1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/f93ecd917348/ changeset: f93ecd917348 user: jgoecks date: 2012-06-13 18:10:54 summary: Viz framework: (a) JavaScript support for running tools and enhancements to parameter viz. affected #: 5 files

diff -r 7387d416d655e086ad3b792058069ea82ce23a3c -r f93ecd917348aeef6332a6d441300ab505daad73 static/scripts/mvc/data.js --- /dev/null +++ b/static/scripts/mvc/data.js @@ -0,0 +1,16 @@ +/** + * A dataset. In Galaxy, datasets are associated with a history, so + * this object is also known as a HistoryDatasetAssociation. + */ +var Dataset = Backbone.Model.extend({ + defaults: { + id: "", + type: "", + name: "", + hda_ldda: "" + } +}); + +var DatasetCollection = Backbone.Collection.extend({ + model: Dataset +}); \ No newline at end of file

diff -r 7387d416d655e086ad3b792058069ea82ce23a3c -r f93ecd917348aeef6332a6d441300ab505daad73 static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -51,11 +51,78 @@ } ],

- urlRoot: galaxy_paths.attributes.root_path + 'api/tools', + urlRoot: galaxy_paths.get('tool_url'),

apply_search_results: function(results) { ( _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide() ); return this.is_visible(); + }, + + /** + * Set a tool input's value. + */ + set_input_value: function(name, value) { + this.get('inputs').find(function(input) { + return input.get('name') === name; + }).set('value', value); + }, + + /** + * Run tool; returns a Deferred that resolves to the tool's output(s). + */ + run: function() { + return this._run() + }, + + /** + * Rerun tool using regions and a target dataset. + */ + rerun: function(target_dataset, regions) { + return this._run({ + action: 'rerun', + target_dataset_id: target_dataset.id, + regions: JSON.stringify(regions) + }); + }, + + /** + * Run tool; returns a Deferred that resolves to the tool's output(s). + * NOTE: this method is a helper method and should not be called directly. + */ + _run: function(additional_params) { + // Create payload. + var payload = _.extend({ + tool_id: this.id + }, additional_params), + input_dict = {}; + this.get('inputs').each(function(input) { + input_dict[input.get('name')] = input.get('value'); + }); + payload.inputs = input_dict; + + // Because job may require indexing datasets, use server-side + // deferred to ensure that job is run. Also use deferred that + // resolves to outputs from tool. + var run_deferred = $.Deferred(), + ss_deferred = new ServerStateDeferred({ + ajax_settings: { + url: this.urlRoot, + data: JSON.stringify(payload), + dataType: "json", + contentType: 'application/json', + type: "POST" + }, + interval: 2000, + success_fn: function(response) { + return response !== "pending"; + } + }); + + // Run job and resolve run_deferred to tool outputs. + $.when(ss_deferred.go()).then(function(result) { + run_deferred.resolve(new DatasetCollection().reset(result)); + }); + return run_deferred; } });

@@ -65,7 +132,9 @@ var ToolInput = Backbone.RelationalModel.extend({ defaults: { name: null, - type: null + label: null, + type: null, + value: null, },

initialize: function() {

diff -r 7387d416d655e086ad3b792058069ea82ce23a3c -r f93ecd917348aeef6332a6d441300ab505daad73 static/scripts/viz/paramamonster.js --- a/static/scripts/viz/paramamonster.js +++ b/static/scripts/viz/paramamonster.js @@ -38,15 +38,16 @@ var param_samples = params_samples[index], param = param_samples.get('param'), - param_name = param.get('name'), + param_label = param.get('label'), settings = param_samples.get('samples');

// Create leaves when last parameter setting is reached. if (params_samples.length - 1 === index) { return _.map(settings, function(setting) { return { - name: param_name + '=' + setting, - param: param + name: param_label + '=' + setting, + param: param, + value: setting } }); } @@ -54,8 +55,9 @@ // Recurse to handle other parameters. return _.map(settings, function(setting) { return { - name: param_name + '=' + setting, + name: param_label + '=' + setting, param: param, + value: setting, children: create_tree_data(filtered_params_samples, index + 1) } }); @@ -94,104 +96,17 @@ });

/** - * A track in a genome browser. + * ParamaMonster visualization model. */ -var Track = Backbone.Model.extend({ - defaults: { - dataset: null - } -}); - -var FeatureTrack = Track.extend({ - defaults: { - track: null - }, +var ParamaMonsterVisualization = Visualization.extend({ + defaults: _.extend({}, Visualization.prototype.defaults, { + tool: null, + parameter_tree: null, + regions: null + }),

- /** - * Draw FeatureTrack tile. - * @param result result from server - * @param cxt canvas context to draw on - * @param mode mode to draw in - * @param resolution view resolution - * @param region region to draw - * @param w_scale pixels per base - * @param ref_seq reference sequence data - */ - draw_tile: function(result, ctx, mode, resolution, region, w_scale, ref_seq) { - var track = this, - canvas = ctx.canvas, - tile_low = region.get('start'), - tile_high = region.get('end'), - min_height = 25, - left_offset = this.left_offset; - - // Drawing the summary tree (feature coverage histogram) - if (mode === "summary_tree" || mode === "Histogram") { - // Get summary tree data if necessary and set max if there is one. - if (result.dataset_type !== "summary_tree") { - var st_data = this.get_summary_tree_data(result.data, tile_low, tile_high, 200); - if (result.max) { - st_data.max = result.max; - } - result = st_data; - } - // Paint summary tree into canvas - var painter = new painters.SummaryTreePainter(result, tile_low, tile_high, this.prefs); - painter.draw(ctx, canvas.width, canvas.height, w_scale); - return new SummaryTreeTile(track, tile_index, resolution, canvas, result.data, result.max); - } - - // Handle row-by-row tracks - - // Preprocessing: filter features and determine whether all unfiltered features have been slotted. - var - filtered = [], - slots = this.slotters[w_scale].slots; - all_slotted = true; - if ( result.data ) { - var filters = this.filters_manager.filters; - for (var i = 0, len = result.data.length; i < len; i++) { - var feature = result.data[i]; - var hide_feature = false; - var filter; - for (var f = 0, flen = filters.length; f < flen; f++) { - filter = filters[f]; - filter.update_attrs(feature); - if (!filter.keep(feature)) { - hide_feature = true; - break; - } - } - if (!hide_feature) { - // Feature visible. - filtered.push(feature); - // Set flag if not slotted. - if ( !(feature[0] in slots) ) { - all_slotted = false; - } - } - } - } - - // Create painter. - var filter_alpha_scaler = (this.filters_manager.alpha_filter ? new FilterScaler(this.filters_manager.alpha_filter) : null); - var filter_height_scaler = (this.filters_manager.height_filter ? new FilterScaler(this.filters_manager.height_filter) : null); - // HACK: ref_seq will only be defined for ReadTracks, and only the ReadPainter accepts that argument - var painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_scaler, filter_height_scaler, ref_seq); - var feature_mapper = null; - - // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); - ctx.fillStyle = this.prefs.block_color; - ctx.font = ctx.canvas.manager.default_font; - ctx.textAlign = "right"; - - if (result.data) { - // Draw features. - feature_mapper = painter.draw(ctx, canvas.width, canvas.height, w_scale, slots); - feature_mapper.translation = -left_offset; - } - - return new FeatureTrackTile(track, tile_index, resolution, canvas, result.data, w_scale, mode, result.message, all_slotted, feature_mapper); + initialize: function(options) { + this.set('parameter_tree', new ToolParameterTree({ tool: this.get('tool') })); } });

@@ -207,7 +122,6 @@ className: 'tool-parameter-tree',

initialize: function(options) { - this.model = options.model; },

render: function() { @@ -244,7 +158,32 @@ .attr("class", "node") .attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; });

- // Set up behavior when node is clicked. + node.append("circle") + .attr("r", 4.5); + + node.append("text") + .attr("dx", function(d) { return d.children ? -8 : 8; }) + .attr("dy", 3) + .attr("text-anchor", function(d) { return d.children ? "end" : "start"; }) + .text(function(d) { return d.name; }); + } +}); + +var ParamaMonsterVisualizationView = Backbone.View.extend({ + className: 'paramamonster', + + initialize: function(options) { + + }, + + render: function() { + // Set up tool parameter tree. + var tool_param_tree_view = new ToolParameterTreeView({ model: this.model.get('parameter_tree') }); + tool_param_tree_view.render(); + this.$el.append(tool_param_tree_view.$el); + + // When node clicked in tree, run tool and show tiles. + var node = d3.select(tool_param_tree_view.$el[0]).selectAll("g.node") node.on("click", function(d, i) { console.log(d, i);

@@ -256,14 +195,6 @@

// Display tiles for region(s) of interest. }); - - node.append("circle") - .attr("r", 4.5); - - node.append("text") - .attr("dx", function(d) { return d.children ? -8 : 8; }) - .attr("dy", 3) - .attr("text-anchor", function(d) { return d.children ? "end" : "start"; }) - .text(function(d) { return d.name; }); - } + + }, }); \ No newline at end of file

diff -r 7387d416d655e086ad3b792058069ea82ce23a3c -r f93ecd917348aeef6332a6d441300ab505daad73 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -11,11 +11,10 @@ /** * 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: { - url: null, - url_params: {}, + ajax_settings: {}, interval: 1000, success_fn: function(result) { return true; } }, @@ -26,10 +25,11 @@ 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() { - $.getJSON(self.get('url'), self.get('url_params'), function(result) { + $.ajax(ajax_settings).success(function(result) { if (success_fn(result)) { // Result is good, so resolve. deferred.resolve(result); @@ -372,6 +372,14 @@ return this.get('chrom') + ":" + this.get('start') + "-" + this.get('end'); },

+ toJSON: function() { + return { + chrom: this.get('chrom'), + start: this.get('start'), + end: this.get('end') + } + }, + /** * Compute the type of overlap between this region and another region. The overlap is computed relative to the given/second region; * hence, OVERLAP_START indicates that the first region overlaps the start (but not the end) of the second region. @@ -495,19 +503,6 @@ });

/** - * A dataset. In Galaxy, datasets are associated with a history, so - * this object is also known as a HistoryDatasetAssociation. - */ -var Dataset = Backbone.Model.extend({ - defaults: { - id: "", - type: "", - name: "", - hda_ldda: "" - } -}); - -/** * A histogram dataset. */ var HistogramDataset = Backbone.Model.extend({

diff -r 7387d416d655e086ad3b792058069ea82ce23a3c -r f93ecd917348aeef6332a6d441300ab505daad73 templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -52,7 +52,8 @@ // Set up needed paths. var galaxy_paths = new GalaxyPaths({ root_path: '${h.url_for( "/" )}', - image_path: '${h.url_for( "/static/images" )}' + image_path: '${h.url_for( "/static/images" )}', + tool_url: '${h.url_for( controller="/api/tools" )}' }); </script></%def>

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

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