September 2012 - galaxy-commits - lists.galaxyproject.org

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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