": { exports: "d3" }, + "libs/backbone/backbone": { exports: "Backbone" } + } + }); + + require(["libs/d3", "viz/visualization", "viz/sweepster"], function(d3, visualization, sweepster) { + + var viz; + $(function() { + // -- Viz set up. -- + var viz = new sweepster.SweepsterVisualization( + ${ h.to_json_string( config ).replace('\\', '\\\\' )} + ); + var viz_view = new sweepster.SweepsterVisualizationView({ model: viz }); + viz_view.render(); + }); }); </script></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: smcmanus: Fixed call to check_tool_output for TaskWrapper.
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3f12146d6d81/ changeset: 3f12146d6d81 user: smcmanus date: 2012-09-18 20:10:56 summary: Fixed call to check_tool_output for TaskWrapper. affected #: 1 file diff -r 23107188eab8aa8f0c5ed721af30ff13b19bd61c -r 3f12146d6d81e08f662ada2011a6973e4230512d lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1048,7 +1048,7 @@ # Check what the tool returned. If the stdout or stderr matched # regular expressions that indicate errors, then set an error. # The same goes if the tool's exit code was in a given range. - if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): + if ( self.check_tool_output( stdout, stderr, tool_exit_code, task ) ): task.state = task.states.OK else: task.state = task.states.ERROR Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for getting updates for tool shed repositories installed into a local Galaxy instance.
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/23107188eab8/ changeset: 23107188eab8 user: greg date: 2012-09-18 19:54:19 summary: Fix for getting updates for tool shed repositories installed into a local Galaxy instance. affected #: 1 file diff -r 2f655fb9e6a8873f1faff3b0fed4c0288a2e4c2b -r 23107188eab8aa8f0c5ed721af30ff13b19bd61c lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -795,19 +795,25 @@ changeset_hash = str( repo.changectx( changeset ) ) ctx = get_changectx_for_changeset( repo, changeset_hash ) if update_to_changeset_hash: - if get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_hash ): - # We found a RepositoryMetadata record. - if changeset_hash == repository.tip: - # The current ctx is the repository tip, so use it. + if changeset_hash == repository.tip: + update_to_ctx = get_changectx_for_changeset( repo, changeset_hash ) + latest_changeset_revision = changeset_hash + break + else: + repository_metadata = get_repository_metadata_by_changeset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_hash ) + if repository_metadata: + # We found a RepositoryMetadata record. update_to_ctx = get_changectx_for_changeset( repo, changeset_hash ) latest_changeset_revision = changeset_hash + break else: - update_to_ctx = get_changectx_for_changeset( repo, update_to_changeset_hash ) - latest_changeset_revision = update_to_changeset_hash - break - elif not update_to_changeset_hash and changeset_hash == changeset_revision: - # We've found the changeset in the changelog for which we need to get the next update. - update_to_changeset_hash = changeset_hash + update_to_changeset_hash = changeset_hash + else: + if changeset_hash == changeset_revision: + # We've found the changeset in the changelog for which we need to get the next update. + update_to_changeset_hash = changeset_hash if from_update_manager: if latest_changeset_revision == changeset_revision: return no_update Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix bugs in Trackster refactoring.
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2f655fb9e6a8/ changeset: 2f655fb9e6a8 user: jgoecks date: 2012-09-18 19:48:06 summary: Fix bugs in Trackster refactoring. affected #: 1 file diff -r aa1ad2112bb7918987dc31250ac214e45ba75641 -r 2f655fb9e6a8873f1faff3b0fed4c0288a2e4c2b static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ b/static/scripts/viz/trackster_ui.js @@ -12,12 +12,12 @@ this.baseURL = baseURL; }, - /** * Create button menu */ createButtonMenu: function() { - var menu = create_icon_buttons_menu([ + var self = this, + menu = create_icon_buttons_menu([ { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { add_datasets(add_datasets_url, add_track_async_url, function(tracks) { _.each(tracks, function(track) { @@ -36,8 +36,7 @@ icon_class: 'globe', title: 'Circster', on_click: function() { - // Add viz id dynamically so that newly saved visualizations work as well. - window.location = "${h.url_for( controller='visualization', action='circster' )}?id=" + view.vis_id; + window.location = self.baseURL + 'visualization/circster?id=' + view.vis_id; } }, { icon_class: 'disk--arrow', title: 'Save', on_click: function() { @@ -86,7 +85,7 @@ }); } }, { icon_class: 'cross-circle', title: 'Close', on_click: function() { - window.location = "${h.url_for( controller='visualization', action='list' )}"; + window.location = self.baseURL + "visualization/list"; } } ], { @@ -126,7 +125,7 @@ $.ajax({ url: this.baseURL + "/visualization/bookmarks_from_dataset", data: data, - dataType: "json", + dataType: "json" }).then( function(data) { for( i = 0; i < data.data.length; i++ ) { var row = data.data[i]; @@ -254,7 +253,7 @@ switch(e.which) { case 37: view.move_fraction(0.25); - break + break; case 38: var change = Math.round(view.viewport_container.height()/15.0); view.viewport_container.scrollTop( view.viewport_container.scrollTop() - 20); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Remove dubugging statement from last commit.
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/aa1ad2112bb7/ changeset: aa1ad2112bb7 user: jgoecks date: 2012-09-18 19:14:49 summary: Remove dubugging statement from last commit. affected #: 2 files diff -r aa0469dd0078fd792ff34db8cd8ee36ae0e9c9be -r aa1ad2112bb7918987dc31250ac214e45ba75641 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -313,8 +313,6 @@ if col_type in [ 'int', 'float' ]: num_numerical_cols += 1 - print dataset.name, num_numerical_cols - vizs = super( Tabular, self ).get_visualizations( dataset ) if num_numerical_cols >= 2: vizs.append( 'scatterplot' ) diff -r aa0469dd0078fd792ff34db8cd8ee36ae0e9c9be -r aa1ad2112bb7918987dc31250ac214e45ba75641 templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -232,8 +232,8 @@ visualizations = data.get_visualizations() ## HACK: if there are visualizations, only provide trackster for now since others ## are not ready. - if visualizations: - visualizations = [ 'trackster' ] + #if visualizations: + # visualizations = [ 'trackster' ] %> %if visualizations: <a href="${h.url_for( controller='visualization' )}" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Enhancements for finding available visualizations: (a) use dataset rather than datatype and (b) only show scatterplot for tabular datasets with >=2 numerical columns.
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/aa0469dd0078/ changeset: aa0469dd0078 user: jgoecks date: 2012-09-18 19:10:04 summary: Enhancements for finding available visualizations: (a) use dataset rather than datatype and (b) only show scatterplot for tabular datasets with >=2 numerical columns. affected #: 4 files diff -r 5cdb0038c89d1396755b2c7e371bde63b221b8df -r aa0469dd0078fd792ff34db8cd8ee36ae0e9c9be lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -545,7 +545,7 @@ raise Exception('Result %s from %s' % (result, cmd)) merge = staticmethod(merge) - def get_visualizations( self ): + def get_visualizations( self, dataset ): """ Returns a list of visualizations for datatype. """ diff -r 5cdb0038c89d1396755b2c7e371bde63b221b8df -r aa0469dd0078fd792ff34db8cd8ee36ae0e9c9be lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -301,11 +301,25 @@ def as_ucsc_display_file( self, dataset, **kwd ): return open( dataset.file_name ) - def get_visualizations( self ): + def get_visualizations( self, dataset ): """ Returns a list of visualizations for datatype. """ - return super( Tabular, self ).get_visualizations() + [ 'scatterplot' ] + + # Can visualize tabular data as scatterplot if there are 2+ numerical + # columns. + num_numerical_cols = 0 + for col_type in dataset.metadata.column_types: + if col_type in [ 'int', 'float' ]: + num_numerical_cols += 1 + + print dataset.name, num_numerical_cols + + vizs = super( Tabular, self ).get_visualizations( dataset ) + if num_numerical_cols >= 2: + vizs.append( 'scatterplot' ) + + return vizs class Taxonomy( Tabular ): def __init__(self, **kwd): diff -r 5cdb0038c89d1396755b2c7e371bde63b221b8df -r aa0469dd0078fd792ff34db8cd8ee36ae0e9c9be lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1245,6 +1245,9 @@ def get_display_applications( self, trans ): return self.datatype.get_display_applications_by_dataset( self, trans ) + def get_visualizations( self ): + return self.datatype.get_visualizations( self ) + class HistoryDatasetAssociation( DatasetInstance ): def __init__( self, hid = None, diff -r 5cdb0038c89d1396755b2c7e371bde63b221b8df -r aa0469dd0078fd792ff34db8cd8ee36ae0e9c9be templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -229,7 +229,7 @@ ## Visualization icon + visualizations. Using anchor attributes is a HACK to encode needed ## information--URL base, dataset id, dbkey, visualizations--in anchor. <% - visualizations = data.datatype.get_visualizations() + visualizations = data.get_visualizations() ## HACK: if there are visualizations, only provide trackster for now since others ## are not ready. if visualizations: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: fix to apply tooltips to running/queued datasets in history panel
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5cdb0038c89d/ changeset: 5cdb0038c89d user: carlfeberhard date: 2012-09-18 18:39:13 summary: fix to apply tooltips to running/queued datasets in history panel affected #: 1 file diff -r 069768b7833ebae78f1c7c7aa97904627540ac3a -r 5cdb0038c89d1396755b2c7e371bde63b221b8df templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -116,6 +116,43 @@ }); }; +// ----------------------------------------------------------------------------- +function applyTooltip( elem ){ + // apply twitter bootstrap tooltip to elem + + //!! 2 line tooltips placed above do not render properly + //TODO: hack (github has an issue on this - see how it's resolved) + var $this = $( elem ); + if( $this.hasClass( 'tooltip' ) ){ + + // remove original tooltip + if( $this.attr( 'data-original-title' ) ){ + // documented method - that doesn't seem to work + //$( this ).tooltip( 'destroy' ); + $this.data( 'tooltip', false ); + + // swap title back + var title = $this.attr( 'data-original-title' ); + $this.attr( 'data-original-title', null ); + $this.attr( 'title', title ); + } + + // (re-)apply tooltip + // place them on the bottom for now + $this.tooltip({ placement : 'bottom' }); + } + return this; +} + +function applyTooltips( elem ){ + // apply twitter bootstrap tooltips to this element and all children + $( $( elem ).find( '.tooltip' ).andSelf() ).each( function(){ + applyTooltip( this ); + }); + return this; +} + +// ----------------------------------------------------------------------------- // Create trackster action function. function create_trackster_action_fn(vis_url, dataset_params, dbkey) { return function() { @@ -327,24 +364,7 @@ tag_handling(this); annotation_handling(this); - - //TODO: hack (github has an issue on this - see how it's resolved) - // fix for two line bootstrap tooltips when placement: above - $( this ).find( '.tooltip' ).each( function(){ - var $this = $( this ); - - // documented method - that doesn't seem to work - //$( this ).tooltip( 'destroy' ); - - $this.data( 'tooltip', false ); - var title = $this.attr( 'data-original-title' ); - $this.attr( 'data-original-title', null ); - $this.attr( 'title', title ); - - // place them on the bottom for now - $this.tooltip({ placement : 'bottom' }); - }); - + applyTooltips( this ); }); _.each( $(".visualize-icon"), function(icon) { @@ -469,8 +489,12 @@ var container = $("#historyItemContainer-" + id); container.html( val.html ); init_history_items( $("div.historyItemWrapper"), "noinit" ); + + // apply ui element behaviors tag_handling(container); annotation_handling(container); + applyTooltips( container ); + var viz_icon = container.find(".visualize-icon")[0]; if (viz_icon) { init_viz_icon(viz_icon); } @@ -674,4 +698,4 @@ </div></body> -</html> +</html> \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Add $__user_name__ to job template.
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/069768b7833e/ changeset: 069768b7833e user: natefoo date: 2012-09-18 18:13:02 summary: Add $__user_name__ to job template. affected #: 1 file diff -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a -r 069768b7833ebae78f1c7c7aa97904627540ac3a lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -155,15 +155,18 @@ if special: out_data[ "output_file" ] = FakeDatasetAssociation( dataset=special.dataset ) - # These can be passed on the command line if wanted as $userId $userEmail - if job.history and job.history.user: # check for anonymous user! - userId = '%d' % job.history.user.id - userEmail = str(job.history.user.email) + # These can be passed on the command line if wanted as $__user_*__ + if job.history and job.history.user: + user_id = '%d' % job.history.user.id + user_email = str(job.history.user.email) + user_name = str(job.history.user.username) else: - userId = 'Anonymous' - userEmail = 'Anonymous' - incoming['__user_id__'] = incoming['userId'] = userId - incoming['__user_email__'] = incoming['userEmail'] = userEmail + user_id = 'Anonymous' + user_email = 'Anonymous' + user_name = 'Anonymous' + incoming['__user_id__'] = incoming['userId'] = user_id + incoming['__user_email__'] = incoming['userEmail'] = user_email + incoming['__user_name__'] = user_name # Build params, done before hook so hook can use param_dict = self.tool.build_param_dict( incoming, inp_data, out_data, self.get_output_fnames(), self.working_directory ) # Certain tools require tasks to be completed prior to job execution Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Viz framework: (a) add generic method to datatypes to get available visualizations and (b) attach available visualizations to dataset visualization icon.
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/32091cc60876/ changeset: 32091cc60876 user: jgoecks date: 2012-09-18 17:40:57 summary: Viz framework: (a) add generic method to datatypes to get available visualizations and (b) attach available visualizations to dataset visualization icon. affected #: 5 files diff -r 5359d1066d91849fbf075f95f4999613d17a9c45 -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -545,6 +545,15 @@ raise Exception('Result %s from %s' % (result, cmd)) merge = staticmethod(merge) + def get_visualizations( self ): + """ + Returns a list of visualizations for datatype. + """ + + if hasattr( self, 'get_track_type' ): + return [ 'trackster', 'circster' ] + return [] + class Text( Data ): file_ext = 'txt' line_class = 'line' diff -r 5359d1066d91849fbf075f95f4999613d17a9c45 -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -301,6 +301,12 @@ def as_ucsc_display_file( self, dataset, **kwd ): return open( dataset.file_name ) + def get_visualizations( self ): + """ + Returns a list of visualizations for datatype. + """ + return super( Tabular, self ).get_visualizations() + [ 'scatterplot' ] + class Taxonomy( Tabular ): def __init__(self, **kwd): """Initialize taxonomy datatype""" diff -r 5359d1066d91849fbf075f95f4999613d17a9c45 -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -708,9 +708,12 @@ # Get new dataset if specified. new_dataset = kwargs.get("dataset_id", None) + ''' + FIXME: if new_dataset is not None: if trans.security.decode_id(new_dataset) in [ d["dataset_id"] for d in viz_config.get("tracks") ]: new_dataset = None # Already in browser, so don't add + ''' return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset ) @web.json diff -r 5359d1066d91849fbf075f95f4999613d17a9c45 -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a templates/root/history.mako --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -116,6 +116,95 @@ }); }; +// Create trackster action function. +function create_trackster_action_fn(vis_url, dataset_params, dbkey) { + return function() { + var params = {}; + if (dbkey) { params['dbkey'] = dbkey; } + $.ajax({ + url: vis_url + '/list_tracks?f-' + $.param(params), + dataType: "html", + error: function() { alert( "Could not add this dataset to browser." ); }, + success: function(table_html) { + var parent = window.parent; + + parent.show_modal("View Data in a New or Saved Visualization", "", { + "Cancel": function() { + parent.hide_modal(); + }, + "View in saved visualization": function() { + // Show new modal with saved visualizations. + parent.show_modal("Add Data to Saved Visualization", table_html, { + "Cancel": function() { + parent.hide_modal(); + }, + "Add to visualization": function() { + $(parent.document).find('input[name=id]:checked').each(function() { + var vis_id = $(this).val(); + dataset_params['id'] = vis_id + parent.location = vis_url + "/trackster?" + $.param(dataset_params); + }); + }, + }); + }, + "View in new visualization": function() { + parent.location = vis_url + "/trackster?" + $.param(dataset_params); + } + }); + } + }); + return false; + }; +}; + +/** + * Create popup menu for visualization icon. + */ +function init_viz_icon(icon) { + var icon = $(icon), + vis_url = icon.attr('href'), + dataset_id = icon.attr('dataset_id'), + visualizations = icon.attr('visualizations').split(','), + dbkey = icon.attr('dbkey'), + popup_menu_dict = {}, + + // Create visualization action. + create_viz_action = function(visualization) { + var action; + if (visualization === 'trackster') { + action = create_trackster_action_fn(vis_url, params, dbkey); + } + else { + action = function() { + window.parent.location = vis_url + '/' + visualization + '?' + + $.param(params); + }; + } + return action; + }, + params = {dataset_id: dataset_id}; + + // Add dbkey to params if it exists. + if (dbkey) { params['dbkey'] = dbkey; } + + // Populate menu dict with visualizations. + _.each(visualizations, function(visualization) { + popup_menu_dict[ + visualization.charAt(0).toUpperCase() + visualization.slice(1) + ] = create_viz_action(visualization); + }); + + // Set up action or menu. + if (visualizations.length === 1) { + // No need for popup menu because there's a single visualization. + icon.click(create_viz_action(visualizations[0])); + } + else { + make_popupmenu(icon, popup_menu_dict); + } +}; + + // Update the message for async operations function render_message(message, status) { $("div#message-container").html( "<div class=\"" + status + "message\">" + message + "</div><br/>" ); @@ -258,96 +347,6 @@ }); - // Trackster links - function init_trackster_links() { - // Add to trackster browser functionality - $(".trackster-add").live("click", function() { - var dataset = this, - dataset_jquery = $(this); - $.ajax({ - url: dataset_jquery.attr("data-url"), - dataType: "html", - error: function() { alert( "Could not add this dataset to browser." ); }, - success: function(table_html) { - var parent = window.parent; - - parent.show_modal("View Data in a New or Saved Visualization", "", { - "Cancel": function() { - parent.hide_modal(); - }, - "View in saved visualization": function() { - // Show new modal with saved visualizations. - parent.show_modal("Add Data to Saved Visualization", table_html, { - "Cancel": function() { - parent.hide_modal(); - }, - "Add to visualization": function() { - $(parent.document).find('input[name=id]:checked').each(function() { - var vis_id = $(this).val(); - parent.location = dataset_jquery.attr("action-url") + "&id=" + vis_id; - }); - }, - }); - }, - "View in new visualization": function() { - parent.location = dataset_jquery.attr("new-url"); - } - }); - } - }); - }); - } - - /** - * Create popup menu for visualization icon. - */ - function init_viz_icon(icon) { - var icon_link = $(icon); - make_popupmenu( icon_link , { - "${_("Trackster")}": function() { - $.ajax({ - url: icon_link.attr("data-url"), - dataType: "html", - error: function() { alert( "Could not add this dataset to browser." ); }, - success: function(table_html) { - var parent = window.parent; - - parent.show_modal("View Data in a New or Saved Visualization", "", { - "Cancel": function() { - parent.hide_modal(); - }, - "View in saved visualization": function() { - // Show new modal with saved visualizations. - parent.hide_modal(); - parent.show_modal("Add Data to Saved Visualization", table_html, { - "Cancel": function() { - parent.hide_modal(); - }, - "Add to visualization": function() { - $(parent.document).find('input[name=id]:checked').each(function() { - var vis_id = $(this).val(); - parent.location = icon_link.attr("action-url") + "&id=" + vis_id; - }); - }, - }); - }, - "View in new visualization": function() { - parent.location = icon_link.attr("new-url"); - } - }); - } - }); - }, - //"${_("Scatterplot")}": function() { - // var data_id = icon_link.parents(".historyItemContainer").attr("id").split("-")[1]; - // parent.galaxy_main.location = - // "${h.url_for( controller='visualization', action='scatterplot', col1=9, col2=13 )}" - // + "&dataset_id=" + data_id; - //} - } ); - return icon; - }; - _.each( $(".visualize-icon"), function(icon) { init_viz_icon(icon); }); @@ -472,6 +471,9 @@ init_history_items( $("div.historyItemWrapper"), "noinit" ); tag_handling(container); annotation_handling(container); + var viz_icon = container.find(".visualize-icon")[0]; + if (viz_icon) { init_viz_icon(viz_icon); } + // If new state is terminal, stop tracking if (TERMINAL_STATES.indexOf(val.state) !== -1) { if ( val.force_history_refresh ){ diff -r 5359d1066d91849fbf075f95f4999613d17a9c45 -r 32091cc60876e9720f2ae2b855e9e7f43e8c775a templates/root/history_common.mako --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -226,17 +226,24 @@ %if for_editing: <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title='${_("Run this job again")}' class="icon-button arrow-circle tooltip"></a> - %if data.ext in app.datatypes_registry.get_available_tracks(): - <% - if data.dbkey != '?': - data_url = h.url_for( controller='visualization', action='list_tracks', dbkey=data.dbkey ) - data_url = data_url.replace( 'dbkey', 'f-dbkey' ) - else: - data_url = h.url_for( controller='visualization', action='list_tracks' ) - %> - <a href="javascript:void(0)" data-url="${data_url}" class="icon-button chart_curve tooltip visualize-icon" - action-url="${h.url_for( controller='tracks', action='browser', dataset_id=dataset_id)}" - new-url="${h.url_for( controller='tracks', action='index', dataset_id=dataset_id, default_dbkey=data.dbkey)}" title="Visualize"></a> + ## Visualization icon + visualizations. Using anchor attributes is a HACK to encode needed + ## information--URL base, dataset id, dbkey, visualizations--in anchor. + <% + visualizations = data.datatype.get_visualizations() + ## HACK: if there are visualizations, only provide trackster for now since others + ## are not ready. + if visualizations: + visualizations = [ 'trackster' ] + %> + %if visualizations: + <a href="${h.url_for( controller='visualization' )}" + class="icon-button chart_curve tooltip visualize-icon" + title="Visualize" + dataset_id="${dataset_id}" + %if data.dbkey != '?': + dbkey="${data.dbkey}" + %endif + visualizations="${','.join(visualizations)}"></a> %endif <% isPhylogenyData = isinstance(data.datatype, (Phyloxml, Nexus, Newick)) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Grammar. it's -> its in admin panel (and tests)
by Bitbucket 18 Sep '12

18 Sep '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5359d1066d91/ changeset: 5359d1066d91 user: dannon date: 2012-09-18 15:34:51 summary: Grammar. it's -> its in admin panel (and tests) affected #: 2 files diff -r ba64c2178fbee9a83f79580c434ab280d8a0b738 -r 5359d1066d91849fbf075f95f4999613d17a9c45 templates/webapps/galaxy/admin/center.mako --- a/templates/webapps/galaxy/admin/center.mako +++ b/templates/webapps/galaxy/admin/center.mako @@ -51,7 +51,7 @@ then users that have Role2 will be able to access the library, but will not see those contained datasets whose [dataset] "access" permission is associated with only Role1. <p/> - In addition to the "access library" permission, permission to perform the following functions on the data library (and it's contents) can + In addition to the "access library" permission, permission to perform the following functions on the data library (and its contents) can be granted to users (a library item is one of: a data library, a library folder, a library dataset). <p/><ul> diff -r ba64c2178fbee9a83f79580c434ab280d8a0b738 -r 5359d1066d91849fbf075f95f4999613d17a9c45 test/functional/test_library_security.py --- a/test/functional/test_library_security.py +++ b/test/functional/test_library_security.py @@ -93,7 +93,7 @@ permissions_in = [ k for k, v in galaxy.model.Library.permitted_actions.items() ] permissions_out = [] # Role1 members are: admin_user, regular_user1, regular_user3. Each of these users will be permitted for - # LIBRARY_ACCESS, LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE on library1 and it's contents. + # LIBRARY_ACCESS, LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE on library1 and its contents. self.library_permissions( self.security.encode_id( library1.id ), library1.name, str( role1.id ), @@ -163,7 +163,7 @@ # Logged in as admin_user # # LIBRARY_ACCESS = Role1: admin_user, regular_user1, regular_user3. Each of these users will be permitted for - # LIBRARY_ACCESS, LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE on this library and it's contents. + # LIBRARY_ACCESS, LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE on this library and its contents. # # Legitimate roles displayed on the permission form are as follows: # 'Role1' since the LIBRARY_ACCESS permission is associated with Role1. # Role one members are: admin_user, regular_user1, regular_user3. @@ -239,7 +239,7 @@ # groups: group1 # users: test(a)bx.psu.edu, test1(a)bx.psu.edu via group1 # - # We first need to make library1 public, but leave it's contents permissions unchanged + # We first need to make library1 public, but leave its contents permissions unchanged self.make_library_item_public( self.security.encode_id( library1.id ), self.security.encode_id( library1.id ), item_type='library', @@ -433,7 +433,7 @@ permissions_in = [ k for k, v in galaxy.model.Library.permitted_actions.items() ] permissions_out = [] # Only admin_user will be permitted for - # LIBRARY_ACCESS, LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE on library2 and it's contents. + # LIBRARY_ACCESS, LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE on library2 and its contents. self.library_permissions( self.security.encode_id( library1.id ), library1.name, str( admin_user_private_role.id ), @@ -526,7 +526,7 @@ ldda8 = get_latest_ldda_by_name( filename ) assert ldda8 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda8 from the database' def test_090_make_library2_and_contents_public( self ): - """Testing making library2 and all of it's contents public""" + """Testing making library2 and all of its contents public""" self.make_library_item_public( self.security.encode_id( library2.id ), self.security.encode_id( library2.id ), item_type='library', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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