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commit/galaxy-central: 2 new changesets
by Bitbucket 13 Apr '11

13 Apr '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/74875168e6da/ changeset: r5381:74875168e6da user: Martijn Vermaat date: 2011-04-14 01:13:10 summary: Typo. affected #: 1 file (1 byte) --- a/static/june_2007_style/blue/base.css Thu Apr 14 01:04:40 2011 +0200 +++ b/static/june_2007_style/blue/base.css Thu Apr 14 01:13:10 2011 +0200 @@ -172,4 +172,4 @@ .text-and-autocomplete-select{background:url(fugue.png) no-repeat right -364px;} .icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} .icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} -.worflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;} +.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;} http://bitbucket.org/galaxy/galaxy-central/changeset/8a0522fff4f7/ changeset: r5382:8a0522fff4f7 user: dannon date: 2011-04-14 01:14:21 summary: Merge. affected #: 1 file (1 byte) --- a/static/june_2007_style/blue/base.css Wed Apr 13 19:07:22 2011 -0400 +++ b/static/june_2007_style/blue/base.css Wed Apr 13 19:14:21 2011 -0400 @@ -172,4 +172,4 @@ .text-and-autocomplete-select{background:url(fugue.png) no-repeat right -364px;} .icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} .icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} -.worflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;} +.workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;} 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: 5 new changesets
by Bitbucket 13 Apr '11

13 Apr '11

5 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/56fc50970fc3/ changeset: r5376:56fc50970fc3 user: dannon date: 2011-04-13 22:35:08 summary: Bugfix for workflow run not reloading history, icon for document stack. affected #: 2 files (803 bytes) Binary file static/images/documents-stack.png has changed --- a/templates/workflow/run_complete.mako Wed Apr 13 16:05:34 2011 -0400 +++ b/templates/workflow/run_complete.mako Wed Apr 13 16:35:08 2011 -0400 @@ -17,4 +17,10 @@ %endfor %endfor </div> -</div> \ No newline at end of file +</div> + +<script type="text/javascript"> + if ( parent.frames && parent.frames.galaxy_history ) { + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history' )}"; + } +</script> http://bitbucket.org/galaxy/galaxy-central/changeset/9a72df515de1/ changeset: r5377:9a72df515de1 user: dannon date: 2011-04-13 22:46:36 summary: Faded document stack icon. affected #: 1 file (587 bytes) Binary file static/images/documents-stack-faded.png has changed http://bitbucket.org/galaxy/galaxy-central/changeset/a946c7e60d1f/ changeset: r5378:a946c7e60d1f user: dannon date: 2011-04-14 01:05:45 summary: Merge. affected #: 1 file (1.8 KB) --- a/static/scripts/trackster.js Wed Apr 13 16:46:36 2011 -0400 +++ b/static/scripts/trackster.js Wed Apr 13 19:05:45 2011 -0400 @@ -741,7 +741,7 @@ this.high = Math.ceil(high); // 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width - this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / 200 ) / Math.LN10 ) ); + this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.LN10 ) ); this.zoom_res = Math.pow( FEATURE_LEVELS, Math.max(0,Math.ceil( Math.log( this.resolution, FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) ))); // Overview @@ -1016,14 +1016,16 @@ return false; }, /** - * Returns true iff element is in [low, high]; range is inclusive. + * Returns true if (a) element's value is in [low, high] (range is inclusive) + * or (b) if value is non-numeric and hence unfilterable. */ keep: function(element) { if ( !this.applies_to( element ) ) { // No element to filter on. return true; } - return (element[this.index] >= this.low && element[this.index] <= this.high); + var val = parseInt(element[this.index]); + return (isNaN(val) || (val >= this.low && val <= this.high)); }, /** * Update filter's min and max values based on element's values. @@ -1306,11 +1308,22 @@ }); /** - * Tiles for TiledTracks. + * Tiles drawn by tracks. */ -var Tile = function(track, canvas) { - this.track = track; - this.canvas = canvas; +var Tile = function(index, resolution, canvas) { + // Wrap element in div for background + this.index = index; + this.resolution = resolution; + this.canvas = $("<div class='track-tile'/>").append(canvas); +}; + +var SummaryTreeTile = function(index, resolution, canvas, max_val) { + Tile.call(this, index, resolution, canvas); + this.max_val = max_val; +}; + +var FeatureTrackTile = function(index, resolution, canvas) { + Tile.call(this, index, resolution, canvas); }; /** @@ -1669,30 +1682,33 @@ // w_scale units are pixels per base. w_scale = width / range, resolution = this.view.resolution, - parent_element = $("<div style='position: relative;'></div>"); + parent_element = $("<div style='position: relative;'></div>"), + gen_key = function(width, w_scale, tile_index) { + return width + '_' + w_scale + '_' + tile_index; + }; if (!clear_after) { this.content_div.children().remove(); } this.content_div.append( parent_element ); this.max_height = 0; // Index of first tile that overlaps visible region var tile_index = Math.floor( low / resolution / DENSITY ); - // A set of setTimeout() ids used when drawing tiles. Each ID indicates - // a tile has been requested to be drawn or is being drawn. - var draw_tile_dict = {}; + // A list of tiles drawn/retrieved. + var drawn_tiles = []; + var tile_count = 0 while ( ( tile_index * DENSITY * resolution ) < high ) { // Check in cache - var key = width + '_' + w_scale + '_' + tile_index; + var key = gen_key(width, w_scale, tile_index); var cached = this.tile_cache.get(key); var tile_low = tile_index * DENSITY * this.view.resolution; var tile_high = tile_low + DENSITY * this.view.resolution; - // console.log(cached, this.tile_cache); if ( !force && cached ) { + drawn_tiles[drawn_tiles.length] = cached; this.show_tile(cached, parent_element, tile_low, w_scale); } else { - this.delayed_draw(force, key, tile_low, tile_high, tile_index, - resolution, parent_element, w_scale, draw_tile_dict); + this.delayed_draw(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles); } tile_index += 1; + tile_count++; } // @@ -1700,7 +1716,7 @@ // var track = this; var intervalId = setInterval(function() { - if (obj_length(draw_tile_dict) === 0) { + if (drawn_tiles.length === tile_count) { // All tiles have been drawn. clearInterval(intervalId); @@ -1725,6 +1741,29 @@ } // + // If mode is Histogram and tiles do not share max, redraw tiles as necessary using new max. + // + if (track.mode == "Histogram") { + // Get global max. + var global_max = -1; + for (var i = 0; i < drawn_tiles.length; i++) { + var cur_max = drawn_tiles[i].max_val; + if (cur_max > global_max) { + global_max = cur_max; + } + } + + for (var i = 0; i < drawn_tiles.length; i++) { + if (drawn_tiles[i].max_val !== global_max) { + var tile = drawn_tiles[i]; + tile.canvas.remove(); + track.delayed_draw(true, gen_key(width, w_scale, tile.index), tile.index, + tile.resolution, parent_element, w_scale, [], { max: global_max }); + } + } + } + + // // Update filter attributes, UI. // @@ -1755,6 +1794,19 @@ track.make_name_popup_menu(); } } + + // Store initial canvas in case we need to use it for overview + /* This is completely broken, just saves the first tile it sees + regardless of if it should be the overview + if (!track.initial_canvas && !window.G_vmlCanvasManager) { + track.initial_canvas = $(tile_element).clone(); + var src_ctx = tile_element.get(0).getContext("2d"); + var tgt_ctx = track.initial_canvas.get(0).getContext("2d"); + var data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height); + tgt_ctx.putImageData(data, 0, 0); + track.set_overview(); + } + */ } }, 50); @@ -1765,44 +1817,28 @@ this.child_tracks[i].draw(force, clear_after); } }, - delayed_draw: function(force, key, tile_low, tile_high, tile_index, resolution, parent_element, w_scale, draw_tile_dict) { - var track = this; - // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data + delayed_draw: function(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) { + var track = this, + tile_low = tile_index * DENSITY * resolution, + tile_high = tile_low + DENSITY * resolution; + + // Helper method. var draw_and_show_tile = function(id, result, resolution, tile_index, parent_element, w_scale, seq_data) { // DEBUG: this is still called too many times when moving slowly, // console.log( "draw_and_show_tile", resolution, tile_index, w_scale ); - returned_tile = track.draw_tile(result, resolution, tile_index, parent_element, w_scale, seq_data) - - // Wrap element in div for background - var wrapper_element = $("<div class='track-tile'>").prepend(returned_tile); - tile_element = wrapper_element; - - track.tile_cache.set(key, tile_element); - track.show_tile(tile_element, parent_element, tile_low, w_scale); - - // TODO: this should go in a post-draw function. - // Store initial canvas in case we need to use it for overview - /* This is completely broken, just saves the first tile it sees - regardless of if it should be the overview - if (!track.initial_canvas && !window.G_vmlCanvasManager) { - track.initial_canvas = $(tile_element).clone(); - var src_ctx = tile_element.get(0).getContext("2d"); - var tgt_ctx = track.initial_canvas.get(0).getContext("2d"); - var data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height); - tgt_ctx.putImageData(data, 0, 0); - track.set_overview(); - } - */ - - delete draw_tile_dict[id]; + var tile = track.draw_tile(result, resolution, tile_index, parent_element, w_scale, seq_data); + track.tile_cache.set(key, tile); + track.show_tile(tile, parent_element, tile_low, w_scale); + drawn_tiles[drawn_tiles.length] = tile; }; + // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data var id = setTimeout(function() { if (tile_low <= track.view.high && tile_high >= track.view.low) { // Show/draw tile: check cache for tile; if tile not in cache, draw it. - var tile_element = (force ? undefined : track.tile_cache.get(key)); - if (tile_element) { - track.show_tile(tile_element, parent_element, tile_low, w_scale); - delete draw_tile_dict[id]; + var tile = (force ? undefined : track.tile_cache.get(key)); + if (tile) { + track.show_tile(tile, parent_element, tile_low, w_scale); + drawn_tiles[drawn_tiles.length] = tile; } else { // @@ -1810,6 +1846,7 @@ // $.when(track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, resolution, track.data_url_extra_params)).then(function(tile_data) { + extend(tile_data, more_tile_data); // If sequence data needed, get that and draw. Otherwise draw. if (view.reference_track && w_scale > view.canvas_manager.char_width_px) { $.when(view.reference_track.data_cache.get_data(view.chrom, tile_low, tile_high, @@ -1825,12 +1862,11 @@ } } }, 50); - draw_tile_dict[id] = true; }, /** * Show track tile and perform associated actions. */ - show_tile: function(tile_element, parent_element, tile_low, w_scale) { + show_tile: function(tile, parent_element, tile_low, w_scale) { // Readability. var track = this; @@ -1844,6 +1880,7 @@ if (this.left_offset) { left -= this.left_offset; } + var tile_element = tile.canvas; tile_element.css({ position: 'absolute', top: 0, left: left, height: '' }); // Setup and show tile element. @@ -1966,7 +2003,7 @@ var c_start = Math.round(c * w_scale); ctx.fillText(seq[c], c_start + track.left_offset, 10); } - return canvas; + return new Tile(tile_index, resolution, canvas); } this.content_div.css("height", "0px"); } @@ -2106,7 +2143,7 @@ this.prefs, this.mode ); painter.draw( ctx, width, height ); - return canvas; + return new Tile(tile_length, resolution, canvas); } }); @@ -2196,11 +2233,14 @@ * position. Return value is a dict with keys 'data', 'delta' (bin size) and 'max.' Data * is a two-item list; first item is bin start, second is bin's count. */ - get_summary_tree_data: function(data, low, high, bin_size) { - var num_bins = Math.floor((high - low)/bin_size), + get_summary_tree_data: function(data, low, high, num_bins) { + if (num_bins > high - low) { + num_bins = high - low; + } + var bin_size = Math.floor((high - low)/num_bins), bins = [], max_count = 0; - + /* // For debugging: for (var i = 0; i < data.length; i++) @@ -2335,8 +2375,7 @@ // Deal with left_offset by translating ctx.translate( left_offset, SUMMARY_TREE_TOP_PADDING ); painter.draw( ctx, width, required_height ); - // Canvas element is returned - return canvas; + return new SummaryTreeTile(tile_index, resolution, canvas, result.max); } // Drawing coverage histogram. This is different from summary tree because data can feature @@ -2359,13 +2398,15 @@ canvas.height = required_height + SUMMARY_TREE_TOP_PADDING; // Paint summary tree into canvas. var binned_data = this.get_summary_tree_data(result.data, tile_low, tile_high, 200); + if (result.max) { + binned_data.max = result.max; + } var painter = new painters.SummaryTreePainter(binned_data, tile_low, tile_high, this.prefs); var ctx = canvas.getContext("2d"); // Deal with left_offset by translating ctx.translate(left_offset, SUMMARY_TREE_TOP_PADDING); painter.draw(ctx, width, required_height); - // Canvas element is returned - return canvas; + return new SummaryTreeTile(tile_index, resolution, canvas, binned_data.max); } // Start dealing with row-by-row tracks @@ -2433,7 +2474,7 @@ // If there's no data, return. if (!result.data) { - return canvas; + return new Tile(tile_index, resolution, canvas); } } @@ -2444,7 +2485,7 @@ ctx.translate( left_offset, ERROR_PADDING ); painter.draw( ctx, width, required_height, slots ); - return canvas; + return new FeatureTrackTile(tile_index, resolution, canvas); } }); @@ -2558,7 +2599,7 @@ this.include_label = include_label; this.max_rows = max_rows; this.measureText = measureText; -} +}; /** * Slot a set of features, `this.slots` will be updated with slots by id, and @@ -2704,7 +2745,7 @@ // ---- Painters ---- var painters_module = function(require, exports){ - + /** * Draw a dashed line on a canvas using filled rectangles. This function is based on: * http://vetruvet.blogspot.com/2010/10/drawing-dashed-lines-on-html5-canvas.h… @@ -2776,7 +2817,7 @@ Painter.call( this, data, view_start, view_end, prefs, mode ); } -SummaryTreePainter.prototype.default_prefis = { show_counts: false }; +SummaryTreePainter.prototype.default_prefs = { show_counts: false }; SummaryTreePainter.prototype.draw = function( ctx, width, height ) { @@ -2790,16 +2831,15 @@ // max rectangle is required_height. base_y = height; delta_x_px = Math.ceil(delta * w_scale); - ctx.save(); for (var i = 0, len = points.length; i < len; i++) { - var x = Math.floor( (points[i][0] - view_start) * w_scale ); var y = points[i][1]; if (!y) { continue; } - var y_px = y / max * height; + var y_px = y / max * height + if (y !== 0 && y_px < 1) { y_px = 1; } ctx.fillStyle = "black"; ctx.fillRect( x, base_y - y_px, delta_x_px, y_px ); @@ -2991,7 +3031,7 @@ } }); -// Contstants specific to feature tracks moved here (HACKING, these should +// Constants specific to feature tracks moved here (HACKING, these should // basically all be configuration options) var DENSE_TRACK_HEIGHT = 10, NO_DETAIL_TRACK_HEIGHT = 3, @@ -3034,8 +3074,7 @@ var feature_uid = feature[0], feature_start = feature[1], - // -1 b/c intervals are half-open. - feature_end = feature[2] - 1, + feature_end = feature[2], feature_name = feature[3], f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), @@ -3134,8 +3173,7 @@ for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) { var block = feature_blocks[k], block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), - // -1 b/c intervals are half-open. - block_end = Math.ceil( Math.min(width, Math.max((block[1] - 1 - tile_low) * w_scale)) ); + block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) ); // Skip drawing if block not on tile. if (block_start > block_end) { continue; } @@ -3199,8 +3237,7 @@ var feature = data[i], feature_uid = feature[0], feature_start = feature[1], - // -1 b/c intervals are half-open. - feature_end = feature[2] - 1, + feature_end = feature[2], feature_name = feature[3], // All features need a start, end, and vertical center. f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), http://bitbucket.org/galaxy/galaxy-central/changeset/1c5796258fb5/ changeset: r5379:1c5796258fb5 user: Martijn Vermaat date: 2011-04-14 01:04:40 summary: Run a workflow on a selection of multiple inputs, one invocation for each. - Makes input selections in the run workflow form support multiple selection. - If multiple inputs are selected, a workflow invocation is executed for each selected input. - Only of of the workflow inputs can have a multiple selection. affected #: 6 files (3.8 KB) --- a/lib/galaxy/tools/parameters/basic.py Wed Apr 13 16:46:36 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Thu Apr 14 01:04:40 2011 +0200 @@ -1421,6 +1421,14 @@ else: return "No dataset" + def validate( self, value, history=None ): + for validator in self.validators: + if value and self.multiple and isinstance(value, list): + for v in value: + validator.validate( v, history ) + else: + validator.validate( value, history ) + def get_dependencies( self ): """ Get the *names* of the other params this param depends on. --- a/lib/galaxy/web/controllers/workflow.py Wed Apr 13 16:46:36 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Thu Apr 14 01:04:40 2011 +0200 @@ -1262,96 +1262,117 @@ if kwargs: # If kwargs were provided, the states for each step should have # been POSTed - for step in workflow.steps: - step.upgrade_messages = {} - # Connections by input name - step.input_connections_by_name = \ - dict( ( conn.input_name, conn ) for conn in step.input_connections ) - # Extract just the arguments for this step by prefix - p = "%s|" % step.id - l = len(p) - step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) ) - step_errors = None - if step.type == 'tool' or step.type is None: - module = module_factory.from_workflow_step( trans, step ) - # Fix any missing parameters - step.upgrade_messages = module.check_and_update_state() - if step.upgrade_messages: - has_upgrade_messages = True - # 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 ) - # Get the tool - tool = module.tool - # Get the state - step.state = state = module.state - # Get old errors - old_errors = state.inputs.pop( "__errors__", {} ) - # Update the state - step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args, - update_only=True, old_errors=old_errors ) - else: - module = step.module = module_factory.from_workflow_step( trans, step ) - state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) ) - step_errors = module.update_runtime_state( trans, state, step_args ) - if step_errors: - errors[step.id] = state.inputs["__errors__"] = step_errors - if 'run_workflow' in kwargs and not errors: - new_history = None - if 'new_history' in kwargs: - if 'new_history_name' in kwargs and kwargs['new_history_name'] != '': - nh_name = kwargs['new_history_name'] + # Get the kwarg keys for data inputs + input_keys = filter(lambda a: a.endswith('|input'), kwargs) + # Example: prefixed='2|input' + # Check if one of them is a list + multiple_input_key = None + multiple_inputs = [None] + for input_key in input_keys: + if isinstance(kwargs[input_key], list): + multiple_input_key = input_key + multiple_inputs = kwargs[input_key] + # List to gather values for the template + invocations=[] + for input_number, single_input in enumerate(multiple_inputs): + # Example: single_input='1', single_input='2', etc... + # 'Fix' the kwargs, to have only the input for this iteration + if multiple_input_key: + kwargs[multiple_input_key] = single_input + for step in workflow.steps: + step.upgrade_messages = {} + # Connections by input name + step.input_connections_by_name = \ + dict( ( conn.input_name, conn ) for conn in step.input_connections ) + # Extract just the arguments for this step by prefix + p = "%s|" % step.id + l = len(p) + step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) ) + step_errors = None + if step.type == 'tool' or step.type is None: + module = module_factory.from_workflow_step( trans, step ) + # Fix any missing parameters + step.upgrade_messages = module.check_and_update_state() + if step.upgrade_messages: + has_upgrade_messages = True + # 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 ) + # Get the tool + tool = module.tool + # Get the state + step.state = state = module.state + # Get old errors + old_errors = state.inputs.pop( "__errors__", {} ) + # Update the state + step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args, + update_only=True, old_errors=old_errors ) else: - nh_name = "History from %s workflow" % workflow.name - new_history = trans.app.model.History( user=trans.user, name=nh_name ) - trans.sa_session.add( new_history ) - # Run each step, connecting outputs to inputs - workflow_invocation = model.WorkflowInvocation() - workflow_invocation.workflow = workflow - outputs = odict() - for i, step in enumerate( workflow.steps ): - # Execute module - job = None - if step.type == 'tool' or step.type is None: - tool = trans.app.toolbox.tools_by_id[ step.tool_id ] - input_values = step.state.inputs - # Connect up - def callback( input, value, prefixed_name, prefixed_label ): - if isinstance( input, DataToolParameter ): - if prefixed_name in step.input_connections_by_name: - conn = step.input_connections_by_name[ prefixed_name ] - return outputs[ conn.output_step.id ][ conn.output_name ] - visit_input_values( tool.inputs, step.state.inputs, callback ) - # Execute it - job, out_data = tool.execute( trans, step.state.inputs, history=new_history) - outputs[ step.id ] = out_data - # Create new PJA associations with the created job, to be run on completion. - # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) - # Pass along replacement dict with the execution of the PJA so we don't have to modify the object. - replacement_dict = {} - for k, v in kwargs.iteritems(): - if k.startswith('wf_parm|'): - replacement_dict[k[8:]] = v - for pja in step.post_job_actions: - if pja.action_type in ActionBox.immediate_actions: - ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict) - else: - job.add_post_job_action(pja) - else: - job, out_data = step.module.execute( trans, step.state ) - outputs[ step.id ] = out_data - # Record invocation - workflow_invocation_step = model.WorkflowInvocationStep() - workflow_invocation_step.workflow_invocation = workflow_invocation - workflow_invocation_step.workflow_step = step - workflow_invocation_step.job = job - # All jobs ran sucessfully, so we can save now - trans.sa_session.add( workflow_invocation ) - trans.sa_session.flush() - return trans.fill_template( "workflow/run_complete.mako", - workflow=stored, - outputs=outputs, - new_history=new_history ) + # Fix this for multiple inputs + module = step.module = module_factory.from_workflow_step( trans, step ) + state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) ) + step_errors = module.update_runtime_state( trans, state, step_args ) + if step_errors: + errors[step.id] = state.inputs["__errors__"] = step_errors + if 'run_workflow' in kwargs and not errors: + new_history = None + if 'new_history' in kwargs: + if 'new_history_name' in kwargs and kwargs['new_history_name'] != '': + nh_name = kwargs['new_history_name'] + else: + nh_name = "History from %s workflow" % workflow.name + if multiple_input_key: + nh_name = '%s %d' % (nh_name, input_number + 1) + new_history = trans.app.model.History( user=trans.user, name=nh_name ) + trans.sa_session.add( new_history ) + # Run each step, connecting outputs to inputs + workflow_invocation = model.WorkflowInvocation() + workflow_invocation.workflow = workflow + outputs = odict() + for i, step in enumerate( workflow.steps ): + # Execute module + job = None + if step.type == 'tool' or step.type is None: + tool = trans.app.toolbox.tools_by_id[ step.tool_id ] + input_values = step.state.inputs + # Connect up + def callback( input, value, prefixed_name, prefixed_label ): + if isinstance( input, DataToolParameter ): + if prefixed_name in step.input_connections_by_name: + conn = step.input_connections_by_name[ prefixed_name ] + return outputs[ conn.output_step.id ][ conn.output_name ] + visit_input_values( tool.inputs, step.state.inputs, callback ) + # Execute it + job, out_data = tool.execute( trans, step.state.inputs, history=new_history) + outputs[ step.id ] = out_data + # Create new PJA associations with the created job, to be run on completion. + # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) + # Pass along replacement dict with the execution of the PJA so we don't have to modify the object. + replacement_dict = {} + for k, v in kwargs.iteritems(): + if k.startswith('wf_parm|'): + replacement_dict[k[8:]] = v + for pja in step.post_job_actions: + if pja.action_type in ActionBox.immediate_actions: + ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict) + else: + job.add_post_job_action(pja) + else: + job, out_data = step.module.execute( trans, step.state ) + outputs[ step.id ] = out_data + # Record invocation + workflow_invocation_step = model.WorkflowInvocationStep() + workflow_invocation_step.workflow_invocation = workflow_invocation + workflow_invocation_step.workflow_step = step + workflow_invocation_step.job = job + # All jobs ran sucessfully, so we can save now + trans.sa_session.add( workflow_invocation ) + invocations.append({'outputs': outputs, + 'new_history': new_history}) + trans.sa_session.flush() + return trans.fill_template( "workflow/run_complete.mako", + workflow=stored, + invocations=invocations ) else: # Prepare each step missing_tools = [] @@ -1816,4 +1837,4 @@ cleanup( prefix, input.cases[current_case].inputs, group_values ) cleanup( "", inputs, values ) return associations - \ No newline at end of file + --- a/lib/galaxy/workflow/modules.py Wed Apr 13 16:46:36 2011 -0400 +++ b/lib/galaxy/workflow/modules.py Thu Apr 14 01:04:40 2011 +0200 @@ -131,7 +131,7 @@ def get_runtime_inputs( self, filter_set=['data'] ): label = self.state.get( "name", "Input Dataset" ) - return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, type="data", format=', '.join(filter_set) ) ) ) + return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, multiple=True, type="data", format=', '.join(filter_set) ) ) ) def get_runtime_state( self ): state = DefaultToolState() state.inputs = dict( input=None ) --- a/static/june_2007_style/blue/base.css Wed Apr 13 16:46:36 2011 -0400 +++ b/static/june_2007_style/blue/base.css Thu Apr 14 01:04:40 2011 +0200 @@ -170,3 +170,6 @@ .editable-text{cursor:pointer;} .editable-text:hover{cursor:text;border:dotted #999999 1px;} .text-and-autocomplete-select{background:url(fugue.png) no-repeat right -364px;} +.icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} +.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} +.worflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;} --- a/templates/workflow/run.mako Wed Apr 13 16:46:36 2011 -0400 +++ b/templates/workflow/run.mako Thu Apr 14 01:04:40 2011 +0200 @@ -2,7 +2,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "jquery.autocomplete" )} + ${h.js( "jquery.autocomplete", "jquery.tipsy" )} <script type="text/javascript"> $( function() { function show_tool_body(title){ @@ -20,6 +20,21 @@ show_tool_body(title); } } + function toggle_multiinput(select) { + if (select.attr('multiple')) { + $('.multiinput').removeClass('disabled'); + if (select.val()) { + select.val(select.val()[0]); + } else { + select.val($('option:last', select).val()); + } + select.removeAttr('multiple'); + } else { + $('.multiinput').addClass('disabled'); + $('.multiinput', select.parent().prev()).removeClass('disabled'); + select.attr('multiple', 'multiple'); + } + } $( "select[refresh_on_change='true']").change( function() { $( "#tool_form" ).submit(); }); @@ -41,6 +56,19 @@ $("#new_history_cbx").click(function(){ $("#new_history_input").toggle(this.checked); }); + $('select[name*="|input"]').removeAttr('multiple').each(function(i, s) { + var select = $(s); + select.parent().prev().append( + $('<span class="icon-button multiinput"></span>').click(function() { + if ($(this).hasClass('disabled')) return; + toggle_multiinput(select); + select.focus(); + }).attr('original-title', + 'Enable/disable selection of multiple input ' + + 'files. Each selected file will have an ' + + 'instance of the workflow.').tipsy({gravity:'s'}) + ); + }); }); </script></%def> --- a/templates/workflow/run_complete.mako Wed Apr 13 16:46:36 2011 -0400 +++ b/templates/workflow/run_complete.mako Thu Apr 14 01:04:40 2011 +0200 @@ -2,21 +2,25 @@ <div class="donemessagelarge"> Successfully ran workflow "${workflow.name}". The following datasets have been added to the queue: - %if new_history: - These datasets will appear in a new history: - <a target='galaxy_history' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(new_history.id), use_panels=False, show_deleted=False )}"> - '${h.to_unicode(new_history.name)}'. - </a> - %endif - <div style="padding-left: 10px;"> - %for step_outputs in outputs.itervalues(): - %for data in step_outputs.itervalues(): - %if not new_history or data.history == new_history: - <p><strong>${data.hid}</strong>: ${data.name}</p> - %endif - %endfor - %endfor - </div> + %for invocation in invocations: + <div class="workflow-invocation-complete"> + %if invocation['new_history']: + <p>These datasets will appear in a new history: + <a target='galaxy_history' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(invocation['new_history'].id), use_panels=False, show_deleted=False )}"> + '${h.to_unicode(invocation['new_history'].name)}'. + </a></p> + %endif + <div style="padding-left: 10px;"> + %for step_outputs in invocation['outputs'].itervalues(): + %for data in step_outputs.itervalues(): + %if not invocation['new_history'] or data.history == invocation['new_history']: + <p><strong>${data.hid}</strong>: ${data.name}</p> + %endif + %endfor + %endfor + </div> + </div> + %endfor </div><script type="text/javascript"> http://bitbucket.org/galaxy/galaxy-central/changeset/383258d637cb/ changeset: r5380:383258d637cb user: dannon date: 2011-04-14 01:07:22 summary: Merge. affected #: 6 files (3.8 KB) --- a/lib/galaxy/tools/parameters/basic.py Wed Apr 13 19:05:45 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Wed Apr 13 19:07:22 2011 -0400 @@ -1421,6 +1421,14 @@ else: return "No dataset" + def validate( self, value, history=None ): + for validator in self.validators: + if value and self.multiple and isinstance(value, list): + for v in value: + validator.validate( v, history ) + else: + validator.validate( value, history ) + def get_dependencies( self ): """ Get the *names* of the other params this param depends on. --- a/lib/galaxy/web/controllers/workflow.py Wed Apr 13 19:05:45 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Wed Apr 13 19:07:22 2011 -0400 @@ -1262,96 +1262,117 @@ if kwargs: # If kwargs were provided, the states for each step should have # been POSTed - for step in workflow.steps: - step.upgrade_messages = {} - # Connections by input name - step.input_connections_by_name = \ - dict( ( conn.input_name, conn ) for conn in step.input_connections ) - # Extract just the arguments for this step by prefix - p = "%s|" % step.id - l = len(p) - step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) ) - step_errors = None - if step.type == 'tool' or step.type is None: - module = module_factory.from_workflow_step( trans, step ) - # Fix any missing parameters - step.upgrade_messages = module.check_and_update_state() - if step.upgrade_messages: - has_upgrade_messages = True - # 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 ) - # Get the tool - tool = module.tool - # Get the state - step.state = state = module.state - # Get old errors - old_errors = state.inputs.pop( "__errors__", {} ) - # Update the state - step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args, - update_only=True, old_errors=old_errors ) - else: - module = step.module = module_factory.from_workflow_step( trans, step ) - state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) ) - step_errors = module.update_runtime_state( trans, state, step_args ) - if step_errors: - errors[step.id] = state.inputs["__errors__"] = step_errors - if 'run_workflow' in kwargs and not errors: - new_history = None - if 'new_history' in kwargs: - if 'new_history_name' in kwargs and kwargs['new_history_name'] != '': - nh_name = kwargs['new_history_name'] + # Get the kwarg keys for data inputs + input_keys = filter(lambda a: a.endswith('|input'), kwargs) + # Example: prefixed='2|input' + # Check if one of them is a list + multiple_input_key = None + multiple_inputs = [None] + for input_key in input_keys: + if isinstance(kwargs[input_key], list): + multiple_input_key = input_key + multiple_inputs = kwargs[input_key] + # List to gather values for the template + invocations=[] + for input_number, single_input in enumerate(multiple_inputs): + # Example: single_input='1', single_input='2', etc... + # 'Fix' the kwargs, to have only the input for this iteration + if multiple_input_key: + kwargs[multiple_input_key] = single_input + for step in workflow.steps: + step.upgrade_messages = {} + # Connections by input name + step.input_connections_by_name = \ + dict( ( conn.input_name, conn ) for conn in step.input_connections ) + # Extract just the arguments for this step by prefix + p = "%s|" % step.id + l = len(p) + step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) ) + step_errors = None + if step.type == 'tool' or step.type is None: + module = module_factory.from_workflow_step( trans, step ) + # Fix any missing parameters + step.upgrade_messages = module.check_and_update_state() + if step.upgrade_messages: + has_upgrade_messages = True + # 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 ) + # Get the tool + tool = module.tool + # Get the state + step.state = state = module.state + # Get old errors + old_errors = state.inputs.pop( "__errors__", {} ) + # Update the state + step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args, + update_only=True, old_errors=old_errors ) else: - nh_name = "History from %s workflow" % workflow.name - new_history = trans.app.model.History( user=trans.user, name=nh_name ) - trans.sa_session.add( new_history ) - # Run each step, connecting outputs to inputs - workflow_invocation = model.WorkflowInvocation() - workflow_invocation.workflow = workflow - outputs = odict() - for i, step in enumerate( workflow.steps ): - # Execute module - job = None - if step.type == 'tool' or step.type is None: - tool = trans.app.toolbox.tools_by_id[ step.tool_id ] - input_values = step.state.inputs - # Connect up - def callback( input, value, prefixed_name, prefixed_label ): - if isinstance( input, DataToolParameter ): - if prefixed_name in step.input_connections_by_name: - conn = step.input_connections_by_name[ prefixed_name ] - return outputs[ conn.output_step.id ][ conn.output_name ] - visit_input_values( tool.inputs, step.state.inputs, callback ) - # Execute it - job, out_data = tool.execute( trans, step.state.inputs, history=new_history) - outputs[ step.id ] = out_data - # Create new PJA associations with the created job, to be run on completion. - # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) - # Pass along replacement dict with the execution of the PJA so we don't have to modify the object. - replacement_dict = {} - for k, v in kwargs.iteritems(): - if k.startswith('wf_parm|'): - replacement_dict[k[8:]] = v - for pja in step.post_job_actions: - if pja.action_type in ActionBox.immediate_actions: - ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict) - else: - job.add_post_job_action(pja) - else: - job, out_data = step.module.execute( trans, step.state ) - outputs[ step.id ] = out_data - # Record invocation - workflow_invocation_step = model.WorkflowInvocationStep() - workflow_invocation_step.workflow_invocation = workflow_invocation - workflow_invocation_step.workflow_step = step - workflow_invocation_step.job = job - # All jobs ran sucessfully, so we can save now - trans.sa_session.add( workflow_invocation ) - trans.sa_session.flush() - return trans.fill_template( "workflow/run_complete.mako", - workflow=stored, - outputs=outputs, - new_history=new_history ) + # Fix this for multiple inputs + module = step.module = module_factory.from_workflow_step( trans, step ) + state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) ) + step_errors = module.update_runtime_state( trans, state, step_args ) + if step_errors: + errors[step.id] = state.inputs["__errors__"] = step_errors + if 'run_workflow' in kwargs and not errors: + new_history = None + if 'new_history' in kwargs: + if 'new_history_name' in kwargs and kwargs['new_history_name'] != '': + nh_name = kwargs['new_history_name'] + else: + nh_name = "History from %s workflow" % workflow.name + if multiple_input_key: + nh_name = '%s %d' % (nh_name, input_number + 1) + new_history = trans.app.model.History( user=trans.user, name=nh_name ) + trans.sa_session.add( new_history ) + # Run each step, connecting outputs to inputs + workflow_invocation = model.WorkflowInvocation() + workflow_invocation.workflow = workflow + outputs = odict() + for i, step in enumerate( workflow.steps ): + # Execute module + job = None + if step.type == 'tool' or step.type is None: + tool = trans.app.toolbox.tools_by_id[ step.tool_id ] + input_values = step.state.inputs + # Connect up + def callback( input, value, prefixed_name, prefixed_label ): + if isinstance( input, DataToolParameter ): + if prefixed_name in step.input_connections_by_name: + conn = step.input_connections_by_name[ prefixed_name ] + return outputs[ conn.output_step.id ][ conn.output_name ] + visit_input_values( tool.inputs, step.state.inputs, callback ) + # Execute it + job, out_data = tool.execute( trans, step.state.inputs, history=new_history) + outputs[ step.id ] = out_data + # Create new PJA associations with the created job, to be run on completion. + # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) + # Pass along replacement dict with the execution of the PJA so we don't have to modify the object. + replacement_dict = {} + for k, v in kwargs.iteritems(): + if k.startswith('wf_parm|'): + replacement_dict[k[8:]] = v + for pja in step.post_job_actions: + if pja.action_type in ActionBox.immediate_actions: + ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict) + else: + job.add_post_job_action(pja) + else: + job, out_data = step.module.execute( trans, step.state ) + outputs[ step.id ] = out_data + # Record invocation + workflow_invocation_step = model.WorkflowInvocationStep() + workflow_invocation_step.workflow_invocation = workflow_invocation + workflow_invocation_step.workflow_step = step + workflow_invocation_step.job = job + # All jobs ran sucessfully, so we can save now + trans.sa_session.add( workflow_invocation ) + invocations.append({'outputs': outputs, + 'new_history': new_history}) + trans.sa_session.flush() + return trans.fill_template( "workflow/run_complete.mako", + workflow=stored, + invocations=invocations ) else: # Prepare each step missing_tools = [] @@ -1816,4 +1837,4 @@ cleanup( prefix, input.cases[current_case].inputs, group_values ) cleanup( "", inputs, values ) return associations - \ No newline at end of file + --- a/lib/galaxy/workflow/modules.py Wed Apr 13 19:05:45 2011 -0400 +++ b/lib/galaxy/workflow/modules.py Wed Apr 13 19:07:22 2011 -0400 @@ -131,7 +131,7 @@ def get_runtime_inputs( self, filter_set=['data'] ): label = self.state.get( "name", "Input Dataset" ) - return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, type="data", format=', '.join(filter_set) ) ) ) + return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, multiple=True, type="data", format=', '.join(filter_set) ) ) ) def get_runtime_state( self ): state = DefaultToolState() state.inputs = dict( input=None ) --- a/static/june_2007_style/blue/base.css Wed Apr 13 19:05:45 2011 -0400 +++ b/static/june_2007_style/blue/base.css Wed Apr 13 19:07:22 2011 -0400 @@ -170,3 +170,6 @@ .editable-text{cursor:pointer;} .editable-text:hover{cursor:text;border:dotted #999999 1px;} .text-and-autocomplete-select{background:url(fugue.png) no-repeat right -364px;} +.icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px;} +.icon-button.multiinput.disabled{background:url(../images/documents-stack-faded.png) no-repeat;cursor:auto;} +.worflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;} --- a/templates/workflow/run.mako Wed Apr 13 19:05:45 2011 -0400 +++ b/templates/workflow/run.mako Wed Apr 13 19:07:22 2011 -0400 @@ -2,7 +2,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "jquery.autocomplete" )} + ${h.js( "jquery.autocomplete", "jquery.tipsy" )} <script type="text/javascript"> $( function() { function show_tool_body(title){ @@ -20,6 +20,21 @@ show_tool_body(title); } } + function toggle_multiinput(select) { + if (select.attr('multiple')) { + $('.multiinput').removeClass('disabled'); + if (select.val()) { + select.val(select.val()[0]); + } else { + select.val($('option:last', select).val()); + } + select.removeAttr('multiple'); + } else { + $('.multiinput').addClass('disabled'); + $('.multiinput', select.parent().prev()).removeClass('disabled'); + select.attr('multiple', 'multiple'); + } + } $( "select[refresh_on_change='true']").change( function() { $( "#tool_form" ).submit(); }); @@ -41,6 +56,19 @@ $("#new_history_cbx").click(function(){ $("#new_history_input").toggle(this.checked); }); + $('select[name*="|input"]').removeAttr('multiple').each(function(i, s) { + var select = $(s); + select.parent().prev().append( + $('<span class="icon-button multiinput"></span>').click(function() { + if ($(this).hasClass('disabled')) return; + toggle_multiinput(select); + select.focus(); + }).attr('original-title', + 'Enable/disable selection of multiple input ' + + 'files. Each selected file will have an ' + + 'instance of the workflow.').tipsy({gravity:'s'}) + ); + }); }); </script></%def> --- a/templates/workflow/run_complete.mako Wed Apr 13 19:05:45 2011 -0400 +++ b/templates/workflow/run_complete.mako Wed Apr 13 19:07:22 2011 -0400 @@ -2,21 +2,25 @@ <div class="donemessagelarge"> Successfully ran workflow "${workflow.name}". The following datasets have been added to the queue: - %if new_history: - These datasets will appear in a new history: - <a target='galaxy_history' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(new_history.id), use_panels=False, show_deleted=False )}"> - '${h.to_unicode(new_history.name)}'. - </a> - %endif - <div style="padding-left: 10px;"> - %for step_outputs in outputs.itervalues(): - %for data in step_outputs.itervalues(): - %if not new_history or data.history == new_history: - <p><strong>${data.hid}</strong>: ${data.name}</p> - %endif - %endfor - %endfor - </div> + %for invocation in invocations: + <div class="workflow-invocation-complete"> + %if invocation['new_history']: + <p>These datasets will appear in a new history: + <a target='galaxy_history' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(invocation['new_history'].id), use_panels=False, show_deleted=False )}"> + '${h.to_unicode(invocation['new_history'].name)}'. + </a></p> + %endif + <div style="padding-left: 10px;"> + %for step_outputs in invocation['outputs'].itervalues(): + %for data in step_outputs.itervalues(): + %if not invocation['new_history'] or data.history == invocation['new_history']: + <p><strong>${data.hid}</strong>: ${data.name}</p> + %endif + %endfor + %endfor + </div> + </div> + %endfor </div><script type="text/javascript"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Add Tile objects to trackster to support better tracking of Tile data properties; use SummaryTreeTile objects to ensure that feature track coverage histograms are drawn with the same max. Some refactoring of TiledTrack.draw() done as well for simplicity. Finally, fixed typos and GFF display bugs.
by Bitbucket 13 Apr '11

13 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/acee660871cd/ changeset: r5375:acee660871cd user: jgoecks date: 2011-04-14 00:09:07 summary: Add Tile objects to trackster to support better tracking of Tile data properties; use SummaryTreeTile objects to ensure that feature track coverage histograms are drawn with the same max. Some refactoring of TiledTrack.draw() done as well for simplicity. Finally, fixed typos and GFF display bugs. affected #: 1 file (1.8 KB) --- a/static/scripts/trackster.js Wed Apr 13 16:05:34 2011 -0400 +++ b/static/scripts/trackster.js Wed Apr 13 18:09:07 2011 -0400 @@ -741,7 +741,7 @@ this.high = Math.ceil(high); // 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width - this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / 200 ) / Math.LN10 ) ); + this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.LN10 ) ); this.zoom_res = Math.pow( FEATURE_LEVELS, Math.max(0,Math.ceil( Math.log( this.resolution, FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) ))); // Overview @@ -1016,14 +1016,16 @@ return false; }, /** - * Returns true iff element is in [low, high]; range is inclusive. + * Returns true if (a) element's value is in [low, high] (range is inclusive) + * or (b) if value is non-numeric and hence unfilterable. */ keep: function(element) { if ( !this.applies_to( element ) ) { // No element to filter on. return true; } - return (element[this.index] >= this.low && element[this.index] <= this.high); + var val = parseInt(element[this.index]); + return (isNaN(val) || (val >= this.low && val <= this.high)); }, /** * Update filter's min and max values based on element's values. @@ -1306,11 +1308,22 @@ }); /** - * Tiles for TiledTracks. + * Tiles drawn by tracks. */ -var Tile = function(track, canvas) { - this.track = track; - this.canvas = canvas; +var Tile = function(index, resolution, canvas) { + // Wrap element in div for background + this.index = index; + this.resolution = resolution; + this.canvas = $("<div class='track-tile'/>").append(canvas); +}; + +var SummaryTreeTile = function(index, resolution, canvas, max_val) { + Tile.call(this, index, resolution, canvas); + this.max_val = max_val; +}; + +var FeatureTrackTile = function(index, resolution, canvas) { + Tile.call(this, index, resolution, canvas); }; /** @@ -1669,30 +1682,33 @@ // w_scale units are pixels per base. w_scale = width / range, resolution = this.view.resolution, - parent_element = $("<div style='position: relative;'></div>"); + parent_element = $("<div style='position: relative;'></div>"), + gen_key = function(width, w_scale, tile_index) { + return width + '_' + w_scale + '_' + tile_index; + }; if (!clear_after) { this.content_div.children().remove(); } this.content_div.append( parent_element ); this.max_height = 0; // Index of first tile that overlaps visible region var tile_index = Math.floor( low / resolution / DENSITY ); - // A set of setTimeout() ids used when drawing tiles. Each ID indicates - // a tile has been requested to be drawn or is being drawn. - var draw_tile_dict = {}; + // A list of tiles drawn/retrieved. + var drawn_tiles = []; + var tile_count = 0 while ( ( tile_index * DENSITY * resolution ) < high ) { // Check in cache - var key = width + '_' + w_scale + '_' + tile_index; + var key = gen_key(width, w_scale, tile_index); var cached = this.tile_cache.get(key); var tile_low = tile_index * DENSITY * this.view.resolution; var tile_high = tile_low + DENSITY * this.view.resolution; - // console.log(cached, this.tile_cache); if ( !force && cached ) { + drawn_tiles[drawn_tiles.length] = cached; this.show_tile(cached, parent_element, tile_low, w_scale); } else { - this.delayed_draw(force, key, tile_low, tile_high, tile_index, - resolution, parent_element, w_scale, draw_tile_dict); + this.delayed_draw(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles); } tile_index += 1; + tile_count++; } // @@ -1700,7 +1716,7 @@ // var track = this; var intervalId = setInterval(function() { - if (obj_length(draw_tile_dict) === 0) { + if (drawn_tiles.length === tile_count) { // All tiles have been drawn. clearInterval(intervalId); @@ -1725,6 +1741,29 @@ } // + // If mode is Histogram and tiles do not share max, redraw tiles as necessary using new max. + // + if (track.mode == "Histogram") { + // Get global max. + var global_max = -1; + for (var i = 0; i < drawn_tiles.length; i++) { + var cur_max = drawn_tiles[i].max_val; + if (cur_max > global_max) { + global_max = cur_max; + } + } + + for (var i = 0; i < drawn_tiles.length; i++) { + if (drawn_tiles[i].max_val !== global_max) { + var tile = drawn_tiles[i]; + tile.canvas.remove(); + track.delayed_draw(true, gen_key(width, w_scale, tile.index), tile.index, + tile.resolution, parent_element, w_scale, [], { max: global_max }); + } + } + } + + // // Update filter attributes, UI. // @@ -1755,6 +1794,19 @@ track.make_name_popup_menu(); } } + + // Store initial canvas in case we need to use it for overview + /* This is completely broken, just saves the first tile it sees + regardless of if it should be the overview + if (!track.initial_canvas && !window.G_vmlCanvasManager) { + track.initial_canvas = $(tile_element).clone(); + var src_ctx = tile_element.get(0).getContext("2d"); + var tgt_ctx = track.initial_canvas.get(0).getContext("2d"); + var data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height); + tgt_ctx.putImageData(data, 0, 0); + track.set_overview(); + } + */ } }, 50); @@ -1765,44 +1817,28 @@ this.child_tracks[i].draw(force, clear_after); } }, - delayed_draw: function(force, key, tile_low, tile_high, tile_index, resolution, parent_element, w_scale, draw_tile_dict) { - var track = this; - // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data + delayed_draw: function(force, key, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) { + var track = this, + tile_low = tile_index * DENSITY * resolution, + tile_high = tile_low + DENSITY * resolution; + + // Helper method. var draw_and_show_tile = function(id, result, resolution, tile_index, parent_element, w_scale, seq_data) { // DEBUG: this is still called too many times when moving slowly, // console.log( "draw_and_show_tile", resolution, tile_index, w_scale ); - returned_tile = track.draw_tile(result, resolution, tile_index, parent_element, w_scale, seq_data) - - // Wrap element in div for background - var wrapper_element = $("<div class='track-tile'>").prepend(returned_tile); - tile_element = wrapper_element; - - track.tile_cache.set(key, tile_element); - track.show_tile(tile_element, parent_element, tile_low, w_scale); - - // TODO: this should go in a post-draw function. - // Store initial canvas in case we need to use it for overview - /* This is completely broken, just saves the first tile it sees - regardless of if it should be the overview - if (!track.initial_canvas && !window.G_vmlCanvasManager) { - track.initial_canvas = $(tile_element).clone(); - var src_ctx = tile_element.get(0).getContext("2d"); - var tgt_ctx = track.initial_canvas.get(0).getContext("2d"); - var data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height); - tgt_ctx.putImageData(data, 0, 0); - track.set_overview(); - } - */ - - delete draw_tile_dict[id]; + var tile = track.draw_tile(result, resolution, tile_index, parent_element, w_scale, seq_data); + track.tile_cache.set(key, tile); + track.show_tile(tile, parent_element, tile_low, w_scale); + drawn_tiles[drawn_tiles.length] = tile; }; + // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data var id = setTimeout(function() { if (tile_low <= track.view.high && tile_high >= track.view.low) { // Show/draw tile: check cache for tile; if tile not in cache, draw it. - var tile_element = (force ? undefined : track.tile_cache.get(key)); - if (tile_element) { - track.show_tile(tile_element, parent_element, tile_low, w_scale); - delete draw_tile_dict[id]; + var tile = (force ? undefined : track.tile_cache.get(key)); + if (tile) { + track.show_tile(tile, parent_element, tile_low, w_scale); + drawn_tiles[drawn_tiles.length] = tile; } else { // @@ -1810,6 +1846,7 @@ // $.when(track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, resolution, track.data_url_extra_params)).then(function(tile_data) { + extend(tile_data, more_tile_data); // If sequence data needed, get that and draw. Otherwise draw. if (view.reference_track && w_scale > view.canvas_manager.char_width_px) { $.when(view.reference_track.data_cache.get_data(view.chrom, tile_low, tile_high, @@ -1825,12 +1862,11 @@ } } }, 50); - draw_tile_dict[id] = true; }, /** * Show track tile and perform associated actions. */ - show_tile: function(tile_element, parent_element, tile_low, w_scale) { + show_tile: function(tile, parent_element, tile_low, w_scale) { // Readability. var track = this; @@ -1844,6 +1880,7 @@ if (this.left_offset) { left -= this.left_offset; } + var tile_element = tile.canvas; tile_element.css({ position: 'absolute', top: 0, left: left, height: '' }); // Setup and show tile element. @@ -1966,7 +2003,7 @@ var c_start = Math.round(c * w_scale); ctx.fillText(seq[c], c_start + track.left_offset, 10); } - return canvas; + return new Tile(tile_index, resolution, canvas); } this.content_div.css("height", "0px"); } @@ -2106,7 +2143,7 @@ this.prefs, this.mode ); painter.draw( ctx, width, height ); - return canvas; + return new Tile(tile_length, resolution, canvas); } }); @@ -2196,11 +2233,14 @@ * position. Return value is a dict with keys 'data', 'delta' (bin size) and 'max.' Data * is a two-item list; first item is bin start, second is bin's count. */ - get_summary_tree_data: function(data, low, high, bin_size) { - var num_bins = Math.floor((high - low)/bin_size), + get_summary_tree_data: function(data, low, high, num_bins) { + if (num_bins > high - low) { + num_bins = high - low; + } + var bin_size = Math.floor((high - low)/num_bins), bins = [], max_count = 0; - + /* // For debugging: for (var i = 0; i < data.length; i++) @@ -2335,8 +2375,7 @@ // Deal with left_offset by translating ctx.translate( left_offset, SUMMARY_TREE_TOP_PADDING ); painter.draw( ctx, width, required_height ); - // Canvas element is returned - return canvas; + return new SummaryTreeTile(tile_index, resolution, canvas, result.max); } // Drawing coverage histogram. This is different from summary tree because data can feature @@ -2359,13 +2398,15 @@ canvas.height = required_height + SUMMARY_TREE_TOP_PADDING; // Paint summary tree into canvas. var binned_data = this.get_summary_tree_data(result.data, tile_low, tile_high, 200); + if (result.max) { + binned_data.max = result.max; + } var painter = new painters.SummaryTreePainter(binned_data, tile_low, tile_high, this.prefs); var ctx = canvas.getContext("2d"); // Deal with left_offset by translating ctx.translate(left_offset, SUMMARY_TREE_TOP_PADDING); painter.draw(ctx, width, required_height); - // Canvas element is returned - return canvas; + return new SummaryTreeTile(tile_index, resolution, canvas, binned_data.max); } // Start dealing with row-by-row tracks @@ -2433,7 +2474,7 @@ // If there's no data, return. if (!result.data) { - return canvas; + return new Tile(tile_index, resolution, canvas); } } @@ -2444,7 +2485,7 @@ ctx.translate( left_offset, ERROR_PADDING ); painter.draw( ctx, width, required_height, slots ); - return canvas; + return new FeatureTrackTile(tile_index, resolution, canvas); } }); @@ -2558,7 +2599,7 @@ this.include_label = include_label; this.max_rows = max_rows; this.measureText = measureText; -} +}; /** * Slot a set of features, `this.slots` will be updated with slots by id, and @@ -2704,7 +2745,7 @@ // ---- Painters ---- var painters_module = function(require, exports){ - + /** * Draw a dashed line on a canvas using filled rectangles. This function is based on: * http://vetruvet.blogspot.com/2010/10/drawing-dashed-lines-on-html5-canvas.h… @@ -2776,7 +2817,7 @@ Painter.call( this, data, view_start, view_end, prefs, mode ); } -SummaryTreePainter.prototype.default_prefis = { show_counts: false }; +SummaryTreePainter.prototype.default_prefs = { show_counts: false }; SummaryTreePainter.prototype.draw = function( ctx, width, height ) { @@ -2790,16 +2831,15 @@ // max rectangle is required_height. base_y = height; delta_x_px = Math.ceil(delta * w_scale); - ctx.save(); for (var i = 0, len = points.length; i < len; i++) { - var x = Math.floor( (points[i][0] - view_start) * w_scale ); var y = points[i][1]; if (!y) { continue; } - var y_px = y / max * height; + var y_px = y / max * height + if (y !== 0 && y_px < 1) { y_px = 1; } ctx.fillStyle = "black"; ctx.fillRect( x, base_y - y_px, delta_x_px, y_px ); @@ -2991,7 +3031,7 @@ } }); -// Contstants specific to feature tracks moved here (HACKING, these should +// Constants specific to feature tracks moved here (HACKING, these should // basically all be configuration options) var DENSE_TRACK_HEIGHT = 10, NO_DETAIL_TRACK_HEIGHT = 3, @@ -3034,8 +3074,7 @@ var feature_uid = feature[0], feature_start = feature[1], - // -1 b/c intervals are half-open. - feature_end = feature[2] - 1, + feature_end = feature[2], feature_name = feature[3], f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ), @@ -3134,8 +3173,7 @@ for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) { var block = feature_blocks[k], block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), - // -1 b/c intervals are half-open. - block_end = Math.ceil( Math.min(width, Math.max((block[1] - 1 - tile_low) * w_scale)) ); + block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) ); // Skip drawing if block not on tile. if (block_start > block_end) { continue; } @@ -3199,8 +3237,7 @@ var feature = data[i], feature_uid = feature[0], feature_start = feature[1], - // -1 b/c intervals are half-open. - feature_end = feature[2] - 1, + feature_end = feature[2], feature_name = feature[3], // All features need a start, end, and vertical center. f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Streamline the process of importing library datasets into histories:
by Bitbucket 13 Apr '11

13 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1ff9cb03b742/ changeset: r5374:1ff9cb03b742 user: greg date: 2011-04-13 22:05:34 summary: Streamline the process of importing library datasets into histories: 1) Allow imports from the admin view instead of just the Data Libraries view. 2) Add a new 1-click option when acting on multiple selected library datasets to import them into the current history. 3) when importing selected library datasets into selected histories, make the current history selected by default. 4) Add the ability to import the current library dataset into a selected history when viewing the library dataset info page. affected #: 4 files (2.0 KB) --- a/lib/galaxy/web/controllers/library_common.py Wed Apr 13 13:52:05 2011 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Wed Apr 13 16:05:34 2011 -0400 @@ -858,7 +858,7 @@ message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." default_action = 'manage_permissions' else: - default_action = 'import_to_histories' + default_action = 'import_to_current_history' trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, @@ -1238,7 +1238,7 @@ message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." default_action = 'manage_permissions' else: - default_action = 'import_to_histories' + default_action = 'import_to_current_history' return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, @@ -1547,6 +1547,7 @@ error = False is_admin = trans.user_is_admin() and cntrller == 'library_admin' current_user_roles = trans.get_current_user_roles() + current_history = trans.get_history() if not ldda_ids: error = True message = 'You must select at least one dataset.' @@ -1554,16 +1555,27 @@ error = True message = 'You must select an action to perform on the selected datasets.' else: - if action == 'import_to_histories': + if action in [ 'import_to_current_history', 'import_to_histories' ]: + new_kwd = {} + if action == 'import_to_current_history': + encoded_current_history_id = trans.security.encode_id( current_history.id ) + selected_history_id = encoded_current_history_id + new_kwd[ 'do_action' ] = action + new_kwd[ 'target_history_ids' ] = encoded_current_history_id + new_kwd[ 'import_datasets_to_histories_button' ] = 'Import library datasets' + else: + selected_history_id = '' return trans.response.send_redirect( web.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=library_id, + selected_history_id=selected_history_id, ldda_ids=ldda_ids, use_panels=use_panels, show_deleted=show_deleted, message=message, - status=status ) ) + status=status, + **new_kwd ) ) if action == 'move': if library_id in [ 'none', 'None', None ]: source_library_id = '' @@ -1808,8 +1820,10 @@ status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) + action = params.get( 'do_action', None ) user = trans.get_user() current_history = trans.get_history() + selected_history_id = params.get( 'selected_history_id', trans.security.encode_id( current_history.id ) ) if library_id: library = trans.sa_session.query( trans.model.Library ).get( trans.security.decode_id( library_id ) ) else: @@ -1886,11 +1900,20 @@ target_histories = [ current_history ] if user: target_histories = user.active_histories + if action == 'import_to_current_history' and library_id: + # To streamline this as much as possible, go back to browsing the library. + return trans.response.send_redirect( web.url_for( controller='library_common', + action='browse_library', + cntrller=cntrller, + id=library_id, + message=util.sanitize_text( message ), + status=status ) ) return trans.fill_template( "/library/common/import_datasets_to_histories.mako", cntrller=cntrller, library=library, - current_history=trans.get_history(), + current_history=current_history, ldda_ids=ldda_ids, + selected_history_id=selected_history_id, target_history_ids=target_history_ids, source_lddas=source_lddas, target_histories=target_histories, --- a/templates/library/common/common.mako Wed Apr 13 13:52:05 2011 -0400 +++ b/templates/library/common/common.mako Wed Apr 13 16:05:34 2011 -0400 @@ -403,11 +403,12 @@ For selected datasets: <select name="do_action" id="action_on_selected_items"> %if can_import_to_histories: - %if not is_admin and default_action == 'import_to_histories': - <option value="import_to_histories" selected>Import to histories</option> + %if default_action == 'import_to_current_history': + <option value="import_to_current_history" selected>Import to current history</option> %else: - <option value="import_to_histories">Import to histories</option> + <option value="import_to_current_history">Import to current history</option> %endif + <option value="import_to_histories">Import to histories</option> %endif %if can_manage_permissions: %if not is_admin and default_action == 'manage_permissions': --- a/templates/library/common/import_datasets_to_histories.mako Wed Apr 13 13:52:05 2011 -0400 +++ b/templates/library/common/import_datasets_to_histories.mako Wed Apr 13 16:05:34 2011 -0400 @@ -50,16 +50,19 @@ <div class="toolFormBody"><div class="form-row" id="single-destination"><select id="single-dest-select" name="target_history_ids"> - <option value=""></option> %for i, target_history in enumerate( target_histories ): <% encoded_id = trans.security.encode_id( target_history.id ) + if encoded_id == selected_history_id: + selected_text = " selected" + else: + selected_text = "" if target_history == current_history: current_history_text = " (current history)" else: current_history_text = "" %> - <option value="${encoded_id}">${i + 1}: ${h.truncate( target_history.name, 30 )}${current_history_text}</option> + <option value="${encoded_id}"${selected_text}>${i + 1}: ${h.truncate( target_history.name, 30 )}${current_history_text}</option> %endfor </select><br/><br/> --- a/templates/library/common/ldda_info.mako Wed Apr 13 13:52:05 2011 -0400 +++ b/templates/library/common/ldda_info.mako Wed Apr 13 16:05:34 2011 -0400 @@ -65,8 +65,8 @@ %if current_version and can_modify: <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), replace_id=trans.security.encode_id( ldda.library_dataset.id ) )}">Upload a new version of this dataset</a> %endif - %if cntrller=='library' and ldda.has_data(): - <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select histories to import this dataset</a> + %if ldda.has_data(): + <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into selected histories</a><a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Download this dataset</a> %endif %if show_associated_hdas_and_lddas: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: 1. Add support for manual file transfer from external services to a Galaxy data library using scp. This is currently enabled via the enable_beta_job_managers flag. This should not currently be used because it hits the db significantly to determine if dererred jobs are queued for running. The plan is to use messaging for this, but that approach is not yet implemented. Rabbit mq is still being used to enable manual file transfer to Galaxy data libraries when the e
by Bitbucket 13 Apr '11

13 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f1a250bbff0b/ changeset: r5373:f1a250bbff0b user: greg date: 2011-04-13 19:52:05 summary: 1. Add support for manual file transfer from external services to a Galaxy data library using scp. This is currently enabled via the enable_beta_job_managers flag. This should not currently be used because it hits the db significantly to determine if dererred jobs are queued for running. The plan is to use messaging for this, but that approach is not yet implemented. Rabbit mq is still being used to enable manual file transfer to Galaxy data libraries when the enable_beta_job_managers flag is not set. 2. Clean up the code that renders the jquery file browser plugin - things work much cleaner now. One remaining item is handing the issue where rsh / ssh keys are not set. Also clean up a lot of code related to manual file transfers in the requests_admin controller. 3. In addition to the new ManualDataTransferPlugin, add the Pacific Biosciences SMRTPortalPlugin that automatically transfers files produced by SMRT Portal to a Galaxy data library. 4. Add the external service type config for Pac Bio SMRT Portal version 1.1.0. affected #: 17 files (6.9 KB) --- a/external_service_types/454_life_sciences.xml Tue Apr 12 23:41:06 2011 -0400 +++ b/external_service_types/454_life_sciences.xml Wed Apr 13 13:52:05 2011 -0400 @@ -3,7 +3,7 @@ <version>1</version><data_transfer_settings> - <data_transfer type='scp' automatic_transfer='False' host='host' user_name='user_name' password='password' data_location='data_location' /> + <data_transfer protocol='scp' automatic_transfer='False' host='host' user_name='user_name' password='password' data_location='data_location' /></data_transfer_settings><run_details> --- a/external_service_types/applied_biosystems_solid.xml Tue Apr 12 23:41:06 2011 -0400 +++ b/external_service_types/applied_biosystems_solid.xml Wed Apr 13 13:52:05 2011 -0400 @@ -3,7 +3,7 @@ <version>3</version><data_transfer_settings> - <data_transfer type='scp' automatic_transfer='False' host='host' user_name='user_name' password='password' data_location='data_location' rename_dataset='rename_dataset' /> + <data_transfer protocol='scp' automatic_transfer='False' host='host' user_name='user_name' password='password' data_location='data_location' rename_dataset='rename_dataset' /></data_transfer_settings><run_details> @@ -31,7 +31,7 @@ <field name="dataset2_name" type="text" label="Sample run output 2" description="" value="Quality file" required="True" /><field name="dataset2_datatype" type="text" label="Sample run datatype 2" description="" value="qual" required="True" /><field name="dataset3_name" type="text" label="Sample run output 3" description="" value="STATS file" required="True" /> - <field name="dataset3_datatype" type="text" label="Sample run datatype 3" description="" value="stats" required="True" /> + <field name="dataset3_datatype" type="text" label="Sample run datatype 3" description="" value="txt" required="True" /></fields></form> --- a/external_service_types/simple_unknown_sequencer.xml Tue Apr 12 23:41:06 2011 -0400 +++ b/external_service_types/simple_unknown_sequencer.xml Wed Apr 13 13:52:05 2011 -0400 @@ -7,7 +7,7 @@ <description></description><version></version><data_transfer_settings> - <data_transfer type='scp' automatic_transfer='False' host='host' user_name='user_name' password='password' data_location='data_location'/> + <data_transfer protocol='scp' automatic_transfer='False' host='host' user_name='user_name' password='password' data_location='data_location'/></data_transfer_settings><form type="external_service" name="Simple unknown sequencer form" description=""><fields> --- a/lib/galaxy/jobs/deferred/__init__.py Tue Apr 12 23:41:06 2011 -0400 +++ b/lib/galaxy/jobs/deferred/__init__.py Wed Apr 13 13:52:05 2011 -0400 @@ -26,7 +26,6 @@ self.monitor_thread = threading.Thread( target=self.__monitor ) self.monitor_thread.start() log.info( 'Deferred job queue started' ) - def _load_plugins( self ): for fname in os.listdir( os.path.dirname( __file__ ) ): if not fname.startswith( '_' ) and fname.endswith( '.py' ): @@ -53,7 +52,6 @@ self.plugins[obj] = plugin( self.app ) self.plugins[obj].job_states = self.job_states log.debug( 'Loaded deferred job plugin: %s' % display_name ) - def __check_jobs_at_startup( self ): waiting_jobs = self.sa_session.query( model.DeferredJob ) \ .filter( model.DeferredJob.state == model.DeferredJob.states.WAITING ).all() @@ -66,7 +64,6 @@ # Pass the job ID as opposed to the job, since the monitor thread # needs to load it in its own threadlocal scoped session. self.waiting_jobs.append( job.id ) - def __monitor( self ): while self.running: try: @@ -75,7 +72,6 @@ log.exception( 'Exception in monitor_step' ) self.sleeper.sleep( 1 ) log.info( 'job queue stopped' ) - def __monitor_step( self ): # TODO: Querying the database with this frequency is bad, we need message passing new_jobs = self.sa_session.query( model.DeferredJob ) \ @@ -121,7 +117,6 @@ else: new_waiting.append( job ) self.waiting_jobs = new_waiting - def __check_job_plugin( self, job ): if job.plugin not in self.plugins: log.error( 'Invalid deferred job plugin: %s' ) % job.plugin @@ -130,15 +125,12 @@ self.sa_session.flush() return False return True - def __check_if_ready_to_run( self, job ): return self.plugins[job.plugin].check_job( job ) - def __fail_job( self, job ): job.state = model.DeferredJob.states.ERROR self.sa_session.add( job ) self.sa_session.flush() - def shutdown( self ): self.running = False self.sleeper.wake() @@ -158,3 +150,34 @@ self.condition.acquire() self.condition.notify() self.condition.release() + +class FakeTrans( object ): + """A fake trans for calling the external set metadata tool""" + def __init__( self, app, history=None, user=None): + class Dummy( object ): + def __init__( self ): + self.id = None + self.app = app + self.sa_session = app.model.context.current + self.dummy = Dummy() + self.history = history + self.user = user + self.model = app.model + def get_galaxy_session( self ): + return self.dummy + def log_event( self, message, tool_id=None ): + pass + def get_current_user_roles( self ): + if self.user: + return self.user.all_roles() + else: + return [] + def db_dataset_for( self, dbkey ): + if self.history is None: + return None + datasets = self.sa_session.query( self.app.model.HistoryDatasetAssociation ) \ + .filter_by( deleted=False, history_id=self.history.id, extension="len" ) + for ds in datasets: + if dbkey == ds.dbkey: + return ds + return None --- a/lib/galaxy/jobs/transfer_manager.py Tue Apr 12 23:41:06 2011 -0400 +++ b/lib/galaxy/jobs/transfer_manager.py Wed Apr 13 13:52:05 2011 -0400 @@ -24,11 +24,20 @@ self.restarter = threading.Thread( target=self.__restarter ) self.restarter.start() def new( self, path=None, **kwd ): - if 'url' not in kwd: - raise Exception( 'Missing required parameter "url".' ) - # try: except JSON: - transfer_job = self.app.model.TransferJob( state=self.app.model.TransferJob.states.NEW, - params=kwd ) + if 'protocol' not in kwd: + raise Exception( 'Missing required parameter "protocol".' ) + protocol = kwd[ 'protocol' ] + if protocol in [ 'http', 'https' ]: + if 'url' not in kwd: + raise Exception( 'Missing required parameter "url".' ) + transfer_job = self.app.model.TransferJob( state=self.app.model.TransferJob.states.NEW, params=kwd ) + elif protocol == 'scp': + # TODO: add more checks here? + if 'sample_dataset_id' not in kwd: + raise Exception( 'Missing required parameter "sample_dataset_id".' ) + if 'file_path' not in kwd: + raise Exception( 'Missing required parameter "file_path".' ) + transfer_job = self.app.model.TransferJob( state=self.app.model.TransferJob.states.NEW, params=kwd ) self.sa_session.add( transfer_job ) self.sa_session.flush() return transfer_job @@ -48,6 +57,8 @@ self.sa_session.add_all( transfer_jobs ) self.sa_session.flush() for tj in transfer_jobs: + params_dict = tj.params + protocol = params_dict[ 'protocol' ] # The transfer script should daemonize fairly quickly - if this is # not the case, this process will need to be moved to a # non-blocking method. @@ -101,7 +112,7 @@ if tj_state['state'] in self.app.model.TransferJob.terminal_states: log.debug( 'Transfer job %s is in terminal state: %s' % ( tj_state['transfer_job_id'], tj_state['state'] ) ) elif tj_state['state'] == self.app.model.TransferJob.states.PROGRESS and 'percent' in tj_state: - log.debug( 'Transfer job %s is %s%% complete' % ( tj_state['transfer_job_id'], tj_state['percent'] ) ) + log.debug( 'Transfer job %s is %s%% complete' % ( tj_state[ 'transfer_job_id' ], tj_state[ 'percent' ] ) ) if len( rval ) == 1: return rval[0] return rval --- a/lib/galaxy/model/__init__.py Tue Apr 12 23:41:06 2011 -0400 +++ b/lib/galaxy/model/__init__.py Wed Apr 13 13:52:05 2011 -0400 @@ -1796,7 +1796,9 @@ self.comment = comment class ExternalService( object ): - data_transfer_types = Bunch( SCP = 'scp' ) + data_transfer_protocol = Bunch( HTTP = 'http', + HTTPS = 'https', + SCP = 'scp' ) def __init__( self, name=None, description=None, external_service_type_id=None, version=None, form_definition_id=None, form_values_id=None, deleted=None ): self.name = name self.description = description @@ -1812,8 +1814,8 @@ trans.app.external_service_types.reload( self.external_service_type_id ) self.data_transfer = {} external_service_type = self.get_external_service_type( trans ) - for data_transfer_type, data_transfer_obj in external_service_type.data_transfer.items(): - if data_transfer_type == self.data_transfer_types.SCP: + for data_transfer_protocol, data_transfer_obj in external_service_type.data_transfer.items(): + if data_transfer_protocol == self.data_transfer_protocol.SCP: scp_configs = {} automatic_transfer = data_transfer_obj.config.get( 'automatic_transfer', 'false' ) scp_configs[ 'automatic_transfer' ] = util.string_as_bool( automatic_transfer ) @@ -1822,7 +1824,7 @@ scp_configs[ 'password' ] = self.form_values.content.get( data_transfer_obj.config.get( 'password', '' ), '' ) scp_configs[ 'data_location' ] = self.form_values.content.get( data_transfer_obj.config.get( 'data_location', '' ), '' ) scp_configs[ 'rename_dataset' ] = self.form_values.content.get( data_transfer_obj.config.get( 'rename_dataset', '' ), '' ) - self.data_transfer[ self.data_transfer_types.SCP ] = scp_configs + self.data_transfer[ self.data_transfer_protocol.SCP ] = scp_configs def populate_actions( self, trans, item, param_dict=None ): return self.get_external_service_type( trans ).actions.populate( self, item, param_dict=param_dict ) @@ -1992,14 +1994,14 @@ def print_ticks( d ): pass error_msg = 'Error encountered in determining the file size of %s on the external_service.' % filepath - if not scp_configs['host'] or not scp_configs['user_name'] or not scp_configs['password']: + if not scp_configs[ 'host' ] or not scp_configs[ 'user_name' ] or not scp_configs[ 'password' ]: return error_msg login_str = '%s@%s' % ( scp_configs['user_name'], scp_configs['host'] ) cmd = 'ssh %s "du -sh \'%s\'"' % ( login_str, filepath ) try: output = pexpect.run( cmd, - events={ '.ssword:*': scp_configs['password']+'\r\n', - pexpect.TIMEOUT:print_ticks}, + events={ '.ssword:*' : scp_configs['password'] + '\r\n', + pexpect.TIMEOUT : print_ticks }, timeout=10 ) except Exception, e: return error_msg @@ -2013,7 +2015,7 @@ def run_details( self ): # self.runs is a list of SampleRunAssociations ordered descending on update_time. if self.runs: - # Always use the lates run details template, self.runs[0] is a SampleRunAssociation + # Always use the latest run details template, self.runs[0] is a SampleRunAssociation return self.runs[0] # Inherit this sample's RequestType run details, if one exists. return self.request.type.run_details --- a/lib/galaxy/sample_tracking/data_transfer.py Tue Apr 12 23:41:06 2011 -0400 +++ b/lib/galaxy/sample_tracking/data_transfer.py Wed Apr 13 13:52:05 2011 -0400 @@ -14,11 +14,11 @@ # TODO: The 'automatic_transfer' setting is for future use. If set to True, we will need to # ensure the sample has an associated destination data library before it moves to a certain state # ( e.g., Run started ). - self.config['automatic_transfer'] = elem.get( 'automatic_transfer' ) - self.config['host'] = elem.get( 'host' ) - self.config['user_name'] = elem.get( 'user_name' ) - self.config['password'] = elem.get( 'password' ) - self.config['data_location'] = elem.get( 'data_location' ) + self.config[ 'automatic_transfer' ] = elem.get( 'automatic_transfer' ) + self.config[ 'host' ] = elem.get( 'host' ) + self.config[ 'user_name' ] = elem.get( 'user_name' ) + self.config[ 'password' ] = elem.get( 'password' ) + self.config[ 'data_location' ] = elem.get( 'data_location' ) # 'rename_dataset' is optional and it may not be defined in all external types # It is only used is AB SOLiD external service type for now rename_dataset = elem.get( 'rename_dataset', None ) --- a/lib/galaxy/sample_tracking/external_service_types.py Tue Apr 12 23:41:06 2011 -0400 +++ b/lib/galaxy/sample_tracking/external_service_types.py Wed Apr 13 13:52:05 2011 -0400 @@ -86,17 +86,18 @@ data_transfer_settings_elem = root.find( 'data_transfer_settings' ) # Currently only data transfer using scp is supported. for data_transfer_elem in data_transfer_settings_elem.findall( "data_transfer" ): - if data_transfer_elem.get( 'type' ) == model.ExternalService.data_transfer_types.SCP: - scp_data_transfer = data_transfer_factories[ model.ExternalService.data_transfer_types.SCP ] + if data_transfer_elem.get( 'protocol' ) == model.ExternalService.data_transfer_protocol.SCP: + scp_data_transfer = data_transfer_factories[ model.ExternalService.data_transfer_protocol.SCP ] scp_data_transfer.parse( self.config_file, data_transfer_elem ) - self.data_transfer[ model.ExternalService.data_transfer_types.SCP ] = scp_data_transfer + self.data_transfer[ model.ExternalService.data_transfer_protocol.SCP ] = scp_data_transfer def parse_run_details( self, root ): self.run_details = {} run_details_elem = root.find( 'run_details' ) if run_details_elem: results_elem = run_details_elem.find( 'results' ) if results_elem: - # get the list of resulting datatypes + # Get the list of resulting datatypes + # TODO: the 'results_urls' attribute is only useful if the transfer protocol is http(s), so check if that is the case. self.run_details[ 'results' ], self.run_details[ 'results_urls' ] = self.parse_run_details_results( results_elem ) def parse_run_details_results( self, root ): datatypes_dict = {} --- a/lib/galaxy/web/controllers/external_service.py Tue Apr 12 23:41:06 2011 -0400 +++ b/lib/galaxy/web/controllers/external_service.py Wed Apr 13 13:52:05 2011 -0400 @@ -176,7 +176,6 @@ trans.sa_session.add( external_service ) trans.sa_session.add( external_service.form_values ) trans.sa_session.flush() - external_service.load_data_transfer_settings( trans ) else: # We're saving a newly created external_service external_service_type = self.get_external_service_type( trans, external_service_type_id ) --- a/lib/galaxy/web/controllers/requests_admin.py Tue Apr 12 23:41:06 2011 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Wed Apr 13 13:52:05 2011 -0400 @@ -351,22 +351,11 @@ request_id = kwd.get( 'request_id', None ) external_service_id = kwd.get( 'external_service_id', None ) files = [] - def handle_error( **kwd ): - kwd[ 'status' ] = 'error' - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='select_datasets_to_transfer', - **kwd ) ) - try: - request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) - except: - return invalid_id_redirect( trans, 'requests_admin', request_id ) - try: - external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) ) - except: - return invalid_id_redirect( trans, 'requests_admin', external_service_id, 'external_service', action='browse_external_services' ) - # load the data transfer settings + request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) + external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) ) + # Load the data transfer settings external_service.load_data_transfer_settings( trans ) - scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_types.SCP ] + scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_protocol.SCP ] selected_datasets_to_transfer = util.restore_text( params.get( 'selected_datasets_to_transfer', '' ) ) if selected_datasets_to_transfer: selected_datasets_to_transfer = selected_datasets_to_transfer.split(',') @@ -383,10 +372,13 @@ if params.get( 'select_datasets_to_transfer_button', False ): # Get the sample that was sequenced to produce these datasets. if sample_id == 'none': + del kwd[ 'select_datasets_to_transfer_button' ] message = 'Select the sample that was sequenced to produce the datasets you want to transfer.' kwd[ 'message' ] = message - del kwd[ 'select_datasets_to_transfer_button' ] - handle_error( **kwd ) + kwd[ 'status' ] = 'error' + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='select_datasets_to_transfer', + **kwd ) ) if not sample.library: # Display an error if a sample has been selected that # has not yet been associated with a destination library. @@ -399,7 +391,7 @@ status=status, message=message ) ) # Save the sample datasets - sample_dataset_file_names = self.__save_sample_datasets( trans, sample, selected_datasets_to_transfer, external_service ) + sample_dataset_file_names = self.__create_sample_datasets( trans, sample, selected_datasets_to_transfer, external_service ) if sample_dataset_file_names: message = 'Datasets (%s) have been selected for sample (%s)' % \ ( str( sample_dataset_file_names )[1:-1].replace( "'", "" ), sample.name ) @@ -426,24 +418,31 @@ # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' - request = trans.sa_session.query( trans.model.Request ).get( int( id ) ) - external_service = trans.sa_session.query( trans.model.ExternalService ).get( int( external_service_id ) ) + request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) + external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) ) external_service.load_data_transfer_settings( trans ) - scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_types.SCP ] - cmd = 'ssh %s@%s "ls -oghp \'%s\'"' % ( scp_configs['user_name'], - scp_configs['host'], + scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_protocol.SCP ] + cmd = 'ssh %s@%s "ls -oghp \'%s\'"' % ( scp_configs[ 'user_name' ], + scp_configs[ 'host' ], folder_path ) + # TODO: this currently requires rsh / ssh keys to be set. If they are not, the process + # hangs. Add an event that handles the authentication message if keys are not set - the + # message is something like: "Are you sure you want to continue connecting (yes/no)." output = pexpect.run( cmd, - events={ '.ssword:*' : scp_configs[ 'password'] + '\r\n', pexpect.TIMEOUT : print_ticks }, + events={ '.ssword:*' : scp_configs[ 'password' ] + '\r\n', + pexpect.TIMEOUT : print_ticks }, timeout=10 ) + if 'Password:\r\n' in output: + # Eliminate the output created using ssh from the tree + output = output.replace( 'Password:\r\n', '' ) return unicode( output.replace( '\n', '<br/>' ) ) @web.json def open_folder( self, trans, request_id, external_service_id, key ): # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' - request = trans.sa_session.query( trans.model.Request ).get( int( request_id ) ) - external_service = trans.sa_session.query( trans.model.ExternalService ).get( int( external_service_id ) ) + request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) ) + external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) ) folder_path = key files_list = self.__get_files( trans, request, external_service, folder_path ) folder_contents = [] @@ -451,49 +450,57 @@ is_folder = False if filename[-1] == os.sep: is_folder = True - full_path = os.path.join(folder_path, filename) - node = {"title": filename, - "isFolder": is_folder, - "isLazy": is_folder, - "tooltip": full_path, - "key": full_path - } - folder_contents.append(node) + full_path = os.path.join( folder_path, filename ) + node = { "title": filename, + "isFolder": is_folder, + "isLazy": is_folder, + "tooltip": full_path, + "key": full_path } + folder_contents.append( node ) return folder_contents def __get_files( self, trans, request, external_service, folder_path ): # Retrieves the filenames to be transferred from the remote host. ok = True external_service.load_data_transfer_settings( trans ) - scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_types.SCP ] + scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_protocol.SCP ] if not scp_configs[ 'host' ] or not scp_configs[ 'user_name' ] or not scp_configs[ 'password' ]: status = 'error' message = "Error in external service login information." ok = False def print_ticks( d ): pass - cmd = 'ssh %s@%s "ls -p \'%s\'"' % ( scp_configs['user_name'], scp_configs['host'], folder_path ) + cmd = 'ssh %s@%s "ls -p \'%s\'"' % ( scp_configs[ 'user_name' ], scp_configs[ 'host' ], folder_path ) + # TODO: this currently requires rsh / ssh keys to be set. If they are not, the process + # hangs. Add an event that handles the authentication message if keys are not set - the + # message is something like: "Are you sure you want to continue connecting (yes/no)." output = pexpect.run( cmd, - events={ '.ssword:*' : scp_configs['password'] + '\r\n', pexpect.TIMEOUT : print_ticks }, + events={ '.ssword:*' : scp_configs[ 'password' ] + '\r\n', + pexpect.TIMEOUT : print_ticks }, timeout=10 ) if 'No such file or directory' in output: status = 'error' message = "No folder named (%s) exists on the external service." % folder_path ok = False if ok: - return output.splitlines() + if 'Password:' in output: + # Eliminate the output created using ssh from the tree + output_as_list = output.splitlines() + output_as_list.remove( 'Password:' ) + else: + output_as_list = output.splitlines() + return output_as_list return trans.response.send_redirect( web.url_for( controller='requests_admin', action='select_datasets_to_transfer', request_id=trans.security.encode_id( request.id ), status=status, message=message ) ) - def __save_sample_datasets( self, trans, sample, selected_datasets_to_transfer, external_service ): + def __create_sample_datasets( self, trans, sample, selected_datasets_to_transfer, external_service ): external_service.load_data_transfer_settings( trans ) - scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_types.SCP ] + scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_protocol.SCP ] sample_dataset_file_names = [] if selected_datasets_to_transfer: for filepath in selected_datasets_to_transfer: - # FIXME: handle folder selection - # ignore folders for now + # FIXME: handle folder selection - ignore folders for now if filepath[-1] != os.sep: name = self.__rename_dataset( sample, filepath.split( '/' )[-1], scp_configs ) status = trans.app.model.SampleDataset.transfer_status.NOT_STARTED @@ -522,25 +529,26 @@ else: new_name = name return util.sanitize_for_filename( new_name ) - def __check_library_add_permission( self, trans, target_library, target_folder ): + def __ensure_library_add_permission( self, trans, target_library, target_folder ): """ - Checks if the current admin user had ADD_LIBRARY permission on the target library - and the target folder, if not provide the permissions. + Ensures the current admin user has ADD_LIBRARY permission on the target data library and folder. """ current_user_roles = trans.user.all_roles() current_user_private_role = trans.app.security_agent.get_private_user_role( trans.user ) - # Make sure this user has LIBRARY_ADD permissions on the target library and folder. - # If not, give them permission. + flush_needed = False if not trans.app.security_agent.can_add_library_item( current_user_roles, target_library ): lp = trans.model.LibraryPermissions( trans.app.security_agent.permitted_actions.LIBRARY_ADD.action, target_library, current_user_private_role ) trans.sa_session.add( lp ) + flush_needed = True if not trans.app.security_agent.can_add_library_item( current_user_roles, target_folder ): lfp = trans.model.LibraryFolderPermissions( trans.app.security_agent.permitted_actions.LIBRARY_ADD.action, target_folder, current_user_private_role ) trans.sa_session.add( lfp ) + flush_needed = True + if flush_needed: trans.sa_session.flush() def __create_data_transfer_messages( self, trans, sample, selected_sample_datasets ): """ @@ -587,7 +595,7 @@ messages = [] for external_service, dataset_elem in dataset_elements.items(): external_service.load_data_transfer_settings( trans ) - scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_types.SCP ] + scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_protocol.SCP ] # Check data transfer settings err_msg = self.__validate_data_transfer_settings( trans, sample.request.type, scp_configs ) if err_msg: @@ -596,16 +604,16 @@ sample_id=trans.security.encode_id( sample.id ), status='error', message=err_msg ) ) - message = xml % dict( GALAXY_HOST=trans.request.host, - API_KEY=trans.user.api_keys[0].key, - DATA_HOST=scp_configs[ 'host' ], - DATA_USER=scp_configs[ 'user_name' ], - DATA_PASSWORD=scp_configs[ 'password' ], - REQUEST_ID=str( sample.request.id ), - SAMPLE_ID=str( sample.id ), - LIBRARY_ID=str( sample.library.id ), - FOLDER_ID=str( sample.folder.id ), - DATASETS=dataset_elem ) + message = xml % dict( GALAXY_HOST=trans.request.host, + API_KEY=trans.user.api_keys[0].key, + DATA_HOST=scp_configs[ 'host' ], + DATA_USER=scp_configs[ 'user_name' ], + DATA_PASSWORD=scp_configs[ 'password' ], + REQUEST_ID=str( sample.request.id ), + SAMPLE_ID=str( sample.id ), + LIBRARY_ID=str( sample.library.id ), + FOLDER_ID=str( sample.folder.id ), + DATASETS=dataset_elem ) messages.append( message.replace( '\n', '' ).replace( '\r', '' ) ) return messages def __validate_data_transfer_settings( self, trans, request_type, scp_configs ): @@ -620,10 +628,10 @@ err_msg += "The 'enable_api = True' setting is not correctly set in the Galaxy config file. " if not trans.user.api_keys: err_msg += "Set your API Key in your User Preferences to transfer datasets. " - # check if library_import_dir is set + # Check if library_import_dir is set if not trans.app.config.library_import_dir: err_msg = "'The library_import_dir' setting is not correctly set in the Galaxy config file. " - # check the RabbitMQ server settings in the config file + # Check the RabbitMQ server settings in the config file for k, v in trans.app.config.amqp.items(): if not v: err_msg += 'Set RabbitMQ server settings in the "galaxy_amqp" section of the Galaxy config file, specifically "%s" is not set.' % k @@ -632,60 +640,79 @@ @web.expose @web.require_admin def initiate_data_transfer( self, trans, sample_id, sample_datasets=[], sample_dataset_id='' ): - ''' - Initiate the transfer of the datasets from the external service to the target Galaxy data library: - - The admin user must have LIBRARY_ADD permission for the target library and folder - - Create an XML message encapsulating all the data transfer information and send it - to the message queue (RabbitMQ broker). - ''' + # Initiate the transfer of the datasets from the external service to the target Galaxy data library. + # The admin user must have LIBRARY_ADD permission for the target library and folder try: sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) except: return invalid_id_redirect( trans, 'requests_admin', sample_id, 'sample' ) - err_msg = '' - # Make sure the current user has LIBRARY_ADD - # permission on the target library and folder. - self.__check_library_add_permission( trans, sample.library, sample.folder ) + message = "" + status = "done" + # Make sure the current admin user has LIBRARY_ADD permission on the target data library and folder. + self.__ensure_library_add_permission( trans, sample.library, sample.folder ) if sample_dataset_id and not sample_datasets: # Either a list of SampleDataset objects or a comma-separated string of # encoded SampleDataset ids can be received. If the latter, parse the - # sample_dataset_id to build the list of sample_datasets. + # sample_dataset_id string to build the list of sample_datasets. id_list = util.listify( sample_dataset_id ) for sample_dataset_id in id_list: sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) ) sample_datasets.append( sample_dataset ) - # Create the message - messages = self.__create_data_transfer_messages( trans, sample, sample_datasets ) - # Send the messages - for message in messages: - try: - conn = amqp.Connection( host=trans.app.config.amqp[ 'host' ] + ":" + trans.app.config.amqp[ 'port' ], - userid=trans.app.config.amqp[ 'userid' ], - password=trans.app.config.amqp[ 'password' ], - virtual_host=trans.app.config.amqp[ 'virtual_host' ], - insist=False ) - chan = conn.channel() - msg = amqp.Message( message, - content_type='text/plain', - application_headers={ 'msg_type': 'data_transfer' } ) - msg.properties[ "delivery_mode" ] = 2 - chan.basic_publish( msg, - exchange=trans.app.config.amqp[ 'exchange' ], - routing_key=trans.app.config.amqp[ 'routing_key' ] ) - chan.close() - conn.close() - except Exception, e: - err_msg = "Error sending the data transfer message to the Galaxy AMQP message queue:<br/>%s" % str(e) - if not err_msg: - err_msg = "%i datasets have been queued for transfer from the external service." % len( sample_datasets ) - status = "done" + if trans.app.config.enable_beta_job_managers: + # For now, assume that all SampleDatasets use the same external service ( this may not be optimal ). + if sample_datasets: + external_service_type_id = sample_datasets[0].external_service.external_service_type_id + # Here external_service_type_id will be something like '454_life_sciences' + external_service = sample.request.type.get_external_service( external_service_type_id ) + external_service_type = external_service.get_external_service_type( trans ) + external_service.load_data_transfer_settings( trans ) + # For now only scp is supported. + scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_protocol.SCP ] + if not scp_configs[ 'automatic_transfer' ]: + deferred_plugin = 'ManualDataTransferPlugin' + else: + raise Exception( "Automatic data transfer using scp is not yet suppored." ) + trans.app.job_manager.deferred_job_queue.plugins[ deferred_plugin ].create_job( trans, + sample=sample, + sample_datasets=sample_datasets, + external_service=external_service, + external_service_type=external_service_type ) else: - status = 'error' + # TODO: Using RabbitMq for now, but eliminate this entire block when we replace RabbitMq with Galaxy's + # own messaging engine. We're holding off on using the new way to transfer files manually until we + # implement a Galaxy-proprietary messaging engine because the deferred job plugins currently perform + # constant db hits to check for deferred jobs that are not in a finished state. + # Create the message + messages = self.__create_data_transfer_messages( trans, sample, sample_datasets ) + # Send the messages + for rmq_msg in messages: + try: + conn = amqp.Connection( host=trans.app.config.amqp[ 'host' ] + ":" + trans.app.config.amqp[ 'port' ], + userid=trans.app.config.amqp[ 'userid' ], + password=trans.app.config.amqp[ 'password' ], + virtual_host=trans.app.config.amqp[ 'virtual_host' ], + insist=False ) + chan = conn.channel() + msg = amqp.Message( rmq_msg, + content_type='text/plain', + application_headers={ 'msg_type': 'data_transfer' } ) + msg.properties[ "delivery_mode" ] = 2 + chan.basic_publish( msg, + exchange=trans.app.config.amqp[ 'exchange' ], + routing_key=trans.app.config.amqp[ 'routing_key' ] ) + chan.close() + conn.close() + except Exception, e: + message = "Error sending the data transfer message to the Galaxy AMQP message queue:<br/>%s" % str(e) + status = "error" + if not message: + message = "%i datasets have been queued for transfer from the external service." % len( sample_datasets ) + status = "done" return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_datasets', sample_id=trans.security.encode_id( sample.id ), - status=status, - message=err_msg ) ) + message=message, + status=status ) ) @web.expose def update_sample_dataset_status(self, trans, cntrller, sample_dataset_ids, new_status, error_msg=None ): # check if the new status is a valid transfer status --- a/scripts/galaxy_messaging/server/amqp_consumer.py Tue Apr 12 23:41:06 2011 -0400 +++ b/scripts/galaxy_messaging/server/amqp_consumer.py Wed Apr 13 13:52:05 2011 -0400 @@ -3,7 +3,7 @@ Galaxy uses AMQ protocol to receive messages from external sources like bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. For Galaxy to receive messages from a message queue the RabbitMQ server has -to be set up with a user account and other parameters listed in the [galaxy:amq] +to be set up with a user account and other parameters listed in the [galaxy_amqp] section in the universe_wsgi.ini config file Once the RabbitMQ server has been setup and started with the given parameters, this script can be run to receive messages and update the Galaxy database accordingly --- a/scripts/transfer.py Tue Apr 12 23:41:06 2011 -0400 +++ b/scripts/transfer.py Wed Apr 13 13:52:05 2011 -0400 @@ -4,22 +4,17 @@ Manager (galaxy.jobs.transfer_manager) and should not normally be invoked by hand. """ - -import os, sys, optparse, ConfigParser, socket, SocketServer, threading, logging, random - -import urllib2, tempfile - -import time - -log = logging.getLogger( __name__ ) -log.setLevel( logging.INFO ) -handler = logging.StreamHandler( sys.stdout ) -log.addHandler( handler ) +import os, sys, optparse, ConfigParser, socket, SocketServer, threading, logging, random, urllib2, tempfile, time galaxy_root = os.path.abspath( os.path.join( os.path.dirname( __file__ ), '..' ) ) sys.path.insert( 0, os.path.abspath( os.path.join( galaxy_root, 'lib' ) ) ) from galaxy import eggs + +import pkg_resources +pkg_resources.require( "pexpect" ) +import pexpect + eggs.require( "SQLAlchemy >= 0.4" ) from sqlalchemy import * @@ -32,6 +27,11 @@ eggs.require( 'python_daemon' ) from daemon import DaemonContext +log = logging.getLogger( __name__ ) +log.setLevel( logging.DEBUG ) +handler = logging.StreamHandler( sys.stdout ) +log.addHandler( handler ) + debug = False slow = False @@ -49,7 +49,7 @@ def parse( self ): self.opts, args = self.parser.parse_args() if len( args ) != 1: - log.error( 'usage: transfer.py [options] <transfer job id>' ) + log.error( 'usage: transfer.py <transfer job id>' ) sys.exit( 1 ) try: self.transfer_job_id = int( args[0] ) @@ -138,57 +138,55 @@ self.result = result def transfer( app, transfer_job_id ): - transfer_job = app.get_transfer_job( transfer_job_id ) if transfer_job is None: log.error( 'Invalid transfer job ID: %s' % transfer_job_id ) return False - port_range = app.config.get( 'app:main', 'transfer_worker_port_range' ) try: port_range = [ int( p ) for p in port_range.split( '-' ) ] except Exception, e: log.error( 'Invalid port range set in transfer_worker_port_range: %s: %s' % ( port_range, str( e ) ) ) return False - - protocol = transfer_job.params['url'].split( '://' )[0] - if protocol not in ( 'http', 'https' ): + protocol = transfer_job.params[ 'protocol' ] + if protocol not in ( 'http', 'https', 'scp' ): log.error( 'Unsupported protocol: %s' % protocol ) return False - state_result = StateResult( result = dict( state = transfer_job.states.RUNNING, info='Transfer process starting up.' ) ) - listener_server = ListenerServer( range( port_range[0], port_range[1] + 1 ), ListenerRequestHandler, app, transfer_job, state_result ) - # daemonize here (if desired) if not debug: daemon_context = DaemonContext( files_preserve=[ listener_server.fileno() ], working_directory=os.getcwd() ) daemon_context.open() - # If this fails, it'll never be detected. Hopefully it won't fail since it succeeded once. app.connect_database() # daemon closed the database fd transfer_job = app.get_transfer_job( transfer_job_id ) - listener_thread = threading.Thread( target=listener_server.serve_forever ) listener_thread.setDaemon( True ) listener_thread.start() - # Store this process' pid so unhandled deaths can be handled by the restarter transfer_job.pid = os.getpid() app.sa_session.add( transfer_job ) app.sa_session.flush() - terminal_state = None - if protocol in ( 'http', 'https' ): - for state in http_transfer( transfer_job ): - state_result.result = state - if state['state'] in transfer_job.terminal_states: - terminal_state = state + if protocol in [ 'http', 'https' ]: + for transfer_result_dict in http_transfer( transfer_job ): + state_result.result = transfer_result_dict + if transfer_result_dict[ 'state' ] in transfer_job.terminal_states: + terminal_state = transfer_result_dict + elif protocol in [ 'scp' ]: + # Transfer the file using scp + transfer_result_dict = scp_transfer( transfer_job ) + # Handle the state of the transfer + state = transfer_result_dict[ 'state' ] + state_result.result = transfer_result_dict + if state in transfer_job.terminal_states: + terminal_state = transfer_result_dict if terminal_state is not None: - transfer_job.state = terminal_state['state'] - for name in ( 'info', 'path' ): + transfer_job.state = terminal_state[ 'state' ] + for name in [ 'info', 'path' ]: if name in terminal_state: - transfer_job.__setattr__( name, terminal_state[name] ) + transfer_job.__setattr__( name, terminal_state[ name ] ) else: transfer_job.state = transfer_job.states.ERROR transfer_job.info = 'Unknown error encountered by transfer worker.' @@ -197,9 +195,7 @@ return True def http_transfer( transfer_job ): - """ - "Plugin" for handling http(s) transfers. - """ + """Plugin" for handling http(s) transfers.""" url = transfer_job.params['url'] try: f = urllib2.urlopen( url ) @@ -243,16 +239,41 @@ return return +def scp_transfer( transfer_job ): + """Plugin" for handling scp transfers using pexpect""" + def print_ticks( d ): + pass + host = transfer_job.params[ 'host' ] + user_name = transfer_job.params[ 'user_name' ] + password = transfer_job.params[ 'password' ] + file_path = transfer_job.params[ 'file_path' ] + try: + fh, fn = tempfile.mkstemp() + except Exception, e: + return dict( state = transfer_job.states.ERROR, info = 'Unable to create temporary file for transfer: %s' % str( e ) ) + try: + # TODO: add the ability to determine progress of the copy here like we do in the http_transfer above. + cmd = "scp %s@%s:'%s' '%s'" % ( user_name, + host, + file_path.replace( ' ', '\ ' ), + fn ) + output = pexpect.run( cmd, + events={ '.ssword:*': password + '\r\n', + pexpect.TIMEOUT: print_ticks }, + timeout=10 ) + return dict( state = transfer_job.states.DONE, path = fn ) + except Exception, e: + return dict( state = transfer_job.states.ERROR, info = 'Error during file transfer: %s' % str( e ) ) + if __name__ == '__main__': - arg_handler = ArgHandler() arg_handler.parse() app = GalaxyApp( arg_handler.opts.config ) - log.debug( 'Initiating transfer' ) + log.debug( 'Initiating transfer...' ) if transfer( app, arg_handler.transfer_job_id ): log.debug( 'Finished' ) else: - log.error( 'Error in transfer process' ) + log.error( 'Error in transfer process...' ) sys.exit( 1 ) sys.exit( 0 ) --- a/templates/admin/requests/select_datasets_to_transfer.mako Tue Apr 12 23:41:06 2011 -0400 +++ b/templates/admin/requests/select_datasets_to_transfer.mako Wed Apr 13 13:52:05 2011 -0400 @@ -23,56 +23,60 @@ minExpandLevel: 0, // 1: root node is not collapsible persist: false, checkbox: true, - selectMode: 3, + selectMode: 3, onPostInit: function(isReloading, isError) { -// alert("reloading: "+isReloading+", error:"+isError); - logMsg("onPostInit(%o, %o) - %o", isReloading, isError, this); - // Re-fire onActivate, so the text is updated - this.reactivate(); + //alert("reloading: "+isReloading+", error:"+isError); + logMsg("onPostInit(%o, %o) - %o", isReloading, isError, this); + // Re-fire onActivate, so the text is updated + this.reactivate(); }, fx: { height: "toggle", duration: 200 }, - // initAjax is hard to fake, so we pass the children as object array: - initAjax: {url: "${h.url_for( controller='requests_admin', action='open_folder' )}", - dataType: "json", - data: { request_id: "${request.id}", external_service_id: "${external_service.id}", key: "${scp_configs['data_location']}" }, - }, - onLazyRead: function(dtnode){ - dtnode.appendAjax({ - url: "${h.url_for( controller='requests_admin', action='open_folder' )}", - dataType: "json", - data: { request_id: "${request.id}", external_service_id: "${external_service.id}", key: dtnode.data.key }, + // initAjax is hard to fake, so we pass the children as object array: + initAjax: {url: "${h.url_for( controller='requests_admin', action='open_folder' )}", + dataType: "json", + data: { request_id: "${trans.security.encode_id( request.id )}", external_service_id: "${trans.security.encode_id( external_service.id )}", key: "${scp_configs['data_location']}" }, + }, + onLazyRead: function(dtnode){ + dtnode.appendAjax({ + url: "${h.url_for( controller='requests_admin', action='open_folder' )}", + dataType: "json", + data: { request_id: "${trans.security.encode_id( request.id )}", external_service_id: "${trans.security.encode_id( external_service.id )}", key: dtnode.data.key }, + }); + }, + onSelect: function(select, dtnode) { + // Display list of selected nodes + var selNodes = dtnode.tree.getSelectedNodes(); + // convert to title/key array + var selKeys = $.map(selNodes, function(node){ + return node.data.key; + }); + document.select_datasets_to_transfer.selected_datasets_to_transfer.value = selKeys.join(",") + }, + onActivate: function(dtnode) { + var cell = $("#file_details"); + var selected_value; + if (dtnode.data.key == 'root') { + selected_value = "${scp_configs['data_location']}/"; + } else { + selected_value = dtnode.data.key; + }; + if (selected_value.charAt(selected_value.length-1) != '/') { + // Make ajax call + $.ajax( { + type: "POST", + url: "${h.url_for( controller='requests_admin', action='get_file_details' )}", + dataType: "json", + data: { request_id: "${trans.security.encode_id(request.id)}", external_service_id: "${trans.security.encode_id(external_service.id)}", folder_path: selected_value }, + success : function ( data ) { + cell.html( '<label>'+data+'</label>' ) + } }); - }, - onSelect: function(select, dtnode) { - // Display list of selected nodes - var selNodes = dtnode.tree.getSelectedNodes(); - // convert to title/key array - var selKeys = $.map(selNodes, function(node){ - return node.data.key; - }); - document.select_datasets_to_transfer.selected_datasets_to_transfer.value = selKeys.join(",") - }, - onActivate: function(dtnode) { - var cell = $("#file_details"); - var selected_value = dtnode.data.key - if(selected_value.charAt(selected_value.length-1) != '/') { - // Make ajax call - $.ajax( { - type: "POST", - url: "${h.url_for( controller='requests_admin', action='get_file_details' )}", - dataType: "json", - data: { request_id: "${request.id}", external_service_id: "${external_service.id}", folder_path: dtnode.data.key }, - success : function ( data ) { - cell.html( '<label>'+data+'</label>' ) - } - }); } else { - cell.html( '' ) - } - }, - }); + cell.html( '' ); + }; + }, + }); }); - </script><% Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: trackster: Don't load huge reference tracks now that we pre-load data, preventing hang
by Bitbucket 12 Apr '11

12 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9e3864eeeb0a/ changeset: r5372:9e3864eeeb0a user: kanwei date: 2011-04-13 05:41:06 summary: trackster: Don't load huge reference tracks now that we pre-load data, preventing hang affected #: 1 file (240 bytes) --- a/static/scripts/trackster.js Tue Apr 12 22:08:09 2011 -0400 +++ b/static/scripts/trackster.js Tue Apr 12 23:41:06 2011 -0400 @@ -244,6 +244,11 @@ * Load data from server; returns AJAX object so that use of Deferred is possible. */ load_data: function(chrom, low, high, mode, resolution, extra_params) { + if (this.track.track_type == "ReferenceTrack" && resolution > 1) { + // Now that data is pre-fetched before draw, we don't load reference tracks + // unless it's at the bottom level + return; + } // Setup data request params. var params = {"chrom": chrom, "low": low, "high": high, "mode": mode, "resolution": resolution, "dataset_id" : this.track.dataset_id, 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: kanwei: Fix some scramble problems
by Bitbucket 12 Apr '11

12 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/01cb4107bb2d/ changeset: r5371:01cb4107bb2d user: kanwei date: 2011-04-13 04:08:09 summary: Fix some scramble problems affected #: 3 files (46 bytes) --- a/lib/galaxy/eggs/__init__.py Tue Apr 12 17:26:06 2011 -0400 +++ b/lib/galaxy/eggs/__init__.py Tue Apr 12 22:08:09 2011 -0400 @@ -219,7 +219,7 @@ pkg_resources.working_set.entry_keys[entry] = [] if entry in sys.path: sys.path.remove(entry) - # if the conflict is a dpeendent egg, fetch that specific egg + # if the conflict is a dependent egg, fetch that specific egg if egg: # Store the removed path so the fetch method can use it egg.removed_location = location --- a/lib/galaxy/eggs/dist.py Tue Apr 12 17:26:06 2011 -0400 +++ b/lib/galaxy/eggs/dist.py Tue Apr 12 22:08:09 2011 -0400 @@ -84,7 +84,7 @@ for platform in platforms: if name in self.ignore and platform in self.ignore[name].split(): continue - egg = DistScrambleEgg( name, version, tag, url, platform ) + egg = DistScrambleEgg( name, version, tag, url, platform, self ) host_info = self.hosts[platform].split() egg.build_host, egg.python = host_info[:2] egg.sources = sources --- a/scripts/dist-scramble.py Tue Apr 12 17:26:06 2011 -0400 +++ b/scripts/dist-scramble.py Tue Apr 12 22:08:09 2011 -0400 @@ -15,6 +15,7 @@ sys.path.append( lib ) from galaxy.eggs.dist import DistScrambleCrate, ScrambleFailure +from galaxy.eggs import EggNotFetchable if len( sys.argv ) > 3 or len( sys.argv ) < 2: print __doc__ 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: Make changes in ddea56886275 compatible with python 2.4
by Bitbucket 12 Apr '11

12 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1cb94990d839/ changeset: r5370:1cb94990d839 user: jgoecks date: 2011-04-12 23:26:06 summary: Make changes in ddea56886275 compatible with python 2.4 affected #: 1 file (298 bytes) --- a/lib/galaxy/datatypes/util/gff_util.py Tue Apr 12 14:40:59 2011 -0400 +++ b/lib/galaxy/datatypes/util/gff_util.py Tue Apr 12 17:26:06 2011 -0400 @@ -149,8 +149,9 @@ self.seed_interval = GenomicIntervalReader.next( self ) except ParseError, e: handle_parse_error( e ) - finally: - raw_size += len( self.current_line ) + # TODO: When no longer supporting python 2.4 use finally: + #finally: + raw_size += len( self.current_line ) # If header or comment, clear seed interval and return it. if isinstance( self.seed_interval, ( Header, Comment ) ): @@ -170,16 +171,20 @@ while True: try: interval = GenomicIntervalReader.next( self ) + raw_size += len( self.current_line ) except StopIteration, e: # No more intervals to read, but last feature needs to be # returned. interval = None + raw_size += len( self.current_line ) break except ParseError, e: handle_parse_error( e ) + raw_size += len( self.current_line ) continue - finally: - raw_size += len( self.current_line ) + # TODO: When no longer supporting python 2.4 use finally: + #finally: + #raw_size += len( self.current_line ) # If interval not associated with feature, break. group = interval.attributes.get( 'group', None ) 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: Trackster: add histogram mode to feature tracks so that user can generate coverage histogram at any level of data. Refactor overlap computation out of modules for now since it's a general purpose method used in multiple modules.
by Bitbucket 12 Apr '11

12 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/33fe59c762a8/ changeset: r5369:33fe59c762a8 user: jgoecks date: 2011-04-12 20:40:59 summary: Trackster: add histogram mode to feature tracks so that user can generate coverage histogram at any level of data. Refactor overlap computation out of modules for now since it's a general purpose method used in multiple modules. affected #: 1 file (4.6 KB) --- a/static/scripts/trackster.js Tue Apr 12 12:10:48 2011 -0400 +++ b/static/scripts/trackster.js Tue Apr 12 14:40:59 2011 -0400 @@ -14,6 +14,50 @@ return target; }; +/** + * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig. + * The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first + * region overlaps the start (but not the end) of the second region. + */ +var BEFORE = 1001, CONTAINS = 1002, OVERLAP_START = 1003, OVERLAP_END = 1004, CONTAINED_BY = 1005, AFTER = 1006; +var compute_overlap = function(first_region, second_region) { + var + first_start = first_region[0], first_end = first_region[1], + second_start = second_region[0], second_end = second_region[1], + overlap; + if (first_start < second_start) { + if (first_end < second_start) { + overlap = BEFORE; + } + else if (first_end <= second_end) { + overlap = OVERLAP_START; + } + else { // first_end > second_end + overlap = CONTAINS; + } + } + else { // first_start >= second_start + if (first_start > second_end) { + overlap = AFTER; + } + else if (first_end <= second_end) { + overlap = CONTAINED_BY; + } + else { + overlap = OVERLAP_END; + } + } + + return overlap; +}; +/** + * Returns true if regions overlap. + */ +var is_overlap = function(first_region, second_region) { + var overlap = compute_overlap(first_region, second_region); + return (overlap !== BEFORE && overlap !== AFTER); +}; + // Encapsulate -- anything to be availabe outside this block is added to exports var trackster_module = function(require, exports){ @@ -98,7 +142,7 @@ $(this).insertBefore( children.get( i ) ); } }); -} +}; /** * Calculates step for slider with a given min, max. @@ -106,7 +150,7 @@ var get_slider_step = function(min, max) { var range = max - min; return (range <= 2 ? 0.01 : (range <= 100 ? 1 : (range <= 1000 ? 5 : 10))); -} +}; /** * Init constants & functions used throughout trackster. @@ -142,7 +186,7 @@ function round_1000(num) { return Math.round(num * 1000) / 1000; -} +}; /** * Generic cache that handles key/value pairs. @@ -2061,14 +2105,14 @@ } }); -var FeatureTrack = function (name, view, hda_ldda, dataset_id, prefs, filters, tool, parent_track) { +var FeatureTrack = function(name, view, hda_ldda, dataset_id, prefs, filters, tool, parent_track) { // // Preinitialization: do things that need to be done before calling Track and TiledTrack // initialization code. // var track = this; this.track_type = "FeatureTrack"; - this.display_modes = ["Auto", "Dense", "Squish", "Pack"]; + this.display_modes = ["Auto", "Histogram", "Dense", "Squish", "Pack"]; // Define and restore track configuration. this.track_config = new TrackConfig( { track: this, @@ -2143,6 +2187,84 @@ return inc_slots.slot_features( features ); }, /** + * Given feature data, returns summary tree data. Feature data must be sorted by start + * position. Return value is a dict with keys 'data', 'delta' (bin size) and 'max.' Data + * is a two-item list; first item is bin start, second is bin's count. + */ + get_summary_tree_data: function(data, low, high, bin_size) { + var num_bins = Math.floor((high - low)/bin_size), + bins = [], + max_count = 0; + + /* + // For debugging: + for (var i = 0; i < data.length; i++) + console.log("\t", data[i][1], data[i][2], data[i][3]); + */ + + // + // Loop through bins, counting data for each interval. + // + var data_index_start = 0, + data_index = 0, + data_interval, + bin_index = 0, + bin_interval = [], + cur_bin, + overlap; + + // Set bin interval. + var set_bin_interval = function(interval, low, bin_index, bin_size) { + interval[0] = low + bin_index * bin_size; + interval[1] = low + (bin_index + 1) * bin_size; + }; + + // Loop through bins, data to compute bin counts. Only compute bin counts as long + // as there is data. + while (bin_index < num_bins && data_index_start !== data.length) { + // Find next bin that has data. + var bin_has_data = false; + for (; bin_index < num_bins && !bin_has_data; bin_index++) { + set_bin_interval(bin_interval, low, bin_index, bin_size); + // Loop through data and break if data found that goes in bin. + for (data_index = data_index_start; data_index < data.length; data_index++) { + data_interval = data[data_index].slice(1, 3); + if (is_overlap(data_interval, bin_interval)) { + bin_has_data = true; + break; + } + } + // Break from bin loop if this bin has data. + if (bin_has_data) { + break; + } + } + + // Set start index to current data, which is the first to overlap with this bin + // and perhaps with later bins. + data_start_index = data_index; + + // Count intervals that overlap with bin. + bins[bins.length] = cur_bin = [bin_interval[0], 0]; + for (; data_index < data.length; data_index++) { + data_interval = data[data_index].slice(1, 3); + if (is_overlap(data_interval, bin_interval)) { + cur_bin[1]++; + } + else { break; } + } + + // Update max count. + if (cur_bin[1] > max_count) { + max_count = cur_bin[1]; + } + + // Go to next bin. + bin_index++; + } + return {max: max_count, delta: bin_size, data: bins}; + }, + /** * Draw FeatureTrack tile. */ draw_tile: function(result, resolution, tile_index, parent_element, w_scale, ref_seq) { @@ -2156,7 +2278,7 @@ left_offset = this.left_offset, slots, required_height; - + // Set display mode if Auto. if (mode === "Auto") { if (result.dataset_type === "summary_tree") { @@ -2211,6 +2333,35 @@ // Canvas element is returned return canvas; } + + // Drawing coverage histogram. This is different from summary tree because data can feature + // details, but user has requested a histogram. + if (mode === "Histogram") { + // Set height of parent_element + required_height = this.summary_draw_height; + parent_element.parent().css("height", Math.max(this.height_px, required_height) + "px"); + // Add label to container div showing maximum count + // TODO: this shouldn't be done at the tile level + this.container_div.find(".yaxislabel").remove(); + var max_label = $("<div />").addClass('yaxislabel'); + max_label.text( result.max ); + max_label.css({ position: "absolute", top: "22px", left: "10px" }); + max_label.prependTo(this.container_div); + // Create canvas + var canvas = this.view.canvas_manager.new_canvas(); + canvas.width = width + left_offset; + // Extra padding at top of summary tree + canvas.height = required_height + SUMMARY_TREE_TOP_PADDING; + // Paint summary tree into canvas. + var binned_data = this.get_summary_tree_data(result.data, tile_low, tile_high, 200); + var painter = new painters.SummaryTreePainter(binned_data, tile_low, tile_high, this.prefs); + var ctx = canvas.getContext("2d"); + // Deal with left_offset by translating + ctx.translate(left_offset, SUMMARY_TREE_TOP_PADDING); + painter.draw(ctx, width, required_height); + // Canvas element is returned + return canvas; + } // Start dealing with row-by-row tracks @@ -3090,43 +3241,6 @@ } }); -/** - * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig. - * The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first - * region overlaps the start (but not the end) of the second region. - */ -var NO_OVERLAP = 1001, CONTAINS = 1002, OVERLAP_START = 1003, OVERLAP_END = 1004, CONTAINED_BY = 1005; -var compute_overlap = function(first_region, second_region) { - var - first_start = first_region[0], first_end = first_region[1], - second_start = second_region[0], second_end = second_region[1], - overlap; - if (first_start < second_start) { - if (first_end < second_start) { - overlap = NO_OVERLAP; - } - else if (first_end <= second_end) { - overlap = OVERLAP_START; - } - else { // first_end > second_end - overlap = CONTAINS; - } - } - else { // first_start >= second_start - if (first_start > second_end) { - overlap = NO_OVERLAP; - } - else if (first_end <= second_end) { - overlap = CONTAINED_BY; - } - else { - overlap = OVERLAP_END; - } - } - - return overlap; -} - var ReadPainter = function( data, view_start, view_end, prefs, mode, ref_seq ) { FeaturePainter.call( this, data, view_start, view_end, prefs, mode ); this.ref_seq = ref_seq; @@ -3208,8 +3322,7 @@ case "S": // Soft clipping. case "M": // Match. case "=": // Equals. - var seq_tile_overlap = compute_overlap([seq_start, seq_start + cig_len], tile_region); - if (seq_tile_overlap !== NO_OVERLAP) { + if (is_overlap([seq_start, seq_start + cig_len], tile_region)) { // Draw. var seq = orig_seq.slice(seq_offset, seq_offset + cig_len); if (gap > 0) { @@ -3258,11 +3371,9 @@ case "I": // Insertion. // Check to see if sequence should be drawn at all by looking at the overlap between // the sequence region and the tile region. - var - seq_tile_overlap = compute_overlap([seq_start, seq_start + cig_len], tile_region), - insert_x_coord = s_start - gap; + var insert_x_coord = s_start - gap; - if (seq_tile_overlap !== NO_OVERLAP) { + if (is_overlap([seq_start, seq_start + cig_len], tile_region)) { var seq = orig_seq.slice(seq_offset, seq_offset + cig_len); // Insertion point is between the sequence start and the previous base: (-gap) moves // back from sequence start to insertion point. 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: kanwei: update jquery to 1.5.2, pack scripts
by Bitbucket 12 Apr '11

12 Apr '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0f3a0c220945/ changeset: r5368:0f3a0c220945 user: kanwei date: 2011-04-12 18:10:48 summary: update jquery to 1.5.2, pack scripts affected #: 3 files (3.2 KB) --- a/static/scripts/jquery.js Tue Apr 12 09:35:36 2011 -0400 +++ b/static/scripts/jquery.js Tue Apr 12 12:10:48 2011 -0400 @@ -1,5 +1,5 @@ /*! - * jQuery JavaScript Library v1.5.1 + * jQuery JavaScript Library v1.5.2 * http://jquery.com/ * * Copyright 2011, John Resig @@ -11,7 +11,7 @@ * Copyright 2011, The Dojo Foundation * Released under the MIT, BSD, and GPL Licenses. * - * Date: Wed Feb 23 13:55:29 2011 -0500 + * Date: Thu Mar 31 15:28:23 2011 -0400 */ (function( window, undefined ) { @@ -69,15 +69,9 @@ // For matching the engine and version of the browser browserMatch, - // Has the ready events already been bound? - readyBound = false, - // The deferred used on DOM ready readyList, - // Promise methods - promiseMethods = "then done fail isResolved isRejected promise".split( " " ), - // The ready event handler DOMContentLoaded, @@ -202,7 +196,7 @@ selector: "", // The current version of jQuery being used - jquery: "1.5.1", + jquery: "1.5.2", // The default length of a jQuery object is 0 length: 0, @@ -427,11 +421,11 @@ }, bindReady: function() { - if ( readyBound ) { + if ( readyList ) { return; } - readyBound = true; + readyList = jQuery._Deferred(); // Catch cases where $(document).ready() is called after the // browser event has already occurred. @@ -811,6 +805,123 @@ return (new Date()).getTime(); }, + // Use of jQuery.browser is frowned upon. + // More details: http://docs.jquery.com/Utilities/jQuery.browser + uaMatch: function( ua ) { + ua = ua.toLowerCase(); + + var match = rwebkit.exec( ua ) || + ropera.exec( ua ) || + rmsie.exec( ua ) || + ua.indexOf("compatible") < 0 && rmozilla.exec( ua ) || + []; + + return { browser: match[1] || "", version: match[2] || "0" }; + }, + + sub: function() { + function jQuerySubclass( selector, context ) { + return new jQuerySubclass.fn.init( selector, context ); + } + jQuery.extend( true, jQuerySubclass, this ); + jQuerySubclass.superclass = this; + jQuerySubclass.fn = jQuerySubclass.prototype = this(); + jQuerySubclass.fn.constructor = jQuerySubclass; + jQuerySubclass.subclass = this.subclass; + jQuerySubclass.fn.init = function init( selector, context ) { + if ( context && context instanceof jQuery && !(context instanceof jQuerySubclass) ) { + context = jQuerySubclass(context); + } + + return jQuery.fn.init.call( this, selector, context, rootjQuerySubclass ); + }; + jQuerySubclass.fn.init.prototype = jQuerySubclass.fn; + var rootjQuerySubclass = jQuerySubclass(document); + return jQuerySubclass; + }, + + browser: {} +}); + +// Populate the class2type map +jQuery.each("Boolean Number String Function Array Date RegExp Object".split(" "), function(i, name) { + class2type[ "[object " + name + "]" ] = name.toLowerCase(); +}); + +browserMatch = jQuery.uaMatch( userAgent ); +if ( browserMatch.browser ) { + jQuery.browser[ browserMatch.browser ] = true; + jQuery.browser.version = browserMatch.version; +} + +// Deprecated, use jQuery.browser.webkit instead +if ( jQuery.browser.webkit ) { + jQuery.browser.safari = true; +} + +if ( indexOf ) { + jQuery.inArray = function( elem, array ) { + return indexOf.call( array, elem ); + }; +} + +// IE doesn't match non-breaking spaces with \s +if ( rnotwhite.test( "\xA0" ) ) { + trimLeft = /^[\s\xA0]+/; + trimRight = /[\s\xA0]+$/; +} + +// All jQuery objects should point back to these +rootjQuery = jQuery(document); + +// Cleanup functions for the document ready method +if ( document.addEventListener ) { + DOMContentLoaded = function() { + document.removeEventListener( "DOMContentLoaded", DOMContentLoaded, false ); + jQuery.ready(); + }; + +} else if ( document.attachEvent ) { + DOMContentLoaded = function() { + // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443). + if ( document.readyState === "complete" ) { + document.detachEvent( "onreadystatechange", DOMContentLoaded ); + jQuery.ready(); + } + }; +} + +// The DOM ready check for Internet Explorer +function doScrollCheck() { + if ( jQuery.isReady ) { + return; + } + + try { + // If IE is used, use the trick by Diego Perini + // http://javascript.nwbox.com/IEContentLoaded/ + document.documentElement.doScroll("left"); + } catch(e) { + setTimeout( doScrollCheck, 1 ); + return; + } + + // and execute any waiting functions + jQuery.ready(); +} + +// Expose jQuery to the global object +return jQuery; + +})(); + + +var // Promise methods + promiseMethods = "then done fail isResolved isRejected promise".split( " " ), + // Static reference to slice + sliceDeferred = [].slice; + +jQuery.extend({ // Create a simple deferred (one callbacks list) _Deferred: function() { var // callbacks list @@ -856,18 +967,14 @@ // resolve with given context and args resolveWith: function( context, args ) { if ( !cancelled && !fired && !firing ) { + // make sure args are available (#8421) + args = args || []; firing = 1; try { while( callbacks[ 0 ] ) { callbacks.shift().apply( context, args ); } } - // We have to add a catch block for - // IE prior to 8 or else the finally - // block will never get executed - catch (e) { - throw e; - } finally { fired = [ context, args ]; firing = 0; @@ -878,7 +985,7 @@ // resolve with this as context and given arguments resolve: function() { - deferred.resolveWith( jQuery.isFunction( this.promise ) ? this.promise() : this, arguments ); + deferred.resolveWith( this, arguments ); return this; }, @@ -941,153 +1048,44 @@ }, // Deferred helper - when: function( object ) { - var lastIndex = arguments.length, - deferred = lastIndex <= 1 && object && jQuery.isFunction( object.promise ) ? - object : - jQuery.Deferred(), - promise = deferred.promise(); - - if ( lastIndex > 1 ) { - var array = slice.call( arguments, 0 ), - count = lastIndex, - iCallback = function( index ) { - return function( value ) { - array[ index ] = arguments.length > 1 ? slice.call( arguments, 0 ) : value; - if ( !( --count ) ) { - deferred.resolveWith( promise, array ); - } - }; - }; - while( ( lastIndex-- ) ) { - object = array[ lastIndex ]; - if ( object && jQuery.isFunction( object.promise ) ) { - object.promise().then( iCallback(lastIndex), deferred.reject ); + when: function( firstParam ) { + var args = arguments, + i = 0, + length = args.length, + count = length, + deferred = length <= 1 && firstParam && jQuery.isFunction( firstParam.promise ) ? + firstParam : + jQuery.Deferred(); + function resolveFunc( i ) { + return function( value ) { + args[ i ] = arguments.length > 1 ? sliceDeferred.call( arguments, 0 ) : value; + if ( !( --count ) ) { + // Strange bug in FF4: + // Values changed onto the arguments object sometimes end up as undefined values + // outside the $.when method. Cloning the object into a fresh array solves the issue + deferred.resolveWith( deferred, sliceDeferred.call( args, 0 ) ); + } + }; + } + if ( length > 1 ) { + for( ; i < length; i++ ) { + if ( args[ i ] && jQuery.isFunction( args[ i ].promise ) ) { + args[ i ].promise().then( resolveFunc(i), deferred.reject ); } else { --count; } } if ( !count ) { - deferred.resolveWith( promise, array ); - } - } else if ( deferred !== object ) { - deferred.resolve( object ); - } - return promise; - }, - - // Use of jQuery.browser is frowned upon. - // More details: http://docs.jquery.com/Utilities/jQuery.browser - uaMatch: function( ua ) { - ua = ua.toLowerCase(); - - var match = rwebkit.exec( ua ) || - ropera.exec( ua ) || - rmsie.exec( ua ) || - ua.indexOf("compatible") < 0 && rmozilla.exec( ua ) || - []; - - return { browser: match[1] || "", version: match[2] || "0" }; - }, - - sub: function() { - function jQuerySubclass( selector, context ) { - return new jQuerySubclass.fn.init( selector, context ); - } - jQuery.extend( true, jQuerySubclass, this ); - jQuerySubclass.superclass = this; - jQuerySubclass.fn = jQuerySubclass.prototype = this(); - jQuerySubclass.fn.constructor = jQuerySubclass; - jQuerySubclass.subclass = this.subclass; - jQuerySubclass.fn.init = function init( selector, context ) { - if ( context && context instanceof jQuery && !(context instanceof jQuerySubclass) ) { - context = jQuerySubclass(context); - } - - return jQuery.fn.init.call( this, selector, context, rootjQuerySubclass ); - }; - jQuerySubclass.fn.init.prototype = jQuerySubclass.fn; - var rootjQuerySubclass = jQuerySubclass(document); - return jQuerySubclass; - }, - - browser: {} + deferred.resolveWith( deferred, args ); + } + } else if ( deferred !== firstParam ) { + deferred.resolveWith( deferred, length ? [ firstParam ] : [] ); + } + return deferred.promise(); + } }); -// Create readyList deferred -readyList = jQuery._Deferred(); - -// Populate the class2type map -jQuery.each("Boolean Number String Function Array Date RegExp Object".split(" "), function(i, name) { - class2type[ "[object " + name + "]" ] = name.toLowerCase(); -}); - -browserMatch = jQuery.uaMatch( userAgent ); -if ( browserMatch.browser ) { - jQuery.browser[ browserMatch.browser ] = true; - jQuery.browser.version = browserMatch.version; -} - -// Deprecated, use jQuery.browser.webkit instead -if ( jQuery.browser.webkit ) { - jQuery.browser.safari = true; -} - -if ( indexOf ) { - jQuery.inArray = function( elem, array ) { - return indexOf.call( array, elem ); - }; -} - -// IE doesn't match non-breaking spaces with \s -if ( rnotwhite.test( "\xA0" ) ) { - trimLeft = /^[\s\xA0]+/; - trimRight = /[\s\xA0]+$/; -} - -// All jQuery objects should point back to these -rootjQuery = jQuery(document); - -// Cleanup functions for the document ready method -if ( document.addEventListener ) { - DOMContentLoaded = function() { - document.removeEventListener( "DOMContentLoaded", DOMContentLoaded, false ); - jQuery.ready(); - }; - -} else if ( document.attachEvent ) { - DOMContentLoaded = function() { - // Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443). - if ( document.readyState === "complete" ) { - document.detachEvent( "onreadystatechange", DOMContentLoaded ); - jQuery.ready(); - } - }; -} - -// The DOM ready check for Internet Explorer -function doScrollCheck() { - if ( jQuery.isReady ) { - return; - } - - try { - // If IE is used, use the trick by Diego Perini - // http://javascript.nwbox.com/IEContentLoaded/ - document.documentElement.doScroll("left"); - } catch(e) { - setTimeout( doScrollCheck, 1 ); - return; - } - - // and execute any waiting functions - jQuery.ready(); -} - -// Expose jQuery to the global object -return jQuery; - -})(); + (function() { @@ -1157,7 +1155,8 @@ boxModel: null, inlineBlockNeedsLayout: false, shrinkWrapBlocks: false, - reliableHiddenOffsets: true + reliableHiddenOffsets: true, + reliableMarginRight: true }; input.checked = true; @@ -1175,15 +1174,15 @@ script = document.createElement("script"), id = "script" + jQuery.now(); + // Make sure that the execution of code works by injecting a script + // tag with appendChild/createTextNode + // (IE doesn't support this, fails, and uses .text instead) try { script.appendChild( document.createTextNode( "window." + id + "=1;" ) ); } catch(e) {} root.insertBefore( script, root.firstChild ); - // Make sure that the execution of code works by injecting a script - // tag with appendChild/createTextNode - // (IE doesn't support this, fails, and uses .text instead) if ( window[ id ] ) { _scriptEval = true; delete window[ id ]; @@ -1192,8 +1191,6 @@ } root.removeChild( script ); - // release memory in IE - root = script = id = null; } return _scriptEval; @@ -1278,6 +1275,17 @@ jQuery.support.reliableHiddenOffsets = jQuery.support.reliableHiddenOffsets && tds[0].offsetHeight === 0; div.innerHTML = ""; + // Check if div with explicit width and no margin-right incorrectly + // gets computed margin-right based on width of container. For more + // info see bug #3333 + // Fails in WebKit before Feb 2011 nightlies + // WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right + if ( document.defaultView && document.defaultView.getComputedStyle ) { + div.style.width = "1px"; + div.style.marginRight = "0"; + jQuery.support.reliableMarginRight = ( parseInt(document.defaultView.getComputedStyle(div, null).marginRight, 10) || 0 ) === 0; + } + body.removeChild( div ).style.display = "none"; div = tds = null; }); @@ -1301,8 +1309,6 @@ el.setAttribute(eventName, "return;"); isSupported = typeof el[eventName] === "function"; } - el = null; - return isSupported; }; @@ -2194,10 +2200,10 @@ } if ( !eventHandle ) { - elemData.handle = eventHandle = function() { + elemData.handle = eventHandle = function( e ) { // Handle the second event of a trigger and when // an event is called after a page has unloaded - return typeof jQuery !== "undefined" && !jQuery.event.triggered ? + return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ? jQuery.event.handle.apply( eventHandle.elem, arguments ) : undefined; }; @@ -2504,7 +2510,7 @@ target[ "on" + targetType ] = null; } - jQuery.event.triggered = true; + jQuery.event.triggered = event.type; target[ targetType ](); } @@ -2515,7 +2521,7 @@ target[ "on" + targetType ] = old; } - jQuery.event.triggered = false; + jQuery.event.triggered = undefined; } } }, @@ -2785,7 +2791,7 @@ // Chrome does something similar, the parentNode property // can be accessed but is null. - if ( parent !== document && !parent.parentNode ) { + if ( parent && parent !== document && !parent.parentNode ) { return; } // Traverse up the tree @@ -2992,19 +2998,33 @@ // Create "bubbling" focus and blur events if ( document.addEventListener ) { jQuery.each({ focus: "focusin", blur: "focusout" }, function( orig, fix ) { + + // Attach a single capturing handler while someone wants focusin/focusout + var attaches = 0; + jQuery.event.special[ fix ] = { setup: function() { - this.addEventListener( orig, handler, true ); + if ( attaches++ === 0 ) { + document.addEventListener( orig, handler, true ); + } }, teardown: function() { - this.removeEventListener( orig, handler, true ); + if ( --attaches === 0 ) { + document.removeEventListener( orig, handler, true ); + } } }; - function handler( e ) { - e = jQuery.event.fix( e ); + function handler( donor ) { + // Donor event is always a native one; fix it and switch its type. + // Let focusin/out handler cancel the donor focus/blur event. + var e = jQuery.event.fix( donor ); e.type = fix; - return jQuery.event.handle.call( this, e ); + e.originalEvent = {}; + jQuery.event.trigger( e, null, e.target ); + if ( e.isDefaultPrevented() ) { + donor.preventDefault(); + } } }); } @@ -3918,10 +3938,12 @@ }, text: function( elem ) { + var attr = elem.getAttribute( "type" ), type = elem.type; // IE6 and 7 will map elem.type to 'text' for new HTML5 types (search, etc) // use getAttribute instead to test this case - return "text" === elem.getAttribute( 'type' ); + return "text" === type && ( attr === type || attr === null ); }, + radio: function( elem ) { return "radio" === elem.type; }, @@ -4496,19 +4518,23 @@ (function(){ var html = document.documentElement, - matches = html.matchesSelector || html.mozMatchesSelector || html.webkitMatchesSelector || html.msMatchesSelector, - pseudoWorks = false; - - try { - // This should fail with an exception - // Gecko does not error, returns false instead - matches.call( document.documentElement, "[test!='']:sizzle" ); + matches = html.matchesSelector || html.mozMatchesSelector || html.webkitMatchesSelector || html.msMatchesSelector; + + if ( matches ) { + // Check to see if it's possible to do matchesSelector + // on a disconnected node (IE 9 fails this) + var disconnectedMatch = !matches.call( document.createElement( "div" ), "div" ), + pseudoWorks = false; + + try { + // This should fail with an exception + // Gecko does not error, returns false instead + matches.call( document.documentElement, "[test!='']:sizzle" ); - } catch( pseudoError ) { - pseudoWorks = true; - } - - if ( matches ) { + } catch( pseudoError ) { + pseudoWorks = true; + } + Sizzle.matchesSelector = function( node, expr ) { // Make sure that attribute selectors are quoted expr = expr.replace(/\=\s*([^'"\]]*)\s*\]/g, "='$1']"); @@ -4516,7 +4542,15 @@ if ( !Sizzle.isXML( node ) ) { try { if ( pseudoWorks || !Expr.match.PSEUDO.test( expr ) && !/!=/.test( expr ) ) { - return matches.call( node, expr ); + var ret = matches.call( node, expr ); + + // IE 9's matchesSelector returns false on disconnected nodes + if ( ret || !disconnectedMatch || + // As well, disconnected nodes are said to be in a document + // fragment in IE 9, so check for that + node.document && node.document.nodeType !== 11 ) { + return ret; + } } } catch(e) {} } @@ -5260,7 +5294,9 @@ } }); } else { - return this.pushStack( jQuery(jQuery.isFunction(value) ? value() : value), "replaceWith", value ); + return this.length ? + this.pushStack( jQuery(jQuery.isFunction(value) ? value() : value), "replaceWith", value ) : + this; } }, @@ -5707,7 +5743,8 @@ var ralpha = /alpha$[^)]*$/i, ropacity = /opacity=([^)]*)/, rdashAlpha = /-([a-z])/ig, - rupper = /([A-Z])/g, + // fixed for IE9, see #8346 + rupper = /([A-Z]|^ms)/g, rnumpx = /^-?\d+(?:px)?$/i, rnum = /^-?\d/, @@ -5944,6 +5981,28 @@ }; } +jQuery(function() { + // This hook cannot be added until DOM ready because the support test + // for it is not run until after DOM ready + if ( !jQuery.support.reliableMarginRight ) { + jQuery.cssHooks.marginRight = { + get: function( elem, computed ) { + // WebKit Bug 13343 - getComputedStyle returns wrong value for margin-right + // Work around by temporarily setting element display to inline-block + var ret; + jQuery.swap( elem, { "display": "inline-block" }, function() { + if ( computed ) { + ret = curCSS( elem, "margin-right", "marginRight" ); + } else { + ret = elem.style.marginRight; + } + }); + return ret; + } + }; + } +}); + if ( document.defaultView && document.defaultView.getComputedStyle ) { getComputedStyle = function( elem, newName, name ) { var ret, defaultView, computedStyle; @@ -6048,7 +6107,7 @@ rheaders = /^(.*?):[ \t]*([^\r\n]*)\r?$/mg, // IE leaves an \r character at EOL rinput = /^(?:color|date|datetime|email|hidden|month|number|password|range|search|tel|text|time|url|week)$/i, // #7653, #8125, #8152: local protocol detection - rlocalProtocol = /(?:^file|^widget|\-extension):$/, + rlocalProtocol = /^(?:about|app|app\-storage|.+\-extension|file|widget):$/, rnoContent = /^(?:GET|HEAD)$/, rprotocol = /^\/\//, rquery = /\?/, @@ -6060,7 +6119,7 @@ rucHeadersFunc = function( _, $1, $2 ) { return $1 + $2.toUpperCase(); }, - rurl = /^([\w\+\.\-]+:)\/\/([^\/?#:]*)(?::(\d+))?/, + rurl = /^([\w\+\.\-]+:)(?:\/\/([^\/?#:]*)(?::(\d+))?)?/, // Keep a copy of the old load method _load = jQuery.fn.load, @@ -6102,7 +6161,7 @@ } // Segment location into parts -ajaxLocParts = rurl.exec( ajaxLocation.toLowerCase() ); +ajaxLocParts = rurl.exec( ajaxLocation.toLowerCase() ) || []; // Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport function addToPrefiltersOrTransports( structure ) { @@ -6360,7 +6419,6 @@ cache: null, traditional: false, headers: {}, - crossDomain: null, */ accepts: { @@ -6645,7 +6703,7 @@ s.dataTypes = jQuery.trim( s.dataType || "*" ).toLowerCase().split( rspacesAjax ); // Determine if a cross-domain request is in order - if ( !s.crossDomain ) { + if ( s.crossDomain == null ) { parts = rurl.exec( s.url.toLowerCase() ); s.crossDomain = !!( parts && ( parts[ 1 ] != ajaxLocParts[ 1 ] || parts[ 2 ] != ajaxLocParts[ 2 ] || @@ -7024,7 +7082,7 @@ var jsc = jQuery.now(), - jsre = /(\=)\?(&|$)|()\?\?()/i; + jsre = /(\=)\?(&|$)|\?\?/i; // Default jsonp settings jQuery.ajaxSetup({ @@ -7285,11 +7343,12 @@ xhr.overrideMimeType( s.mimeType ); } - // Requested-With header - // Not set for crossDomain requests with no content - // (see why at http://trac.dojotoolkit.org/ticket/9486) - // Won't change header if already provided - if ( !( s.crossDomain && !s.hasContent ) && !headers["X-Requested-With"] ) { + // X-Requested-With header + // For cross-domain requests, seeing as conditions for a preflight are + // akin to a jigsaw puzzle, we simply never set it to be sure. + // (it can always be set on a per-request basis or even using ajaxSetup) + // For same-domain requests, won't change header if already provided. + if ( !s.crossDomain && !headers["X-Requested-With"] ) { headers[ "X-Requested-With" ] = "XMLHttpRequest"; } @@ -7979,8 +8038,8 @@ win = getWindow(doc), clientTop = docElem.clientTop || body.clientTop || 0, clientLeft = docElem.clientLeft || body.clientLeft || 0, - scrollTop = (win.pageYOffset || jQuery.support.boxModel && docElem.scrollTop || body.scrollTop ), - scrollLeft = (win.pageXOffset || jQuery.support.boxModel && docElem.scrollLeft || body.scrollLeft), + scrollTop = win.pageYOffset || jQuery.support.boxModel && docElem.scrollTop || body.scrollTop, + scrollLeft = win.pageXOffset || jQuery.support.boxModel && docElem.scrollLeft || body.scrollLeft, top = box.top + scrollTop - clientTop, left = box.left + scrollLeft - clientLeft; @@ -8093,7 +8152,6 @@ this.doesNotIncludeMarginInBodyOffset = (body.offsetTop !== bodyMarginTop); body.removeChild( container ); - body = container = innerDiv = checkDiv = table = td = null; jQuery.offset.initialize = jQuery.noop; }, @@ -8123,10 +8181,10 @@ curOffset = curElem.offset(), curCSSTop = jQuery.css( elem, "top" ), curCSSLeft = jQuery.css( elem, "left" ), - calculatePosition = (position === "absolute" && jQuery.inArray('auto', [curCSSTop, curCSSLeft]) > -1), + calculatePosition = (position === "absolute" || position === "fixed") && jQuery.inArray('auto', [curCSSTop, curCSSLeft]) > -1, props = {}, curPosition = {}, curTop, curLeft; - // need to be able to calculate position if either top or left is auto and position is absolute + // need to be able to calculate position if either top or left is auto and position is either absolute or fixed if ( calculatePosition ) { curPosition = curElem.position(); } --- a/static/scripts/packed/jquery.js Tue Apr 12 09:35:36 2011 -0400 +++ b/static/scripts/packed/jquery.js Tue Apr 12 12:10:48 2011 -0400 @@ -1,5 +1,5 @@ /* - * jQuery JavaScript Library v1.5.1 + * jQuery JavaScript Library v1.5.2 * http://jquery.com/ * * Copyright 2011, John Resig @@ -11,13 +11,13 @@ * Copyright 2011, The Dojo Foundation * Released under the MIT, BSD, and GPL Licenses. * - * Date: Wed Feb 23 13:55:29 2011 -0500 + * Date: Thu Mar 31 15:28:23 2011 -0400 */ -(function(aY,H){var al=aY.document;var a=(function(){var bn=function(bI,bJ){return new bn.fn.init(bI,bJ,bl)},bD=aY.jQuery,bp=aY.$,bl,bH=/^(?:[^<]*(<[\w\W]+>)[^>]*$|#([\w\-]+)$)/,bv=/\S/,br=/^\s+/,bm=/\s+$/,bq=/\d/,bj=/^<(\w+)\s*\/?>(?:<\/\1>)?$/,bw=/^[\],:{}\s]*$/,bF=/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g,by=/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,bs=/(?:^|:|,)(?:\s*\[)+/g,bh=/(webkit)[ \/]([\w.]+)/,bA=/(opera)(?:.*version)?[ \/]([\w.]+)/,bz=/(msie) ([\w.]+)/,bB=/(mozilla)(?:.*? rv:([\w.]+))?/,bG=navigator.userAgent,bE,bC=false,bk,e="then done fail isResolved isRejected promise".split(" "),bd,bu=Object.prototype.toString,bo=Object.prototype.hasOwnProperty,bi=Array.prototype.push,bt=Array.prototype.slice,bx=String.prototype.trim,be=Array.prototype.indexOf,bg={};bn.fn=bn.prototype={constructor:bn,init:function(bI,bM,bL){var bK,bN,bJ,bO;if(!bI){return this}if(bI.nodeType){this.context=this[0]=bI;this.length=1;return this}if(bI==="body"&&!bM&&al.body){this.context=al;this[0]=al.body;this.selector="body";this.length=1;return this}if(typeof bI==="string"){bK=bH.exec(bI);if(bK&&(bK[1]||!bM)){if(bK[1]){bM=bM instanceof bn?bM[0]:bM;bO=(bM?bM.ownerDocument||bM:al);bJ=bj.exec(bI);if(bJ){if(bn.isPlainObject(bM)){bI=[al.createElement(bJ[1])];bn.fn.attr.call(bI,bM,true)}else{bI=[bO.createElement(bJ[1])]}}else{bJ=bn.buildFragment([bK[1]],[bO]);bI=(bJ.cacheable?bn.clone(bJ.fragment):bJ.fragment).childNodes}return bn.merge(this,bI)}else{bN=al.getElementById(bK[2]);if(bN&&bN.parentNode){if(bN.id!==bK[2]){return bL.find(bI)}this.length=1;this[0]=bN}this.context=al;this.selector=bI;return this}}else{if(!bM||bM.jquery){return(bM||bL).find(bI)}else{return this.constructor(bM).find(bI)}}}else{if(bn.isFunction(bI)){return bL.ready(bI)}}if(bI.selector!==H){this.selector=bI.selector;this.context=bI.context}return bn.makeArray(bI,this)},selector:"",jquery:"1.5.1",length:0,size:function(){return this.length},toArray:function(){return bt.call(this,0)},get:function(bI){return bI==null?this.toArray():(bI<0?this[this.length+bI]:this[bI])},pushStack:function(bJ,bL,bI){var bK=this.constructor();if(bn.isArray(bJ)){bi.apply(bK,bJ)}else{bn.merge(bK,bJ)}bK.prevObject=this;bK.context=this.context;if(bL==="find"){bK.selector=this.selector+(this.selector?" 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at end of file --- a/static/scripts/packed/trackster.js Tue Apr 12 09:35:36 2011 -0400 +++ b/static/scripts/packed/trackster.js Tue Apr 12 12:10:48 2011 -0400 @@ -1,1 +1,1 @@ -var extend=function(){var c=arguments[0];for(var b=1;b<arguments.length;b++){var a=arguments[b];for(key in a){c[key]=a[key]}}return c};var trackster_module=function(f,Q){var o=f("slotting"),G=f("painters");var V=function(W,X){this.document=W;this.default_font=X!==undefined?X:"9px Monaco, Lucida Console, 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Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var X=function(aa){if(aa.type==="focusout"||(aa.keyCode||aa.which)===13||(aa.keyCode||aa.which)===27){if((aa.keyCode||aa.which)!==27){W.go_to($(this).val())}$(this).hide();$(this).val("");W.location_span.show();W.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup 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/>").click(function(){W.zoom_in();W.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},Z);this.chrom_select.bind("change",function(){W.change_chrom(W.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(aa){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(aa){W.zoom_in(aa.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aa,ab){this.current_x=ab.offsetX}).bind("drag",function(aa,ac){var ad=ac.offsetX-this.current_x;this.current_x=ac.offsetX;var ab=Math.round(ad/W.viewport_container.width()*(W.max_high-W.max_low));W.move_delta(-ab)});this.overview_close.bind("click",function(){for(var ab=0,aa=W.tracks.length;ab<aa;ab++){W.tracks[ab].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",W.overview_box.height());W.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(aa,ab){if(aa.clientX>W.viewport_container.width()-16){return false}}).bind("dragstart",function(aa,ab){ab.original_low=W.low;ab.current_height=aa.clientY;ab.current_x=ab.offsetX}).bind("drag",function(ac,ae){var aa=$(this);var af=ae.offsetX-ae.current_x;var ab=aa.scrollTop()-(ac.clientY-ae.current_height);aa.scrollTop(ab);ae.current_height=ac.clientY;ae.current_x=ae.offsetX;var ad=Math.round(af/W.viewport_container.width()*(W.high-W.low));W.move_delta(ad)}).bind("mousewheel",function(ac,ae,ab,aa){if(ab){var ad=Math.round(-ab/W.viewport_container.width()*(W.high-W.low));W.move_delta(ad)}});this.top_labeltrack.bind("dragstart",function(aa,ab){return $("<div />").css({height:W.content_div.height()+W.top_labeltrack.height()+W.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ae,af){$(af.proxy).css({left:Math.min(ae.pageX,af.startX),width:Math.abs(ae.pageX-af.startX)});var ab=Math.min(ae.pageX,af.startX)-W.container.offset().left,aa=Math.max(ae.pageX,af.startX)-W.container.offset().left,ad=(W.high-W.low),ac=W.viewport_container.width();W.update_location(Math.round(ab/ac*ad)+W.low,Math.round(aa/ac*ad)+W.low)}).bind("dragend",function(af,ag){var ab=Math.min(af.pageX,ag.startX),aa=Math.max(af.pageX,ag.startX),ad=(W.high-W.low),ac=W.viewport_container.width(),ae=W.low;W.low=Math.round(ab/ac*ad)+ae;W.high=Math.round(aa/ac*ad)+ae;$(ag.proxy).remove();W.redraw()});this.add_label_track(new T(this,this.top_labeltrack));this.add_label_track(new T(this,this.nav_labeltrack));$(window).bind("resize",function(){W.resize_window()});$(document).bind("redraw",function(){W.redraw()});this.reset();$(window).trigger("resize")},update_location:function(W,X){this.location_span.text(commatize(W)+" - "+commatize(X));this.nav_input.val(this.chrom+":"+commatize(W)+"-"+commatize(X))},load_chroms:function(X,Y){X.num=s;$.extend(X,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var W=this;$.ajax({url:chrom_url,data:X,dataType:"json",success:function(aa){if(aa.chrom_info.length===0){alert("Invalid chromosome: "+X.chrom);return}if(aa.reference){W.add_label_track(new x(W))}W.chrom_data=aa.chrom_info;var ad='<option value="">Select Chrom/Contig</option>';for(var ac=0,Z=W.chrom_data.length;ac<Z;ac++){var ab=W.chrom_data[ac].chrom;ad+='<option value="'+ab+'">'+ab+"</option>"}if(aa.prev_chroms){ad+='<option value="previous">Previous '+s+"</option>"}if(aa.next_chroms){ad+='<option value="next">Next '+s+"</option>"}W.chrom_select.html(ad);if(Y){Y()}W.chrom_start_index=aa.start_index},error:function(){alert("Could not load chroms for this dbkey:",W.dbkey)}})},change_chrom:function(aa,X,ac){if(!aa||aa==="None"){return}var Z=this;if(aa==="previous"){Z.load_chroms({low:this.chrom_start_index-s});return}if(aa==="next"){Z.load_chroms({low:this.chrom_start_index+s});return}var ab=$.grep(Z.chrom_data,function(ae,af){return ae.chrom===aa})[0];if(ab===undefined){Z.load_chroms({chrom:aa},function(){Z.change_chrom(aa,X,ac)});return}else{if(aa!==Z.chrom){Z.chrom=aa;if(!Z.chrom){Z.intro_div.show()}else{Z.intro_div.hide()}Z.chrom_select.val(Z.chrom);Z.max_high=ab.len-1;Z.reset();Z.redraw(true);for(var ad=0,W=Z.tracks.length;ad<W;ad++){var Y=Z.tracks[ad];if(Y.init){Y.init()}}}if(X!==undefined&&ac!==undefined){Z.low=Math.max(X,0);Z.high=Math.min(ac,Z.max_high)}Z.reset_overview();Z.redraw()}},go_to:function(aa){var ae=this,W,Z,X=aa.split(":"),ac=X[0],ad=X[1];if(ad!==undefined){try{var ab=ad.split("-");W=parseInt(ab[0].replace(/,/g,""),10);Z=parseInt(ab[1].replace(/,/g,""),10)}catch(Y){return false}}ae.change_chrom(ac,W,Z)},move_fraction:function(Y){var W=this;var X=W.high-W.low;this.move_delta(Y*X)},move_delta:function(Y){var W=this;var X=W.high-W.low;if(W.low-Y<W.max_low){W.low=W.max_low;W.high=W.max_low+X}else{if(W.high-Y>W.max_high){W.high=W.max_high;W.low=W.max_high-X}else{W.high-=Y;W.low-=Y}}W.redraw()},add_track:function(W){W.view=this;W.track_id=this.track_id_counter;this.tracks.push(W);if(W.init){W.init()}W.container_div.attr("id","track_"+W.track_id);B(W.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(W){W.view=this;this.label_tracks.push(W)},remove_track:function(W){this.has_changes=true;W.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(W)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ad){var ac=this.high-this.low,ab=this.low,X=this.high;if(ab<this.max_low){ab=this.max_low}if(X>this.max_high){X=this.max_high}if(this.high!==0&&ac<this.min_separation){X=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(X);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(r,Math.max(0,Math.ceil(Math.log(this.resolution,r)/Math.log(r))));var W=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aa=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:W,width:Math.max(ae,aa)}).show();if(aa<ae){this.overview_box.css("left",W-(ae-aa)/2)}if(this.overview_highlight){this.overview_highlight.css({left:W,width:aa})}this.update_location(this.low,this.high);if(!ad){for(var Y=0,Z=this.tracks.length;Y<Z;Y++){if(this.tracks[Y]&&this.tracks[Y].enabled){this.tracks[Y].draw()}}for(Y=0,Z=this.label_tracks.length;Y<Z;Y++){this.label_tracks[Y].draw()}}},zoom_in:function(X,Y){if(this.max_high===0||this.high-this.low<this.min_separation){return}var Z=this.high-this.low,aa=Z/2+this.low,W=(Z/this.zoom_factor)/2;if(X){aa=X/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aa-W);this.high=Math.round(aa+W);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var X=this.high-this.low,Y=X/2+this.low,W=(X*this.zoom_factor)/2;this.low=Math.round(Y-W);this.high=Math.round(Y+W);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var n=function(X,aa){this.track=X;this.name=aa.name;this.params=[];var ai=aa.params;for(var Y=0;Y<ai.length;Y++){var ad=ai[Y],W=ad.name,ah=ad.label,Z=unescape(ad.html),af=ad.type;if(af==="number"){this.params[this.params.length]=new g(W,ah,Z,ad.min,ad.max)}else{if(af=="select"){this.params[this.params.length]=new I(W,ah,Z)}else{console.log("WARNING: unrecognized tool parameter type:",W,af)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ak){ak.stopPropagation()}).bind("click",function(ak){ak.stopPropagation()}).bind("dblclick",function(ak){ak.stopPropagation()});var ag=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ae=this.params;var ab=this;$.each(this.params,function(al,ao){var an=$("<div>").addClass("param-row").appendTo(ab.parent_div);var ak=$("<div>").addClass("param-label").text(ao.label).appendTo(an);var am=$("<div/>").addClass("slider").html(ao.html).appendTo(an);$("<div style='clear: both;'/>").appendTo(an)});this.parent_div.find("input").click(function(){$(this).select()});var aj=$("<div>").addClass("slider-row").appendTo(this.parent_div);var ac=$("<input type='submit'>").attr("value","Run").appendTo(aj);var ab=this;ac.click(function(){ab.run()})};extend(n.prototype,{get_param_values_dict:function(){var W={};this.parent_div.find(":input").each(function(){var X=$(this).attr("name"),Y=$(this).val();W[X]=JSON.stringify(Y)});return W},get_param_values:function(){var X=[];var W={};this.parent_div.find(":input").each(function(){var Y=$(this).attr("name"),Z=$(this).val();if(Y){X[X.length]=Z}});return X},run:function(){var X={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name};$.extend(X,this.get_param_values_dict());var Z=this.track,Y=X.tool_id+Z.tool_region_and_parameters_str(X.chrom,X.low,X.high),aa;if(Z.track_type==="FeatureTrack"){aa=new N(Y,view,Z.hda_ldda,undefined,{},{},Z)}this.track.add_track(aa);aa.content_div.text("Starting job.");var W=function(){$.getJSON(run_tool_url,X,function(ab){if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(E)}else{if(ab.error){aa.container_div.addClass("error");aa.content_div.text(u+ab.message)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text("Converting input data so that it can be easily reused.");setTimeout(W,2000)}else{aa.dataset_id=ab.dataset_id;aa.content_div.text("Running job.");aa.init()}}}})};W()}});var I=function(X,W,Y){this.name=X;this.label=W;this.html=Y};var g=function(Y,X,aa,Z,W){I.call(this,Y,X,aa);this.min=Z;this.max=W};var j=function(X,W,Y){this.name=X;this.index=W;this.value=Y};var O=function(X,W){this.name=X;this.index=W;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};extend(O.prototype,{applies_to:function(W){if(W.length>this.index){return true}return false},keep:function(W){if(!this.applies_to(W)){return true}return(W[this.index]>=this.low&&W[this.index]<=this.high)},update_attrs:function(X){var W=false;if(!this.applies_to(X)){return W}if(X[this.index]<this.min){this.min=Math.floor(X[this.index]);W=true}if(X[this.index]>this.max){this.max=Math.ceil(X[this.index]);W=true}return W},update_ui_elt:function(){var X=this.slider.slider("option","min"),W=this.slider.slider("option","max");if(this.min<X||this.max>W){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",h(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var v=function(W){var ac=[];for(var Z=0;Z<W.length;Z++){var ab=W[Z];var Y=ab.name,aa=ab.type,X=ab.index;if(aa==="int"||aa==="float"){ac[Z]=new O(Y,X)}else{ac[Z]=new j(Y,X,aa)}}return ac};var S=function(W){this.track=W.track;this.params=W.params;this.values={};if(W.saved_values){this.restore_values(W.saved_values)}this.onchange=W.onchange};extend(S.prototype,{restore_values:function(W){var X=this;$.each(this.params,function(Y,Z){if(W[Z.key]!==undefined){X.values[Z.key]=W[Z.key]}else{X.values[Z.key]=Z.default_value}})},build_form:function(){var X=this;var W=$("<div />");$.each(this.params,function(ab,Z){if(!Z.hidden){var Y="param_"+ab;var ag=$("<div class='form-row' />").appendTo(W);ag.append($("<label />").attr("for",Y).text(Z.label+":"));if(Z.type==="bool"){ag.append($('<input type="checkbox" />').attr("id",Y).attr("name",Y).attr("checked",X.values[Z.key]))}else{if(Z.type==="color"){var ad=X.values[Z.key];var ac=$("<input />").attr("id",Y).attr("name",Y).val(ad);var ae=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var aa=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ae);var af=$("<div/>").appendTo(aa).farbtastic({width:100,height:100,callback:ac,color:ad});$("<div />").append(ac).append(ae).appendTo(ag).bind("click",function(ah){ae.css({left:$(this).position().left+($(ac).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ae.hide();$(document).unbind("click.color-picker")});ah.stopPropagation()})}else{ag.append($("<input />").attr("id",Y).attr("name",Y).val(X.values[Z.key]))}}}});return W},update_from_form:function(W){var Y=this;var X=false;$.each(this.params,function(Z,ab){if(!ab.hidden){var ac="param_"+Z;var aa=W.find("#"+ac).val();if(ab.type==="float"){aa=parseFloat(aa)}else{if(ab.type==="int"){aa=parseInt(aa)}else{if(ab.type==="bool"){aa=W.find("#"+ac).is(":checked")}}}if(aa!==Y.values[ab.key]){Y.values[ab.key]=aa;X=true}}});if(X){this.onchange()}}});var b=function(W,X){this.track=W;this.canvas=X};var k=function(X,W,aa,Y,Z){this.name=X;this.view=W;this.parent_element=aa;this.data_url=(Y?Y:default_data_url);this.data_url_extra_params={};this.data_query_wait=(Z?Z:F);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};extend(k.prototype,{init:function(){var W=this;W.enabled=false;W.tile_cache.clear();W.data_cache.clear();W.initial_canvas=undefined;W.content_div.css("height","auto");W.container_div.removeClass("nodata error pending");if(!W.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:W.hda_ldda,dataset_id:W.dataset_id,chrom:W.view.chrom},function(X){if(!X||X==="error"||X.kind==="error"){W.container_div.addClass("error");W.content_div.text(m);if(X.message){var Z=W.view.tracks.indexOf(W);var Y=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+X.message+"</pre>",{Close:hide_modal})});W.content_div.append(Y)}}else{if(X==="no converter"){W.container_div.addClass("error");W.content_div.text(E)}else{if(X==="no data"||(X.data!==undefined&&(X.data===null||X.data.length===0))){W.container_div.addClass("nodata");W.content_div.text(A)}else{if(X==="pending"){W.container_div.addClass("pending");W.content_div.text(p);setTimeout(function(){W.init()},W.data_query_wait)}else{if(X.status==="data"){if(X.valid_chroms){W.valid_chroms=X.valid_chroms;W.make_name_popup_menu()}W.content_div.text(R);if(W.view.chrom){W.content_div.text("");W.content_div.css("height",W.height_px+"px");W.enabled=true;$.when(W.predraw_init()).done(function(){W.container_div.removeClass("nodata error pending");W.draw()})}}}}}}})},predraw_init:function(){},update_name:function(W){this.old_name=this.name;this.name=W;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var H=function(X,ad,ag){var Y=this,ah=Y.view;this.filters=(X!==undefined?v(X):[]);this.filters_available=false;this.filters_visible=false;this.tool=(ad!==undefined&&obj_length(ad)>0?new n(this,ad):undefined);this.parent_track=ag;this.child_tracks=[];if(Y.hidden){return}var af=function(ai,aj,ak){ai.click(function(){var al=aj.text();max=parseFloat(ak.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(ak.slider("option","values")){input_size=2*input_size+1;multi_value=true}aj.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",al).appendTo(aj).focus().select().click(function(am){am.stopPropagation()}).blur(function(){$(this).remove();aj.text(al)}).keyup(function(aq){if(aq.keyCode===27){$(this).trigger("blur")}else{if(aq.keyCode===13){var ao=ak.slider("option","min"),am=ak.slider("option","max"),ap=function(ar){return(isNaN(ar)||ar>am||ar<ao)},an=$(this).val();if(!multi_value){an=parseFloat(an);if(ap(an)){alert("Parameter value must be in the range ["+ao+"-"+am+"]");return $(this)}}else{an=an.split("-");an=[parseFloat(an[0]),parseFloat(an[1])];if(ap(an[0])||ap(an[1])){alert("Parameter value must be in the range ["+ao+"-"+am+"]");return $(this)}}ak.slider((multi_value?"values":"value"),an)}}})})};if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(ai){ai.stopPropagation()}).bind("click",function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()});$.each(this.filters,function(ao,aj){var al=$("<div/>").addClass("slider-row").appendTo(Y.filters_div);var ai=$("<div/>").addClass("slider-label").appendTo(al);var aq=$("<span/>").addClass("slider-name").text(aj.name+" ").appendTo(ai);var ak=$("<span/>");var am=$("<span/>").addClass("slider-value").appendTo(ai).append("[").append(ak).append("]");var ap=$("<div/>").addClass("slider").appendTo(al);aj.control_element=$("<div/>").attr("id",aj.name+"-filter-control").appendTo(ap);var an=[0,0];aj.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ar,at){an=at.values;ak.text(at.values[0]+"-"+at.values[1]);setTimeout(function(){if(at.values[0]==an[0]&&at.values[1]==an[1]){var au=at.values;ak.text(au[0]+"-"+au[1]);aj.low=au[0];aj.high=au[1];Y.draw(true,true)}},50)},change:function(ar,at){aj.control_element.slider("option","slide").call(aj.control_element,ar,at)}});aj.slider=aj.control_element;aj.slider_label=ak;af(am,ak,aj.control_element);$("<div style='clear: both;'/>").appendTo(al)});if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}Y.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();Y.container_div.append(Y.child_tracks_container);if(Y.display_modes!==undefined){if(Y.mode_div===undefined){Y.mode_div=$("<div class='right-float menubutton popup' />").appendTo(Y.header_div);var aa=(Y.track_config&&Y.track_config.values.mode?Y.track_config.values.mode:Y.display_modes[0]);Y.mode=aa;Y.mode_div.text(aa);var Z=function(ai){Y.mode_div.text(ai);Y.mode=ai;Y.track_config.values.mode=ai;Y.tile_cache.clear();Y.draw()};var W={};for(var ab=0,ae=Y.display_modes.length;ab<ae;ab++){var ac=Y.display_modes[ab];W[ac]=function(ai){return function(){Z(ai)}}(ac)}make_popupmenu(Y.mode_div,W)}else{Y.mode_div.hide()}}this.make_name_popup_menu()};extend(H.prototype,k.prototype,{make_name_popup_menu:function(){var X=this;var W={};W["Edit configuration"]=function(){var ad=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(){X.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(ae){if((ae.keyCode||ae.which)===27){ad()}else{if((ae.keyCode||ae.which)===13){ab()}}};$(window).bind("keypress.check_enter_esc",ac);show_modal("Configure Track",X.track_config.build_form(),{Cancel:ad,OK:ab})};if(X.filters_available>0){var aa=(X.filters_div.is(":visible")?"Hide filters":"Show filters");W[aa]=function(){X.filters_visible=(X.filters_div.is(":visible"));X.filters_div.toggle();X.make_name_popup_menu()}}if(X.tool){var aa=(X.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");W[aa]=function(){if(!X.dynamic_tool_div.is(":visible")){X.update_name(X.name+X.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";X.revert_name()}X.dynamic_tool_div.toggle();X.make_name_popup_menu()}}if(X.valid_chroms){W["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+X.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var Y=view;var Z=function(){$("#no-tracks").show()};if(this.parent_track){Y=this.parent_track;Z=function(){}}W.Remove=function(){Y.remove_track(X);if(Y.num_tracks===0){Z()}};make_popupmenu(X.name_div,W)},draw:function(W,Z){var an=this.view.low,ac=this.view.high,ae=ac-an,ag=this.view.container.width(),ab=ag/ae,ah=this.view.resolution,aa=$("<div style='position: relative;'></div>");if(!Z){this.content_div.children().remove()}this.content_div.append(aa);this.max_height=0;var aj=Math.floor(an/ah/J);var Y={};while((aj*J*ah)<ac){var am=ag+"_"+ab+"_"+aj;var ad=this.tile_cache.get(am);var ak=aj*J*this.view.resolution;var X=ak+J*this.view.resolution;if(!W&&ad){this.show_tile(ad,aa,ak,ab)}else{this.delayed_draw(W,am,ak,X,aj,ah,aa,ab,Y)}aj+=1}var af=this;var al=setInterval(function(){if(obj_length(Y)===0){clearInterval(al);if(Z){var aq=af.content_div.children();var ap=false;for(var ar=aq.length-1,ao=0;ar>=ao;ar--){var av=$(aq[ar]);if(ap){av.remove()}else{if(av.children().length!==0){ap=true}}}}for(var au=0;au<af.filters.length;au++){af.filters[au].update_ui_elt()}var at=false;if(af.example_feature){for(var au=0;au<af.filters.length;au++){if(af.filters[au].applies_to(af.example_feature)){at=true;break}}}if(af.filters_available!==at){af.filters_available=at;if(!af.filters_available){af.filters_div.hide()}af.make_name_popup_menu()}}},50);for(var ai=0;ai<this.child_tracks.length;ai++){this.child_tracks[ai].draw(W,Z)}},delayed_draw:function(X,ae,ac,ag,Y,aa,af,ah,ab){var Z=this;var ad=function(ap,ai,ak,aj,an,ao,al){returned_tile=Z.draw_tile(ai,ak,aj,an,ao,al);var am=$("<div class='track-tile'>").prepend(returned_tile);tile_element=am;Z.tile_cache.set(ae,tile_element);Z.show_tile(tile_element,an,ac,ao);delete ab[ap]};var W=setTimeout(function(){if(ac<=Z.view.high&&ag>=Z.view.low){var ai=(X?undefined:Z.tile_cache.get(ae));if(ai){Z.show_tile(ai,af,ac,ah);delete ab[W]}else{$.when(Z.data_cache.get_data(view.chrom,ac,ag,Z.mode,aa,Z.data_url_extra_params)).then(function(aj){if(view.reference_track&&ah>view.canvas_manager.char_width_px){$.when(view.reference_track.data_cache.get_data(view.chrom,ac,ag,Z.mode,aa,view.reference_track.data_url_extra_params)).then(function(ak){ad(W,aj,aa,Y,af,ah,ak)})}else{ad(W,aj,aa,Y,af,ah)}})}}},50);ab[W]=true},show_tile:function(W,ab,Z,ac){var X=this;var Y=this.view.high-this.view.low,aa=(Z-this.view.low)*ac;if(this.left_offset){aa-=this.left_offset}W.css({position:"absolute",top:0,left:aa,height:""});ab.append(W);X.max_height=Math.max(X.max_height,W.height());X.content_div.css("height",X.max_height+"px");ab.children().css("height",X.max_height+"px")},set_overview:function(){var W=this.view;if(this.initial_canvas&&this.is_overview){W.overview_close.show();W.overview_viewport.append(this.initial_canvas);W.overview_highlight.show().height(this.initial_canvas.height());W.overview_viewport.height(this.initial_canvas.height()+W.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(Y,W,Z){var X=this,aa=(Y!==undefined&&W!==undefined&&Z!==undefined?Y+":"+W+"-"+Z:"all");return" - region=["+aa+"], parameters=["+X.tool.get_param_values().join(", ")+"]"},add_track:function(W){W.track_id=this.track_id+"_"+this.child_tracks.length;W.container_div.attr("id","track_"+W.track_id);this.child_tracks_container.append(W.container_div);B(W.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(W);this.view.has_changes=true},remove_track:function(W){W.container_div.fadeOut("slow",function(){$(this).remove()})}});var T=function(W,X){this.track_type="LabelTrack";this.hidden=true;k.call(this,null,W,X);this.container_div.addClass("label-track")};extend(T.prototype,k.prototype,{draw:function(){var Y=this.view,Z=Y.high-Y.low,ac=Math.floor(Math.pow(10,Math.floor(Math.log(Z)/Math.log(10)))),W=Math.floor(Y.low/ac)*ac,aa=this.view.container.width(),X=$("<div style='position: relative; height: 1.3em;'></div>");while(W<Y.high){var ab=(W-Y.low)/Z*aa;X.append($("<div class='label'>"+commatize(W)+"</div>").css({position:"absolute",left:ab-1}));W+=ac}this.content_div.children(":first").remove();this.content_div.append(X)}});var x=function(W){this.track_type="ReferenceTrack";this.hidden=true;k.call(this,null,W,W.top_labeltrack);H.call(this);W.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:W.dbkey};this.data_cache=new K(y,this,false);this.tile_cache=new c(q)};extend(x.prototype,H.prototype,{draw_tile:function(ag,ab,X,ad,ah){var aa=this,Y=J*ab;if(ah>this.view.canvas_manager.char_width_px){if(ag===null){aa.content_div.css("height","0px");return}var Z=this.view.canvas_manager.new_canvas();var af=Z.getContext("2d");Z.width=Math.ceil(Y*ah+aa.left_offset);Z.height=aa.height_px;af.font=af.canvas.manager.default_font;af.textAlign="center";for(var ac=0,ae=ag.length;ac<ae;ac++){var W=Math.round(ac*ah);af.fillText(ag[ac],W+aa.left_offset,10)}return Z}this.content_div.css("height","0px")}});var l=function(aa,Y,ab,W,Z){var X=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";k.call(this,aa,Y,Y.viewport_container);H.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ab;this.dataset_id=W;this.original_dataset_id=W;this.data_cache=new K(y,this);this.tile_cache=new c(q);this.track_config=new S({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:Z,onchange:function(){X.vertical_range=X.prefs.max_value-X.prefs.min_value;$("#linetrack_"+X.track_id+"_minval").text(X.prefs.min_value);$("#linetrack_"+X.track_id+"_maxval").text(X.prefs.max_value);X.tile_cache.clear();X.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};extend(l.prototype,H.prototype,{add_resize_handle:function(){var W=this;var Z=false;var Y=false;var X=$("<div class='track-resize'>");$(W.container_div).hover(function(){Z=true;X.show()},function(){Z=false;if(!Y){X.hide()}});X.hide().bind("dragstart",function(aa,ab){Y=true;ab.original_height=$(W.content_div).height()}).bind("drag",function(ab,ac){var aa=Math.min(Math.max(ac.original_height+ac.deltaY,W.min_height_px),W.max_height_px);$(W.content_div).css("height",aa);W.height_px=aa;W.draw(true)}).bind("dragend",function(aa,ab){W.tile_cache.clear();Y=false;if(!Z){X.hide()}W.track_config.values.height=W.height_px}).appendTo(W.container_div)},predraw_init:function(){var W=this,X=W.view.tracks.indexOf(W);W.vertical_range=undefined;return $.getJSON(W.data_url,{stats:true,chrom:W.view.chrom,low:null,high:null,hda_ldda:W.hda_ldda,dataset_id:W.dataset_id},function(Y){W.container_div.addClass("line-track");var aa=Y.data;if(isNaN(parseFloat(W.prefs.min_value))||isNaN(parseFloat(W.prefs.max_value))){W.prefs.min_value=aa.min;W.prefs.max_value=aa.max;$("#track_"+X+"_minval").val(W.prefs.min_value);$("#track_"+X+"_maxval").val(W.prefs.max_value)}W.vertical_range=W.prefs.max_value-W.prefs.min_value;W.total_frequency=aa.total_frequency;W.container_div.find(".yaxislabel").remove();var ab=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+X+"_minval").text(t(W.prefs.min_value));var Z=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+X+"_maxval").text(t(W.prefs.max_value));Z.css({position:"absolute",top:"24px",left:"10px"});Z.prependTo(W.container_div);ab.css({position:"absolute",bottom:"2px",left:"10px"});ab.prependTo(W.container_div)})},draw_tile:function(ah,aa,X,ae,ag){if(this.vertical_range===undefined){return}var ab=X*J*aa,Z=J*aa,W=Math.ceil(Z*ag),ad=this.height_px;var Y=this.view.canvas_manager.new_canvas();Y.width=W,Y.height=ad;var af=Y.getContext("2d");var ac=new G.LinePainter(ah.data,ab,ab+Z,this.prefs,this.mode);ac.draw(af,W,ad);return Y}});var e=function(W,ab,aa,ae,ad,Y,Z,ac){var X=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new S({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ad,onchange:function(){X.tile_cache.clear();X.draw()}});this.prefs=this.track_config.values;k.call(this,W,ab,ab.viewport_container);H.call(this,Y,Z,ac);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=aa;this.dataset_id=ae;this.original_dataset_id=ae;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_cache=new K(20,this);this.left_offset=200;this.painter=G.LinkedFeaturePainter};extend(e.prototype,H.prototype,{update_auto_mode:function(W){if(this.mode=="Auto"){if(W=="no_detail"){W="feature spans"}else{if(W=="summary_tree"){W="coverage histogram"}}this.mode_div.text("Auto ("+W+")")}},incremental_slots:function(aa,X,Z){var Y=this.view.canvas_manager.dummy_context,W=this.inc_slots[aa];if(!W||(W.mode!==Z)){W=new (o.FeatureSlotter)(aa,Z==="Pack",w,function(ab){return Y.measureText(ab)});W.mode=Z;this.inc_slots[aa]=W}return W.slot_features(X)},draw_tile:function(ai,aq,av,ae,ag,Z){var an=this,ax=av*J*aq,X=(av+1)*J*aq,ak=X-ax,ao=Math.ceil(ak*ag),am=this.mode,aB=25,aa=this.left_offset,aj,ab;if(am==="Auto"){if(ai.dataset_type==="summary_tree"){am=ai.dataset_type}else{if(ai.extra_info==="no_detail"){am="no_detail"}else{var aA=ai.data;if(this.view.high-this.view.low>D){am="Squish"}else{am="Pack"}}}this.update_auto_mode(am)}if(am==="summary_tree"){ab=this.summary_draw_height;ae.parent().css("height",Math.max(this.height_px,ab)+"px");this.container_div.find(".yaxislabel").remove();var W=$("<div />").addClass("yaxislabel");W.text(ai.max);W.css({position:"absolute",top:"22px",left:"10px"});W.prependTo(this.container_div);var Y=this.view.canvas_manager.new_canvas();Y.width=ao+aa;Y.height=ab+L;var ay=new G.SummaryTreePainter(ai,ax,X,this.prefs);var ap=Y.getContext("2d");ap.translate(aa,L);ay.draw(ap,ao,ab);return Y}var aj,ad=1;if(am==="no_detail"||am==="Squish"||am==="Pack"){ad=this.incremental_slots(ag,ai.data,am);aj=this.inc_slots[ag].slots}var af=[];if(ai.data){for(var ar=0,au=ai.data.length;ar<au;ar++){var ac=ai.data[ar];var at=false;var ah;for(var aw=0,az=this.filters.length;aw<az;aw++){ah=this.filters[aw];ah.update_attrs(ac);if(!ah.keep(ac)){at=true;break}}if(!at){af.push(ac)}}}var ay=new (this.painter)(af,ax,X,this.prefs,am,Z);var ab=ay.get_required_height(ad)+z;var Y=this.view.canvas_manager.new_canvas();Y.width=ao+aa;Y.height=ab;ae.parent().css("height",Math.max(this.height_px,ab)+"px");var ap=Y.getContext("2d");ap.fillStyle=this.prefs.block_color;ap.font=ap.canvas.manager.default_font;ap.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ai.message){$(Y).css({"border-top":"1px solid red"});ap.fillStyle="red";ap.textAlign="left";var al=ap.textBaseline;ap.textBaseline="top";ap.fillText(ai.message,aa,0);ap.textBaseline=al;if(!ai.data){return Y}}this.example_feature=(ai.data.length?ai.data[0]:undefined);ap.translate(aa,z);ay.draw(ap,ao,ab,aj);return Y}});var M=function(Z,X,ab,W,Y,aa){e.call(this,Z,X,ab,W,Y,aa);this.track_type="VcfTrack";this.painter=G.VariantPainter};extend(M.prototype,H.prototype,e.prototype);var P=function(Z,X,ab,W,Y,aa){e.call(this,Z,X,ab,W,Y,aa);this.track_config=new S({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:Y,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.painter=G.ReadPainter;this.make_name_popup_menu()};extend(P.prototype,H.prototype,e.prototype);var N=function(aa,Y,ac,W,Z,ab,X){e.call(this,aa,Y,ac,W,Z,ab,{},X);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};extend(N.prototype,H.prototype,e.prototype,{predraw_init:function(){var X=this;var W=function(){if(X.data_cache.size()===0){setTimeout(W,300)}else{X.data_url=default_data_url;X.data_query_wait=F;X.dataset_state_url=converted_datasets_state_url;$.getJSON(X.dataset_state_url,{dataset_id:X.dataset_id,hda_ldda:X.hda_ldda},function(Y){})}};W()}});Q.View=U;Q.LineTrack=l;Q.FeatureTrack=e;Q.ReadTrack=P};var slotting_module=function(c,b){var d=2,a=5;b.FeatureSlotter=function(h,g,e,f){this.slots={};this.start_end_dct={};this.w_scale=h;this.include_label=g;this.max_rows=e;this.measureText=f};extend(b.FeatureSlotter.prototype,{slot_features:function(l){var o=this.w_scale,r=this.slots,g=this.start_end_dct,x=[],z=[],m=0,y=this.max_rows;for(var v=0,w=l.length;v<w;v++){var k=l[v],n=k[0];if(r[n]!==undefined){m=Math.max(m,r[n]);z.push(r[n])}else{x.push(v)}}var p=function(F,G){for(var E=0;E<=y;E++){var C=false,H=g[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var A=H[B];if(G>A[0]&&F<A[1]){C=true;break}}}if(!C){return E}}return -1};for(var v=0,w=x.length;v<w;v++){var k=l[x[v]],n=k[0],t=k[1],e=k[2],q=k[3],f=Math.floor(t*o),j=Math.ceil(e*o),u=this.measureText(q).width,h;if(q!==undefined&&this.include_label){u+=(d+a);if(f-u>=0){f-=u;h="left"}else{j+=u;h="right"}}var s=p(f,j);if(s>=0){if(g[s]===undefined){g[s]=[]}g[s].push([f,j]);r[n]=s;m=Math.max(m,s)}else{}}return m+1}})};var painters_module=function(k,B){var r=function(M,E,K,D,J,H){if(H===undefined){H=4}var G=D-E;var F=J-K;var I=Math.floor(Math.sqrt(G*G+F*F)/H);var N=G/I;var L=F/I;var C;for(C=0;C<I;C++,E+=N,K+=L){if(C%2!==0){continue}M.fillRect(E,K,H,1)}};var s=function(E,D,C,H){var G=D-H/2,F=D+H/2,I=C-Math.sqrt(H*3/2);E.beginPath();E.moveTo(G,I);E.lineTo(F,I);E.lineTo(D,C);E.lineTo(G,I);E.strokeStyle=this.fillStyle;E.fill();E.stroke();E.closePath()};var o=function(E,G,C,D,F){this.data=E;this.view_start=G;this.view_end=C;this.prefs=extend({},this.default_prefs,D);this.mode=F};o.prototype.default_prefs={};var w=function(E,G,C,D,F){o.call(this,E,G,C,D,F)};w.prototype.default_prefis={show_counts:false};w.prototype.draw=function(P,C,O){var H=this.view_start,R=this.view_end-this.view_start,Q=C/R;var M=this.data.data,L=this.data.delta,J=this.data.max,E=O;delta_x_px=Math.ceil(L*Q);P.save();for(var F=0,G=M.length;F<G;F++){var K=Math.floor((M[F][0]-H)*Q);var I=M[F][1];if(!I){continue}var N=I/J*O;P.fillStyle="black";P.fillRect(K,E-N,delta_x_px,N);var D=4;if(this.prefs.show_counts&&(P.measureText(I).width+D)<delta_x_px){P.fillStyle="#666";P.textAlign="center";P.fillText(I,K+(delta_x_px/2),10)}}P.restore()};var c=function(E,G,C,D,F){o.call(this,E,G,C,D,F)};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(R,Q,O){var J=false,K=this.prefs.min_value,H=this.prefs.max_value,N=H-K,D=O,E=this.view_start,P=this.view_end-this.view_start,F=Q/P,L=this.mode,V=this.data;R.save();var W=Math.round(O+K/N*O);if(L!=="Intensity"){R.fillStyle="#aaa";R.fillRect(0,W,Q,1)}R.beginPath();R.fillStyle=this.prefs.color;var U,I,G;if(V.length>1){G=Math.ceil((V[1][0]-V[0][0])*F)}else{G=10}for(var S=0,T=V.length;S<T;S++){U=Math.round((V[S][0]-E)*F);I=V[S][1];if(I===null){if(J&&L==="Filled"){R.lineTo(U,D)}J=false;continue}if(I<K){I=K}else{if(I>H){I=H}}if(L==="Histogram"){I=Math.round(I/N*D);R.fillRect(U,W,G,-I)}else{if(L==="Intensity"){I=255-Math.floor((I-K)/N*255);R.fillStyle="rgb("+I+","+I+","+I+")";R.fillRect(U,0,G,D)}else{I=Math.round(D-(I-K)/N*D);if(J){R.lineTo(U,I)}else{J=true;if(L==="Filled"){R.moveTo(U,D);R.lineTo(U,I)}else{R.moveTo(U,I)}}}}}if(L==="Filled"){if(J){R.lineTo(U,W);R.lineTo(0,W)}R.fill()}else{R.stroke()}var C=-1,M=-1;R.fillStyle=this.prefs.overflow_color;for(var S=0,T=V.length;S<T;S++){I=V[S][1];U=Math.round((V[S][0]-E)*F);x_minus_scaled=Math.round((V[S][0]-1-E)*F);if(M>=0&&(I===null||I<H)){R.fillRect(M,0,x_minus_scaled-M+1,2);M=-1}else{if(C>=0&&(I===null||I>K)){R.fillRect(C,O-2,x_minus_scaled-C+1,2);C=-1}}if(I!==null&&I>H&&M<0){M=U}else{if(I!==null&&I<K&&C<0){C=U}}}R.restore()};var q=function(E,G,C,D,F){o.call(this,E,G,C,D,F)};q.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(q.prototype,{get_required_height:function(D){var C=y_scale=this.get_row_height(),E=this.mode;if(E==="no_detail"||E==="Squish"||E==="Pack"){C=D*y_scale}return C+Math.max(Math.round(y_scale/2),5)},draw:function(O,F,N,K){var I=this.data,L=this.view_start,P=this.view_end;O.save();O.fillStyle=this.prefs.block_color;O.textAlign="right";var S=this.view_end-this.view_start,R=F/S,E=this.get_row_height();for(var H=0,J=I.length;H<J;H++){var Q=I[H],G=Q[0],C=Q[1],D=Q[2],M=(K&&K[G]!==undefined?K[G]:null);if((C<P&&D>L)&&(this.mode=="Dense"||M!==null)){this.draw_element(O,this.mode,Q,M,L,P,R,E,F)}}O.restore()}});var d=10,j=3,n=5,A=10,g=1,u=3,f=3,a=9,p=2,h="#ccc";var t=function(E,G,C,D,F){q.call(this,E,G,C,D,F)};extend(t.prototype,q.prototype,{get_row_height:function(){var D=this.mode,C;if(D==="Dense"){C=d}else{if(D==="no_detail"){C=j}else{if(D==="Squish"){C=n}else{C=A}}}return C},draw_element:function(O,H,W,J,Q,ag,ak,al,C){var T=W[0],ai=W[1],aa=W[2]-1,R=W[3],ab=Math.floor(Math.max(0,(ai-Q)*ak)),P=Math.ceil(Math.min(C,Math.max(0,(aa-Q)*ak))),Z=(H==="Dense"?0:(0+J))*al,N,ae,S=null,am=null,F=this.prefs.block_color,ad=this.prefs.label_color;if(H=="Dense"){J=1}if(H==="no_detail"){O.fillStyle=F;O.fillRect(ab,Z+5,P-ab,g)}else{var M=W[4],Y=W[5],ac=W[6],G=W[7];if(Y&&ac){S=Math.floor(Math.max(0,(Y-Q)*ak));am=Math.ceil(Math.min(C,Math.max(0,(ac-Q)*ak)))}var aj,U;if(H==="Squish"||H==="Dense"){aj=1;U=f}else{aj=5;U=a}if(!G){if(W.strand){if(W.strand==="+"){O.fillStyle=O.canvas.manager.get_pattern("right_strand_inv")}else{if(W.strand==="-"){O.fillStyle=O.canvas.manager.get_pattern("left_strand_inv")}}}else{O.fillStyle=F}O.fillRect(ab,Z,P-ab,U)}else{var L,V;if(H==="Squish"||H==="Dense"){O.fillStyle=h;L=Z+Math.floor(f/2)+1;V=1}else{if(M){var L=Z;var 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b=function(E,G,C,D,F){q.call(this,E,G,C,D,F)};extend(b.prototype,q.prototype,{draw_element:function(V,Q,K,G,Y,E,N,W,T){var K=data[i],M=K[0],U=K[1],F=K[2]-1,P=K[3],I=Math.floor(Math.max(0,(U-Y)*N)),L=Math.ceil(Math.min(T,Math.max(0,(F-Y)*N))),H=(Q==="Dense"?0:(0+G))*W,C,Z,D=null,O=null;if(no_label){V.fillStyle=block_color;V.fillRect(I+left_offset,H+5,L-I,1)}else{var X=K[4],S=K[5],J=K[6];C=9;Z=1;V.fillRect(I+left_offset,H,L-I,C);if(Q!=="Dense"&&P!==undefined&&U>Y){V.fillStyle=label_color;if(Y===0&&I-V.measureText(P).width<0){V.textAlign="left";V.fillText(P,L+2+left_offset,H+8)}else{V.textAlign="right";V.fillText(P,I-2+left_offset,H+8)}V.fillStyle=block_color}var R=X+" / "+S;if(U>Y&&V.measureText(R).width<(L-I)){V.fillStyle="white";V.textAlign="center";V.fillText(R,left_offset+I+(L-I)/2,H+8);V.fillStyle=block_color}}}});var z=1001,m=1002,e=1003,y=1004,l=1005;var x=function(G,D){var I=G[0],H=G[1],F=D[0],E=D[1],C;if(I<F){if(H<F){C=z}else{if(H<=E){C=e}else{C=m}}}else{if(I>E){C=z}else{if(H<=E){C=l}else{C=y}}}return C};var v=function(F,H,C,E,G,D){q.call(this,F,H,C,E,G);this.ref_seq=D};v.prototype.default_prefs=extend({},q.prototype.default_prefs,{show_insertions:false});extend(v.prototype,q.prototype,{get_row_height:function(){var C,D=this.mode;if(D==="Dense"){C=d}else{if(D==="Squish"){C=n}else{C=A;if(this.prefs.show_insertions){C*=2}}}return C},draw_read:function(Z,U,P,ae,E,Y,M,J,I){Z.textAlign="center";var X=this,D=[ae,E],S=0,aa=0,W=0;ref_seq=this.ref_seq,char_width_px=Z.canvas.manager.char_width_px;var aj=[];if((U==="Pack"||this.mode==="Auto")&&J!==undefined&&P>char_width_px){W=Math.round(P/2)}if(!M){M=[[0,J.length]]}for(var Q=0,ac=M.length;Q<ac;Q++){var N=M[Q],F="MIDNSHP=X"[N[0]],R=N[1];if(F==="H"||F==="S"){S-=R}var K=Y+S,ai=Math.floor(Math.max(0,(K-ae)*P)),L=Math.floor(Math.max(0,(K+R-ae)*P));if(ai===L){L+=1}switch(F){case"H":break;case"S":case"M":case"=":var 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Array){var R=Math.floor(Math.max(0,(I[4][0]-Y)*M)),P=Math.ceil(Math.min(T,Math.max(0,(I[4][1]-Y)*M))),O=Math.floor(Math.max(0,(I[5][0]-Y)*M)),C=Math.ceil(Math.min(T,Math.max(0,(I[5][1]-Y)*M)));if(I[4][1]>=Y&&I[4][0]<=D&&I[4][2]){this.draw_read(V,Q,M,Y,D,I[4][0],I[4][2],I[4][3],G)}if(I[5][1]>=Y&&I[5][0]<=D&&I[5][2]){this.draw_read(V,Q,M,Y,D,I[5][0],I[5][2],I[5][3],G)}if(O>P){V.fillStyle=h;r(V,P-S,G+5,O-S,G+5)}}else{V.fillStyle=Z;this.draw_read(V,Q,M,Y,D,U,I[4],I[5],G)}if(Q==="Pack"&&U>Y){V.fillStyle=this.prefs.label_color;var X=1;if(X===0&&H-V.measureText(N).width<0){V.textAlign="left";V.fillText(N,J+p-S,G+8)}else{V.textAlign="right";V.fillText(N,H-p-S,G+8)}V.fillStyle=Z}}});B.SummaryTreePainter=w;B.LinePainter=c;B.LinkedFeaturePainter=t;B.ReadPainter=v;B.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var extend=function(){var c=arguments[0];for(var b=1;b<arguments.length;b++){var a=arguments[b];for(key in a){c[key]=a[key]}}return c};var trackster_module=function(f,P){var o=f("slotting"),F=f("painters");var V=function(W,X){this.document=W;this.default_font=X!==undefined?X:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};extend(V.prototype,{load_pattern:function(W,aa){var X=this.patterns,Y=this.dummy_context,Z=new Image();Z.src=image_path+aa;Z.onload=function(){X[W]=Y.createPattern(Z,"repeat")}},get_pattern:function(W){return this.patterns[W]},new_canvas:function(){var W=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(W)}W.manager=this;return W}});var A=function(W,X){W.bind("drag",{handle:X,relative:true},function(ab,ac){var aa=$(this).parent();var Z=aa.children();var Y;for(Y=0;Y<Z.length;Y++){if(ac.offsetY<$(Z.get(Y)).position().top){break}}if(Y===Z.length){if(this!==Z.get(Y-1)){aa.append(this)}}else{if(this!==Z.get(Y)){$(this).insertBefore(Z.get(Y))}}})};var h=function(Y,W){var X=W-Y;return(X<=2?0.01:(X<=100?1:(X<=1000?5:10)))};var B=9,y=10,K=B+2,v=100,C=12000,I=200,r=10,E=5000,s=100,m="There was an error in indexing this dataset. ",D="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",z="No data for this chrom/contig.",p="Currently indexing... please wait",u="Tool cannot be rerun: ",a="Loading data...",Q="Ready for display",d=10,q=5,x=5;function t(W){return Math.round(W*1000)/1000}var c=function(W){this.num_elements=W;this.clear()};extend(c.prototype,{get:function(X){var W=this.key_ary.indexOf(X);if(W!==-1){this.move_key_to_end(X,W)}return this.obj_cache[X]},set:function(X,Y){if(!this.obj_cache[X]){if(this.key_ary.length>=this.num_elements){var W=this.key_ary.shift();delete this.obj_cache[W]}this.key_ary.push(X)}this.obj_cache[X]=Y;return Y},move_key_to_end:function(X,W){this.key_ary.splice(W,1);this.key_ary.push(X)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var J=function(X,W,Y){c.call(this,X);this.track=W;this.subset=(Y!==undefined?Y:true)};extend(J.prototype,c.prototype,{load_data:function(ae,af,aa,ad,X,ac){var Z={chrom:ae,low:af,high:aa,mode:ad,resolution:X,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(Z,ac);if(this.track.filters_manager){var ag=[];var W=this.track.filters_manager.filters;for(var ab=0;ab<W.length;ab++){ag[ag.length]=W[ab].name}Z.filter_cols=JSON.stringify(ag)}var Y=this;return $.getJSON(this.track.data_url,Z,function(ah){Y.set_data(af,aa,ad,ah)})},get_data:function(Y,W,ab,ac,X,aa){var Z=this.get(this.gen_key(W,ab,ac));if(Z){return Z}Z=this.load_data(Y,W,ab,ac,X,aa);this.set_data(W,ab,ac,Z);return Z},set_data:function(X,Y,Z,W){return this.set(this.gen_key(X,Y,Z),W)},gen_key:function(W,Y,Z){var X=W+"_"+Y+"_"+Z;return X},split_key:function(W){return W.split("_")}});var U=function(W,Z,Y,X,aa){this.container=W;this.chrom=null;this.vis_id=Y;this.dbkey=X;this.title=Z;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(aa);this.canvas_manager=new V(W.get(0).ownerDocument);this.reset()};extend(U.prototype,{init:function(Z){var Y=this.container,W=this;this.top_container=$("<div/>").addClass("top-container").appendTo(Y);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(Y);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(Y);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var X=function(aa){if(aa.type==="focusout"||(aa.keyCode||aa.which)===13||(aa.keyCode||aa.which)===27){if((aa.keyCode||aa.which)!==27){W.go_to($(this).val())}$(this).hide();$(this).val("");W.location_span.show();W.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",X).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){W.location_span.hide();W.chrom_select.hide();W.nav_input.val(W.chrom+":"+W.low+"-"+W.high);W.nav_input.css("display","inline-block");W.nav_input.select();W.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){W.zoom_out();W.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){W.zoom_in();W.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},Z);this.chrom_select.bind("change",function(){W.change_chrom(W.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(aa){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(aa){W.zoom_in(aa.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aa,ab){this.current_x=ab.offsetX}).bind("drag",function(aa,ac){var ad=ac.offsetX-this.current_x;this.current_x=ac.offsetX;var ab=Math.round(ad/W.viewport_container.width()*(W.max_high-W.max_low));W.move_delta(-ab)});this.overview_close.bind("click",function(){for(var ab=0,aa=W.tracks.length;ab<aa;ab++){W.tracks[ab].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",W.overview_box.height());W.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(aa,ab){if(aa.clientX>W.viewport_container.width()-16){return false}}).bind("dragstart",function(aa,ab){ab.original_low=W.low;ab.current_height=aa.clientY;ab.current_x=ab.offsetX}).bind("drag",function(ac,ae){var aa=$(this);var af=ae.offsetX-ae.current_x;var ab=aa.scrollTop()-(ac.clientY-ae.current_height);aa.scrollTop(ab);ae.current_height=ac.clientY;ae.current_x=ae.offsetX;var ad=Math.round(af/W.viewport_container.width()*(W.high-W.low));W.move_delta(ad)}).bind("mousewheel",function(ac,ae,ab,aa){if(ab){var ad=Math.round(-ab/W.viewport_container.width()*(W.high-W.low));W.move_delta(ad)}});this.top_labeltrack.bind("dragstart",function(aa,ab){return $("<div />").css({height:W.content_div.height()+W.top_labeltrack.height()+W.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ae,af){$(af.proxy).css({left:Math.min(ae.pageX,af.startX),width:Math.abs(ae.pageX-af.startX)});var ab=Math.min(ae.pageX,af.startX)-W.container.offset().left,aa=Math.max(ae.pageX,af.startX)-W.container.offset().left,ad=(W.high-W.low),ac=W.viewport_container.width();W.update_location(Math.round(ab/ac*ad)+W.low,Math.round(aa/ac*ad)+W.low)}).bind("dragend",function(af,ag){var ab=Math.min(af.pageX,ag.startX),aa=Math.max(af.pageX,ag.startX),ad=(W.high-W.low),ac=W.viewport_container.width(),ae=W.low;W.low=Math.round(ab/ac*ad)+ae;W.high=Math.round(aa/ac*ad)+ae;$(ag.proxy).remove();W.redraw()});this.add_label_track(new T(this,this.top_labeltrack));this.add_label_track(new T(this,this.nav_labeltrack));$(window).bind("resize",function(){W.resize_window()});$(document).bind("redraw",function(){W.redraw()});this.reset();$(window).trigger("resize")},update_location:function(W,X){this.location_span.text(commatize(W)+" - "+commatize(X));this.nav_input.val(this.chrom+":"+commatize(W)+"-"+commatize(X))},load_chroms:function(X,Y){X.num=s;$.extend(X,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var W=this;$.ajax({url:chrom_url,data:X,dataType:"json",success:function(aa){if(aa.chrom_info.length===0){alert("Invalid chromosome: "+X.chrom);return}if(aa.reference){W.add_label_track(new w(W))}W.chrom_data=aa.chrom_info;var ad='<option value="">Select Chrom/Contig</option>';for(var ac=0,Z=W.chrom_data.length;ac<Z;ac++){var ab=W.chrom_data[ac].chrom;ad+='<option value="'+ab+'">'+ab+"</option>"}if(aa.prev_chroms){ad+='<option value="previous">Previous '+s+"</option>"}if(aa.next_chroms){ad+='<option value="next">Next '+s+"</option>"}W.chrom_select.html(ad);if(Y){Y()}W.chrom_start_index=aa.start_index},error:function(){alert("Could not load chroms for this dbkey:",W.dbkey)}})},change_chrom:function(aa,X,ac){if(!aa||aa==="None"){return}var Z=this;if(aa==="previous"){Z.load_chroms({low:this.chrom_start_index-s});return}if(aa==="next"){Z.load_chroms({low:this.chrom_start_index+s});return}var ab=$.grep(Z.chrom_data,function(ae,af){return ae.chrom===aa})[0];if(ab===undefined){Z.load_chroms({chrom:aa},function(){Z.change_chrom(aa,X,ac)});return}else{if(aa!==Z.chrom){Z.chrom=aa;if(!Z.chrom){Z.intro_div.show()}else{Z.intro_div.hide()}Z.chrom_select.val(Z.chrom);Z.max_high=ab.len-1;Z.reset();Z.redraw(true);for(var ad=0,W=Z.tracks.length;ad<W;ad++){var Y=Z.tracks[ad];if(Y.init){Y.init()}}}if(X!==undefined&&ac!==undefined){Z.low=Math.max(X,0);Z.high=Math.min(ac,Z.max_high)}Z.reset_overview();Z.redraw()}},go_to:function(aa){var ae=this,W,Z,X=aa.split(":"),ac=X[0],ad=X[1];if(ad!==undefined){try{var ab=ad.split("-");W=parseInt(ab[0].replace(/,/g,""),10);Z=parseInt(ab[1].replace(/,/g,""),10)}catch(Y){return false}}ae.change_chrom(ac,W,Z)},move_fraction:function(Y){var W=this;var X=W.high-W.low;this.move_delta(Y*X)},move_delta:function(Y){var W=this;var X=W.high-W.low;if(W.low-Y<W.max_low){W.low=W.max_low;W.high=W.max_low+X}else{if(W.high-Y>W.max_high){W.high=W.max_high;W.low=W.max_high-X}else{W.high-=Y;W.low-=Y}}W.redraw()},add_track:function(W){W.view=this;W.track_id=this.track_id_counter;this.tracks.push(W);if(W.init){W.init()}W.container_div.attr("id","track_"+W.track_id);A(W.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(W){W.view=this;this.label_tracks.push(W)},remove_track:function(W){this.has_changes=true;W.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(W)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ad){var ac=this.high-this.low,ab=this.low,X=this.high;if(ab<this.max_low){ab=this.max_low}if(X>this.max_high){X=this.max_high}if(this.high!==0&&ac<this.min_separation){X=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(X);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(r,Math.max(0,Math.ceil(Math.log(this.resolution,r)/Math.log(r))));var W=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aa=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:W,width:Math.max(ae,aa)}).show();if(aa<ae){this.overview_box.css("left",W-(ae-aa)/2)}if(this.overview_highlight){this.overview_highlight.css({left:W,width:aa})}this.update_location(this.low,this.high);if(!ad){for(var Y=0,Z=this.tracks.length;Y<Z;Y++){if(this.tracks[Y]&&this.tracks[Y].enabled){this.tracks[Y].draw()}}for(Y=0,Z=this.label_tracks.length;Y<Z;Y++){this.label_tracks[Y].draw()}}},zoom_in:function(X,Y){if(this.max_high===0||this.high-this.low<this.min_separation){return}var Z=this.high-this.low,aa=Z/2+this.low,W=(Z/this.zoom_factor)/2;if(X){aa=X/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aa-W);this.high=Math.round(aa+W);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var X=this.high-this.low,Y=X/2+this.low,W=(X*this.zoom_factor)/2;this.low=Math.round(Y-W);this.high=Math.round(Y+W);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var n=function(X,aa){this.track=X;this.name=aa.name;this.params=[];var ai=aa.params;for(var Y=0;Y<ai.length;Y++){var ad=ai[Y],W=ad.name,ah=ad.label,Z=unescape(ad.html),af=ad.type;if(af==="number"){this.params[this.params.length]=new g(W,ah,Z,ad.min,ad.max)}else{if(af=="select"){this.params[this.params.length]=new H(W,ah,Z)}else{console.log("WARNING: unrecognized tool parameter type:",W,af)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ak){ak.stopPropagation()}).bind("click",function(ak){ak.stopPropagation()}).bind("dblclick",function(ak){ak.stopPropagation()});var ag=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ae=this.params;var ab=this;$.each(this.params,function(al,ao){var an=$("<div>").addClass("param-row").appendTo(ab.parent_div);var ak=$("<div>").addClass("param-label").text(ao.label).appendTo(an);var am=$("<div/>").addClass("slider").html(ao.html).appendTo(an);$("<div style='clear: both;'/>").appendTo(an)});this.parent_div.find("input").click(function(){$(this).select()});var aj=$("<div>").addClass("slider-row").appendTo(this.parent_div);var ac=$("<input type='submit'>").attr("value","Run").appendTo(aj);var ab=this;ac.click(function(){ab.run()})};extend(n.prototype,{get_param_values_dict:function(){var W={};this.parent_div.find(":input").each(function(){var X=$(this).attr("name"),Y=$(this).val();W[X]=JSON.stringify(Y)});return W},get_param_values:function(){var X=[];var W={};this.parent_div.find(":input").each(function(){var Y=$(this).attr("name"),Z=$(this).val();if(Y){X[X.length]=Z}});return X},run:function(){var X={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name};$.extend(X,this.get_param_values_dict());var Z=this.track,Y=X.tool_id+Z.tool_region_and_parameters_str(X.chrom,X.low,X.high),aa;if(Z.track_type==="FeatureTrack"){aa=new M(Y,view,Z.hda_ldda,undefined,{},{},Z)}this.track.add_track(aa);aa.content_div.text("Starting job.");var W=function(){$.getJSON(run_tool_url,X,function(ab){if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(D)}else{if(ab.error){aa.container_div.addClass("error");aa.content_div.text(u+ab.message)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text("Converting input data so that it can be easily reused.");setTimeout(W,2000)}else{aa.dataset_id=ab.dataset_id;aa.content_div.text("Running job.");aa.init()}}}})};W()}});var H=function(X,W,Y){this.name=X;this.label=W;this.html=Y};var g=function(Y,X,aa,Z,W){H.call(this,Y,X,aa);this.min=Z;this.max=W};var j=function(X,W,Y){this.name=X;this.index=W;this.value=Y};var N=function(X,W){this.name=X;this.index=W;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};extend(N.prototype,{applies_to:function(W){if(W.length>this.index){return true}return false},keep:function(W){if(!this.applies_to(W)){return true}return(W[this.index]>=this.low&&W[this.index]<=this.high)},update_attrs:function(X){var W=false;if(!this.applies_to(X)){return W}if(X[this.index]<this.min){this.min=Math.floor(X[this.index]);W=true}if(X[this.index]>this.max){this.max=Math.ceil(X[this.index]);W=true}return W},update_ui_elt:function(){var X=this.slider.slider("option","min"),W=this.slider.slider("option","max");if(this.min<X||this.max>W){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",h(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var S=function(Y,ae){this.track=Y;this.filters=[];for(var aa=0;aa<ae.length;aa++){var W=ae[aa];var X=W.name,ad=W.type,ab=W.index;if(ad==="int"||ad==="float"){this.filters[aa]=new N(X,ab)}else{this.filters[aa]=new j(X,ab,ad)}}var ac=function(af,ag,ah){af.click(function(){var ai=ag.text();max=parseFloat(ah.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(ah.slider("option","values")){input_size=2*input_size+1;multi_value=true}ag.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ai).appendTo(ag).focus().select().click(function(aj){aj.stopPropagation()}).blur(function(){$(this).remove();ag.text(ai)}).keyup(function(an){if(an.keyCode===27){$(this).trigger("blur")}else{if(an.keyCode===13){var al=ah.slider("option","min"),aj=ah.slider("option","max"),am=function(ao){return(isNaN(ao)||ao>aj||ao<al)},ak=$(this).val();if(!multi_value){ak=parseFloat(ak);if(am(ak)){alert("Parameter value must be in the range ["+al+"-"+aj+"]");return $(this)}}else{ak=ak.split("-");ak=[parseFloat(ak[0]),parseFloat(ak[1])];if(am(ak[0])||am(ak[1])){alert("Parameter value must be in the range ["+al+"-"+aj+"]");return $(this)}}ah.slider((multi_value?"values":"value"),ak)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(af){af.stopPropagation()}).bind("click",function(af){af.stopPropagation()}).bind("dblclick",function(af){af.stopPropagation()});var Z=this;$.each(this.filters,function(al,ag){var ai=$("<div/>").addClass("slider-row").appendTo(Z.parent_div);var af=$("<div/>").addClass("slider-label").appendTo(ai);var an=$("<span/>").addClass("slider-name").text(ag.name+" ").appendTo(af);var ah=$("<span/>");var aj=$("<span/>").addClass("slider-value").appendTo(af).append("[").append(ah).append("]");var am=$("<div/>").addClass("slider").appendTo(ai);ag.control_element=$("<div/>").attr("id",ag.name+"-filter-control").appendTo(am);var ak=[0,0];ag.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ao,ap){ak=ap.values;ah.text(ap.values[0]+"-"+ap.values[1]);setTimeout(function(){if(ap.values[0]==ak[0]&&ap.values[1]==ak[1]){var aq=ap.values;ah.text(aq[0]+"-"+aq[1]);ag.low=aq[0];ag.high=aq[1];Z.track.draw(true,true)}},50)},change:function(ao,ap){ag.control_element.slider("option","slide").call(ag.control_element,ao,ap)}});ag.slider=ag.control_element;ag.slider_label=ah;ac(aj,ah,ag.control_element);$("<div style='clear: both;'/>").appendTo(ai)})};var R=function(W){this.track=W.track;this.params=W.params;this.values={};if(W.saved_values){this.restore_values(W.saved_values)}this.onchange=W.onchange};extend(R.prototype,{restore_values:function(W){var X=this;$.each(this.params,function(Y,Z){if(W[Z.key]!==undefined){X.values[Z.key]=W[Z.key]}else{X.values[Z.key]=Z.default_value}})},build_form:function(){var X=this;var W=$("<div />");$.each(this.params,function(ab,Z){if(!Z.hidden){var Y="param_"+ab;var ag=$("<div class='form-row' />").appendTo(W);ag.append($("<label />").attr("for",Y).text(Z.label+":"));if(Z.type==="bool"){ag.append($('<input type="checkbox" />').attr("id",Y).attr("name",Y).attr("checked",X.values[Z.key]))}else{if(Z.type==="color"){var ad=X.values[Z.key];var ac=$("<input />").attr("id",Y).attr("name",Y).val(ad);var ae=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var aa=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ae);var af=$("<div/>").appendTo(aa).farbtastic({width:100,height:100,callback:ac,color:ad});$("<div />").append(ac).append(ae).appendTo(ag).bind("click",function(ah){ae.css({left:$(this).position().left+($(ac).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ae.hide();$(document).unbind("click.color-picker")});ah.stopPropagation()})}else{ag.append($("<input />").attr("id",Y).attr("name",Y).val(X.values[Z.key]))}}}});return W},update_from_form:function(W){var Y=this;var X=false;$.each(this.params,function(Z,ab){if(!ab.hidden){var ac="param_"+Z;var aa=W.find("#"+ac).val();if(ab.type==="float"){aa=parseFloat(aa)}else{if(ab.type==="int"){aa=parseInt(aa)}else{if(ab.type==="bool"){aa=W.find("#"+ac).is(":checked")}}}if(aa!==Y.values[ab.key]){Y.values[ab.key]=aa;X=true}}});if(X){this.onchange()}}});var b=function(W,X){this.track=W;this.canvas=X};var k=function(X,W,aa,Y,Z){this.name=X;this.view=W;this.parent_element=aa;this.data_url=(Y?Y:default_data_url);this.data_url_extra_params={};this.data_query_wait=(Z?Z:E);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};extend(k.prototype,{init:function(){var W=this;W.enabled=false;W.tile_cache.clear();W.data_cache.clear();W.initial_canvas=undefined;W.content_div.css("height","auto");W.container_div.removeClass("nodata error pending");if(!W.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:W.hda_ldda,dataset_id:W.dataset_id,chrom:W.view.chrom},function(X){if(!X||X==="error"||X.kind==="error"){W.container_div.addClass("error");W.content_div.text(m);if(X.message){var Z=W.view.tracks.indexOf(W);var Y=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+X.message+"</pre>",{Close:hide_modal})});W.content_div.append(Y)}}else{if(X==="no converter"){W.container_div.addClass("error");W.content_div.text(D)}else{if(X==="no data"||(X.data!==undefined&&(X.data===null||X.data.length===0))){W.container_div.addClass("nodata");W.content_div.text(z)}else{if(X==="pending"){W.container_div.addClass("pending");W.content_div.text(p);setTimeout(function(){W.init()},W.data_query_wait)}else{if(X.status==="data"){if(X.valid_chroms){W.valid_chroms=X.valid_chroms;W.make_name_popup_menu()}W.content_div.text(Q);if(W.view.chrom){W.content_div.text("");W.content_div.css("height",W.height_px+"px");W.enabled=true;$.when(W.predraw_init()).done(function(){W.container_div.removeClass("nodata error pending");W.draw()})}}}}}}})},predraw_init:function(){},update_name:function(W){this.old_name=this.name;this.name=W;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var G=function(ae,ac,af){var X=this,ag=X.view;this.filters_manager=(ae!==undefined?new S(this,ae):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(ac!==undefined&&obj_length(ac)>0?new n(this,ac):undefined);this.parent_track=af;this.child_tracks=[];if(X.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}X.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();X.container_div.append(X.child_tracks_container);if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(X.display_modes!==undefined){if(X.mode_div===undefined){X.mode_div=$("<div class='right-float menubutton popup' />").appendTo(X.header_div);var Z=(X.track_config&&X.track_config.values.mode?X.track_config.values.mode:X.display_modes[0]);X.mode=Z;X.mode_div.text(Z);var Y=function(ah){X.mode_div.text(ah);X.mode=ah;X.track_config.values.mode=ah;X.tile_cache.clear();X.draw()};var W={};for(var aa=0,ad=X.display_modes.length;aa<ad;aa++){var ab=X.display_modes[aa];W[ab]=function(ah){return function(){Y(ah)}}(ab)}make_popupmenu(X.mode_div,W)}else{X.mode_div.hide()}}this.make_name_popup_menu()};extend(G.prototype,k.prototype,{make_name_popup_menu:function(){var X=this;var W={};W["Edit configuration"]=function(){var ad=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(){X.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(ae){if((ae.keyCode||ae.which)===27){ad()}else{if((ae.keyCode||ae.which)===13){ab()}}};$(window).bind("keypress.check_enter_esc",ac);show_modal("Configure Track",X.track_config.build_form(),{Cancel:ad,OK:ab})};if(X.filters_available>0){var aa=(X.filters_div.is(":visible")?"Hide filters":"Show filters");W[aa]=function(){X.filters_visible=(X.filters_div.is(":visible"));X.filters_div.toggle();X.make_name_popup_menu()}}if(X.tool){var aa=(X.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");W[aa]=function(){if(!X.dynamic_tool_div.is(":visible")){X.update_name(X.name+X.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";X.revert_name()}X.dynamic_tool_div.toggle();X.make_name_popup_menu()}}if(X.valid_chroms){W["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+X.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var Y=view;var Z=function(){$("#no-tracks").show()};if(this.parent_track){Y=this.parent_track;Z=function(){}}W.Remove=function(){Y.remove_track(X);if(Y.num_tracks===0){Z()}};make_popupmenu(X.name_div,W)},draw:function(W,Z){var an=this.view.low,ac=this.view.high,ae=ac-an,ag=this.view.container.width(),ab=ag/ae,ah=this.view.resolution,aa=$("<div style='position: relative;'></div>");if(!Z){this.content_div.children().remove()}this.content_div.append(aa);this.max_height=0;var aj=Math.floor(an/ah/I);var Y={};while((aj*I*ah)<ac){var am=ag+"_"+ab+"_"+aj;var ad=this.tile_cache.get(am);var ak=aj*I*this.view.resolution;var X=ak+I*this.view.resolution;if(!W&&ad){this.show_tile(ad,aa,ak,ab)}else{this.delayed_draw(W,am,ak,X,aj,ah,aa,ab,Y)}aj+=1}var af=this;var al=setInterval(function(){if(obj_length(Y)===0){clearInterval(al);if(Z){var aq=af.content_div.children();var ap=false;for(var ar=aq.length-1,ao=0;ar>=ao;ar--){var aw=$(aq[ar]);if(ap){aw.remove()}else{if(aw.children().length!==0){ap=true}}}}if(af.filters_manager){var au=af.filters_manager.filters;for(var av=0;av<au.length;av++){au[av].update_ui_elt()}var at=false;if(af.example_feature){for(var av=0;av<au.length;av++){if(au[av].applies_to(af.example_feature)){at=true;break}}}if(af.filters_available!==at){af.filters_available=at;if(!af.filters_available){af.filters_div.hide()}af.make_name_popup_menu()}}}},50);for(var ai=0;ai<this.child_tracks.length;ai++){this.child_tracks[ai].draw(W,Z)}},delayed_draw:function(X,ae,ac,ag,Y,aa,af,ah,ab){var Z=this;var ad=function(ap,ai,ak,aj,an,ao,al){returned_tile=Z.draw_tile(ai,ak,aj,an,ao,al);var am=$("<div class='track-tile'>").prepend(returned_tile);tile_element=am;Z.tile_cache.set(ae,tile_element);Z.show_tile(tile_element,an,ac,ao);delete ab[ap]};var W=setTimeout(function(){if(ac<=Z.view.high&&ag>=Z.view.low){var ai=(X?undefined:Z.tile_cache.get(ae));if(ai){Z.show_tile(ai,af,ac,ah);delete ab[W]}else{$.when(Z.data_cache.get_data(view.chrom,ac,ag,Z.mode,aa,Z.data_url_extra_params)).then(function(aj){if(view.reference_track&&ah>view.canvas_manager.char_width_px){$.when(view.reference_track.data_cache.get_data(view.chrom,ac,ag,Z.mode,aa,view.reference_track.data_url_extra_params)).then(function(ak){ad(W,aj,aa,Y,af,ah,ak)})}else{ad(W,aj,aa,Y,af,ah)}})}}},50);ab[W]=true},show_tile:function(W,ab,Z,ac){var X=this;var Y=this.view.high-this.view.low,aa=(Z-this.view.low)*ac;if(this.left_offset){aa-=this.left_offset}W.css({position:"absolute",top:0,left:aa,height:""});ab.append(W);X.max_height=Math.max(X.max_height,W.height());X.content_div.css("height",X.max_height+"px");ab.children().css("height",X.max_height+"px")},set_overview:function(){var W=this.view;if(this.initial_canvas&&this.is_overview){W.overview_close.show();W.overview_viewport.append(this.initial_canvas);W.overview_highlight.show().height(this.initial_canvas.height());W.overview_viewport.height(this.initial_canvas.height()+W.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(Y,W,Z){var X=this,aa=(Y!==undefined&&W!==undefined&&Z!==undefined?Y+":"+W+"-"+Z:"all");return" - region=["+aa+"], parameters=["+X.tool.get_param_values().join(", ")+"]"},add_track:function(W){W.track_id=this.track_id+"_"+this.child_tracks.length;W.container_div.attr("id","track_"+W.track_id);this.child_tracks_container.append(W.container_div);A(W.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(W);this.view.has_changes=true},remove_track:function(W){W.container_div.fadeOut("slow",function(){$(this).remove()})}});var T=function(W,X){this.track_type="LabelTrack";this.hidden=true;k.call(this,null,W,X);this.container_div.addClass("label-track")};extend(T.prototype,k.prototype,{draw:function(){var Y=this.view,Z=Y.high-Y.low,ac=Math.floor(Math.pow(10,Math.floor(Math.log(Z)/Math.log(10)))),W=Math.floor(Y.low/ac)*ac,aa=this.view.container.width(),X=$("<div style='position: relative; height: 1.3em;'></div>");while(W<Y.high){var ab=(W-Y.low)/Z*aa;X.append($("<div class='label'>"+commatize(W)+"</div>").css({position:"absolute",left:ab-1}));W+=ac}this.content_div.children(":first").remove();this.content_div.append(X)}});var w=function(W){this.track_type="ReferenceTrack";this.hidden=true;k.call(this,null,W,W.top_labeltrack);G.call(this);W.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:W.dbkey};this.data_cache=new J(x,this,false);this.tile_cache=new c(q)};extend(w.prototype,G.prototype,{draw_tile:function(ag,ab,X,ad,ah){var aa=this,Y=I*ab;if(ah>this.view.canvas_manager.char_width_px){if(ag===null){aa.content_div.css("height","0px");return}var Z=this.view.canvas_manager.new_canvas();var af=Z.getContext("2d");Z.width=Math.ceil(Y*ah+aa.left_offset);Z.height=aa.height_px;af.font=af.canvas.manager.default_font;af.textAlign="center";for(var ac=0,ae=ag.length;ac<ae;ac++){var W=Math.round(ac*ah);af.fillText(ag[ac],W+aa.left_offset,10)}return Z}this.content_div.css("height","0px")}});var l=function(aa,Y,ab,W,Z){var X=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";k.call(this,aa,Y,Y.viewport_container);G.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ab;this.dataset_id=W;this.original_dataset_id=W;this.data_cache=new J(x,this);this.tile_cache=new c(q);this.track_config=new R({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:Z,onchange:function(){X.vertical_range=X.prefs.max_value-X.prefs.min_value;$("#linetrack_"+X.track_id+"_minval").text(X.prefs.min_value);$("#linetrack_"+X.track_id+"_maxval").text(X.prefs.max_value);X.tile_cache.clear();X.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};extend(l.prototype,G.prototype,{add_resize_handle:function(){var W=this;var Z=false;var Y=false;var X=$("<div class='track-resize'>");$(W.container_div).hover(function(){Z=true;X.show()},function(){Z=false;if(!Y){X.hide()}});X.hide().bind("dragstart",function(aa,ab){Y=true;ab.original_height=$(W.content_div).height()}).bind("drag",function(ab,ac){var aa=Math.min(Math.max(ac.original_height+ac.deltaY,W.min_height_px),W.max_height_px);$(W.content_div).css("height",aa);W.height_px=aa;W.draw(true)}).bind("dragend",function(aa,ab){W.tile_cache.clear();Y=false;if(!Z){X.hide()}W.track_config.values.height=W.height_px}).appendTo(W.container_div)},predraw_init:function(){var W=this,X=W.view.tracks.indexOf(W);W.vertical_range=undefined;return $.getJSON(W.data_url,{stats:true,chrom:W.view.chrom,low:null,high:null,hda_ldda:W.hda_ldda,dataset_id:W.dataset_id},function(Y){W.container_div.addClass("line-track");var aa=Y.data;if(isNaN(parseFloat(W.prefs.min_value))||isNaN(parseFloat(W.prefs.max_value))){W.prefs.min_value=aa.min;W.prefs.max_value=aa.max;$("#track_"+X+"_minval").val(W.prefs.min_value);$("#track_"+X+"_maxval").val(W.prefs.max_value)}W.vertical_range=W.prefs.max_value-W.prefs.min_value;W.total_frequency=aa.total_frequency;W.container_div.find(".yaxislabel").remove();var ab=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+X+"_minval").text(t(W.prefs.min_value));var Z=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+X+"_maxval").text(t(W.prefs.max_value));Z.css({position:"absolute",top:"24px",left:"10px"});Z.prependTo(W.container_div);ab.css({position:"absolute",bottom:"2px",left:"10px"});ab.prependTo(W.container_div)})},draw_tile:function(ah,aa,X,ae,ag){if(this.vertical_range===undefined){return}var ab=X*I*aa,Z=I*aa,W=Math.ceil(Z*ag),ad=this.height_px;var Y=this.view.canvas_manager.new_canvas();Y.width=W,Y.height=ad;var af=Y.getContext("2d");var ac=new F.LinePainter(ah.data,ab,ab+Z,this.prefs,this.mode);ac.draw(af,W,ad);return Y}});var e=function(W,ab,aa,ae,ad,Y,Z,ac){var X=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new R({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ad,onchange:function(){X.tile_cache.clear();X.draw()}});this.prefs=this.track_config.values;k.call(this,W,ab,ab.viewport_container);G.call(this,Y,Z,ac);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=aa;this.dataset_id=ae;this.original_dataset_id=ae;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_cache=new J(20,this);this.left_offset=200;this.painter=F.LinkedFeaturePainter};extend(e.prototype,G.prototype,{update_auto_mode:function(W){if(this.mode=="Auto"){if(W=="no_detail"){W="feature spans"}else{if(W=="summary_tree"){W="coverage histogram"}}this.mode_div.text("Auto ("+W+")")}},incremental_slots:function(aa,X,Z){var Y=this.view.canvas_manager.dummy_context,W=this.inc_slots[aa];if(!W||(W.mode!==Z)){W=new (o.FeatureSlotter)(aa,Z==="Pack",v,function(ab){return Y.measureText(ab)});W.mode=Z;this.inc_slots[aa]=W}return W.slot_features(X)},draw_tile:function(aj,ar,aw,ae,ag,Z){var ao=this,ay=aw*I*ar,X=(aw+1)*I*ar,al=X-ay,ap=Math.ceil(al*ag),an=this.mode,aC=25,aa=this.left_offset,ak,ab;if(an==="Auto"){if(aj.dataset_type==="summary_tree"){an=aj.dataset_type}else{if(aj.extra_info==="no_detail"){an="no_detail"}else{var aB=aj.data;if(this.view.high-this.view.low>C){an="Squish"}else{an="Pack"}}}this.update_auto_mode(an)}if(an==="summary_tree"){ab=this.summary_draw_height;ae.parent().css("height",Math.max(this.height_px,ab)+"px");this.container_div.find(".yaxislabel").remove();var W=$("<div />").addClass("yaxislabel");W.text(aj.max);W.css({position:"absolute",top:"22px",left:"10px"});W.prependTo(this.container_div);var Y=this.view.canvas_manager.new_canvas();Y.width=ap+aa;Y.height=ab+K;var az=new F.SummaryTreePainter(aj,ay,X,this.prefs);var aq=Y.getContext("2d");aq.translate(aa,K);az.draw(aq,ap,ab);return Y}var ak,ad=1;if(an==="no_detail"||an==="Squish"||an==="Pack"){ad=this.incremental_slots(ag,aj.data,an);ak=this.inc_slots[ag].slots}var af=[];if(aj.data){var ah=this.filters_manager.filters;for(var at=0,av=aj.data.length;at<av;at++){var ac=aj.data[at];var au=false;var ai;for(var ax=0,aA=ah.length;ax<aA;ax++){ai=ah[ax];ai.update_attrs(ac);if(!ai.keep(ac)){au=true;break}}if(!au){af.push(ac)}}}var az=new (this.painter)(af,ay,X,this.prefs,an,Z);var ab=az.get_required_height(ad)+y;var Y=this.view.canvas_manager.new_canvas();Y.width=ap+aa;Y.height=ab;ae.parent().css("height",Math.max(this.height_px,ab)+"px");var aq=Y.getContext("2d");aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aj.message){$(Y).css({"border-top":"1px solid red"});aq.fillStyle="red";aq.textAlign="left";var am=aq.textBaseline;aq.textBaseline="top";aq.fillText(aj.message,aa,0);aq.textBaseline=am;if(!aj.data){return Y}}this.example_feature=(aj.data.length?aj.data[0]:undefined);aq.translate(aa,y);az.draw(aq,ap,ab,ak);return Y}});var L=function(Z,X,ab,W,Y,aa){e.call(this,Z,X,ab,W,Y,aa);this.track_type="VcfTrack";this.painter=F.VariantPainter};extend(L.prototype,G.prototype,e.prototype);var O=function(Z,X,ab,W,Y,aa){e.call(this,Z,X,ab,W,Y,aa);this.track_config=new R({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:Y,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.painter=F.ReadPainter;this.make_name_popup_menu()};extend(O.prototype,G.prototype,e.prototype);var M=function(aa,Y,ac,W,Z,ab,X){e.call(this,aa,Y,ac,W,Z,ab,{},X);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};extend(M.prototype,G.prototype,e.prototype,{predraw_init:function(){var X=this;var W=function(){if(X.data_cache.size()===0){setTimeout(W,300)}else{X.data_url=default_data_url;X.data_query_wait=E;X.dataset_state_url=converted_datasets_state_url;$.getJSON(X.dataset_state_url,{dataset_id:X.dataset_id,hda_ldda:X.hda_ldda},function(Y){})}};W()}});P.View=U;P.LineTrack=l;P.FeatureTrack=e;P.ReadTrack=O};var slotting_module=function(c,b){var d=2,a=5;b.FeatureSlotter=function(h,g,e,f){this.slots={};this.start_end_dct={};this.w_scale=h;this.include_label=g;this.max_rows=e;this.measureText=f};extend(b.FeatureSlotter.prototype,{slot_features:function(l){var o=this.w_scale,r=this.slots,g=this.start_end_dct,x=[],z=[],m=0,y=this.max_rows;for(var v=0,w=l.length;v<w;v++){var k=l[v],n=k[0];if(r[n]!==undefined){m=Math.max(m,r[n]);z.push(r[n])}else{x.push(v)}}var p=function(F,G){for(var E=0;E<=y;E++){var C=false,H=g[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var A=H[B];if(G>A[0]&&F<A[1]){C=true;break}}}if(!C){return E}}return -1};for(var v=0,w=x.length;v<w;v++){var k=l[x[v]],n=k[0],t=k[1],e=k[2],q=k[3],f=Math.floor(t*o),j=Math.ceil(e*o),u=this.measureText(q).width,h;if(q!==undefined&&this.include_label){u+=(d+a);if(f-u>=0){f-=u;h="left"}else{j+=u;h="right"}}var s=p(f,j);if(s>=0){if(g[s]===undefined){g[s]=[]}g[s].push([f,j]);r[n]=s;m=Math.max(m,s)}else{}}return m+1}})};var painters_module=function(k,B){var r=function(M,E,K,D,J,H){if(H===undefined){H=4}var G=D-E;var F=J-K;var I=Math.floor(Math.sqrt(G*G+F*F)/H);var N=G/I;var L=F/I;var C;for(C=0;C<I;C++,E+=N,K+=L){if(C%2!==0){continue}M.fillRect(E,K,H,1)}};var s=function(E,D,C,H){var G=D-H/2,F=D+H/2,I=C-Math.sqrt(H*3/2);E.beginPath();E.moveTo(G,I);E.lineTo(F,I);E.lineTo(D,C);E.lineTo(G,I);E.strokeStyle=this.fillStyle;E.fill();E.stroke();E.closePath()};var o=function(E,G,C,D,F){this.data=E;this.view_start=G;this.view_end=C;this.prefs=extend({},this.default_prefs,D);this.mode=F};o.prototype.default_prefs={};var w=function(E,G,C,D,F){o.call(this,E,G,C,D,F)};w.prototype.default_prefis={show_counts:false};w.prototype.draw=function(P,C,O){var H=this.view_start,R=this.view_end-this.view_start,Q=C/R;var M=this.data.data,L=this.data.delta,J=this.data.max,E=O;delta_x_px=Math.ceil(L*Q);P.save();for(var F=0,G=M.length;F<G;F++){var K=Math.floor((M[F][0]-H)*Q);var I=M[F][1];if(!I){continue}var N=I/J*O;P.fillStyle="black";P.fillRect(K,E-N,delta_x_px,N);var D=4;if(this.prefs.show_counts&&(P.measureText(I).width+D)<delta_x_px){P.fillStyle="#666";P.textAlign="center";P.fillText(I,K+(delta_x_px/2),10)}}P.restore()};var c=function(E,G,C,D,F){o.call(this,E,G,C,D,F)};c.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};c.prototype.draw=function(R,Q,O){var J=false,K=this.prefs.min_value,H=this.prefs.max_value,N=H-K,D=O,E=this.view_start,P=this.view_end-this.view_start,F=Q/P,L=this.mode,V=this.data;R.save();var W=Math.round(O+K/N*O);if(L!=="Intensity"){R.fillStyle="#aaa";R.fillRect(0,W,Q,1)}R.beginPath();R.fillStyle=this.prefs.color;var U,I,G;if(V.length>1){G=Math.ceil((V[1][0]-V[0][0])*F)}else{G=10}for(var 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q=function(E,G,C,D,F){o.call(this,E,G,C,D,F)};q.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(q.prototype,{get_required_height:function(D){var C=y_scale=this.get_row_height(),E=this.mode;if(E==="no_detail"||E==="Squish"||E==="Pack"){C=D*y_scale}return C+Math.max(Math.round(y_scale/2),5)},draw:function(O,F,N,K){var I=this.data,L=this.view_start,P=this.view_end;O.save();O.fillStyle=this.prefs.block_color;O.textAlign="right";var S=this.view_end-this.view_start,R=F/S,E=this.get_row_height();for(var H=0,J=I.length;H<J;H++){var Q=I[H],G=Q[0],C=Q[1],D=Q[2],M=(K&&K[G]!==undefined?K[G]:null);if((C<P&&D>L)&&(this.mode=="Dense"||M!==null)){this.draw_element(O,this.mode,Q,M,L,P,R,E,F)}}O.restore()}});var d=10,j=3,n=5,A=10,g=1,u=3,f=3,a=9,p=2,h="#ccc";var t=function(E,G,C,D,F){q.call(this,E,G,C,D,F)};extend(t.prototype,q.prototype,{get_row_height:function(){var D=this.mode,C;if(D==="Dense"){C=d}else{if(D==="no_detail"){C=j}else{if(D==="Squish"){C=n}else{C=A}}}return 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b=function(E,G,C,D,F){q.call(this,E,G,C,D,F)};extend(b.prototype,q.prototype,{draw_element:function(V,Q,K,G,Y,E,N,W,T){var K=data[i],M=K[0],U=K[1],F=K[2]-1,P=K[3],I=Math.floor(Math.max(0,(U-Y)*N)),L=Math.ceil(Math.min(T,Math.max(0,(F-Y)*N))),H=(Q==="Dense"?0:(0+G))*W,C,Z,D=null,O=null;if(no_label){V.fillStyle=block_color;V.fillRect(I+left_offset,H+5,L-I,1)}else{var X=K[4],S=K[5],J=K[6];C=9;Z=1;V.fillRect(I+left_offset,H,L-I,C);if(Q!=="Dense"&&P!==undefined&&U>Y){V.fillStyle=label_color;if(Y===0&&I-V.measureText(P).width<0){V.textAlign="left";V.fillText(P,L+2+left_offset,H+8)}else{V.textAlign="right";V.fillText(P,I-2+left_offset,H+8)}V.fillStyle=block_color}var R=X+" / "+S;if(U>Y&&V.measureText(R).width<(L-I)){V.fillStyle="white";V.textAlign="center";V.fillText(R,left_offset+I+(L-I)/2,H+8);V.fillStyle=block_color}}}});var z=1001,m=1002,e=1003,y=1004,l=1005;var x=function(G,D){var 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c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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