details: http://www.bx.psu.edu/hg/galaxy/rev/cb842f737d46 changeset: 2837:cb842f737d46 user: Kanwei Li kanwei@gmail.com date: Tue Oct 06 23:47:08 2009 -0400 description: refactor trackster, better failure message

6 file(s) affected in this change:

lib/galaxy/datatypes/indexers/coverage.py lib/galaxy/datatypes/indexers/wiggle.py lib/galaxy/web/controllers/tracks.py static/scripts/trackster.js templates/tracks/browser.mako templates/tracks/new_browser.mako

diffs (252 lines):

diff -r b25297e88f96 -r cb842f737d46 lib/galaxy/datatypes/indexers/coverage.py --- a/lib/galaxy/datatypes/indexers/coverage.py Tue Oct 06 21:25:01 2009 -0400 +++ b/lib/galaxy/datatypes/indexers/coverage.py Tue Oct 06 23:47:08 2009 -0400 @@ -2,7 +2,7 @@

""" Read a chromosome of coverage data, and write it as a npy array, as -well as averages over regions of progessively larger size in powers of 10 +well as averages over regions of progressively larger size in powers of 10 """

from __future__ import division diff -r b25297e88f96 -r cb842f737d46 lib/galaxy/datatypes/indexers/wiggle.py --- a/lib/galaxy/datatypes/indexers/wiggle.py Tue Oct 06 21:25:01 2009 -0400 +++ b/lib/galaxy/datatypes/indexers/wiggle.py Tue Oct 06 23:47:08 2009 -0400 @@ -2,7 +2,7 @@

""" Read a chromosome of wiggle data, and write it as a npy array, as -well as averages over regions of progessively larger size in powers of 10 +well as averages over regions of progressively larger size in powers of 10 """

from __future__ import division diff -r b25297e88f96 -r cb842f737d46 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Tue Oct 06 21:25:01 2009 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Tue Oct 06 23:47:08 2009 -0400 @@ -49,7 +49,8 @@

# FIXME: hardcoding this for now, but it should be derived from the available # converters -browsable_types = set( ["wig", "bed" ] ) +browsable_types = ( "wig", "bed" ) +

class TracksController( BaseController ): """ @@ -92,7 +93,7 @@ if dataset.metadata.dbkey == dbkey and dataset.extension in browsable_types: datasets[dataset.id] = (dataset.extension, dataset.name) # Render the template - return trans.fill_template( "tracks/new_browser.mako", dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets ) + return trans.fill_template( "tracks/new_browser.mako", converters=browsable_types, dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets )

@web.expose def browser(self, trans, dataset_ids, chrom=""): diff -r b25297e88f96 -r cb842f737d46 static/scripts/trackster.js --- a/static/scripts/trackster.js Tue Oct 06 21:25:01 2009 -0400 +++ b/static/scripts/trackster.js Tue Oct 06 23:47:08 2009 -0400 @@ -5,35 +5,6 @@ var DENSITY = 1000, DATA_ERROR = "There was an error in indexing this dataset.", DATA_NONE = "No data for this chrom/contig."; - -var DataCache = function( type, track ) { - this.type = type; - this.track = track; - this.cache = Object(); -}; -$.extend( DataCache.prototype, { - get: function( resolution, position ) { - var cache = this.cache; - if ( !( cache[resolution] && cache[resolution][position] ) ) { - if ( !cache[resolution] ) { - cache[resolution] = Object(); - } - var low = position * DENSITY * resolution; - var high = ( position + 1 ) * DENSITY * resolution; - cache[resolution][position] = { state: "loading" }; - - $.getJSON( data_url, { track_type: this.track.track_type, chrom: this.track.view.chrom, low: low, high: high, dataset_id: this.track.dataset_id }, function ( data ) { - if( data == "pending" ) { - setTimeout( fetcher, 5000 ); - } else { - cache[resolution][position] = { state: "loaded", values: data }; - } - $(document).trigger( "redraw" ); - }); - } - return cache[resolution][position]; - } -});

var View = function( chrom, max_length ) { this.chrom = chrom; @@ -234,7 +205,7 @@ this.container_div.addClass( "line-track" ); this.content_div.css( "height", this.height_px + "px" ); this.dataset_id = dataset_id; - this.cache = new DataCache( "", this ); + this.cache = new Cache(50); }; $.extend( LineTrack.prototype, TiledTrack.prototype, { init: function() { @@ -254,6 +225,21 @@ } }); }, + get_data: function( resolution, position ) { + var key = resolution + '-' + position, + cache = this.cache; + + if ( !cache[key] ) { + var low = position * DENSITY * resolution, + high = ( position + 1 ) * DENSITY * resolution; + + $.getJSON( data_url, { track_type: this.track_type, chrom: this.view.chrom, low: low, high: high, dataset_id: this.dataset_id }, function ( data ) { + cache[key] = data; + $(document).trigger( "redraw" ); + }); + } + return cache[key]; + }, draw_tile: function( resolution, tile_index, parent_element, w_scale, h_scale ) { if (!this.vertical_range) // We don't have the necessary information yet return; @@ -261,13 +247,13 @@ var tile_low = tile_index * DENSITY * resolution, tile_high = ( tile_index + 1 ) * DENSITY * resolution, tile_length = DENSITY * resolution; - var chunk = this.cache.get( resolution, tile_index ); - var element; - if ( chunk.state == "loading" ) { - element = $("<div class='loading tile'></div>"); - } else { - element = $("<canvas class='tile'></canvas>"); + var data = this.get_data( resolution, tile_index ); + if ( !data ) { + in_path = false; + return null; } + var element = $("<canvas class='tile'></canvas>"); + element.css( { position: "absolute", top: 0, @@ -275,18 +261,13 @@ }); parent_element.append( element ); // Chunk is still loading, do nothing - if ( chunk.state == "loading" ) { - in_path = false; - return null; - } + var canvas = element; canvas.get(0).width = Math.ceil( tile_length * w_scale ); canvas.get(0).height = this.height_px; var ctx = canvas.get(0).getContext("2d"); var in_path = false; ctx.beginPath(); - var data = chunk.values; - if (!data) return; for ( var i = 0; i < data.length - 1; i++ ) { var x = data[i][0] - tile_low; var y = data[i][1]; diff -r b25297e88f96 -r cb842f737d46 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Tue Oct 06 21:25:01 2009 -0400 +++ b/templates/tracks/browser.mako Tue Oct 06 23:47:08 2009 -0400 @@ -7,7 +7,7 @@

<%def name="javascripts()"> ${parent.javascripts()} -${h.js( "jquery", "jquery.event.drag", "jquery.mousewheel", "trackster" )} +${h.js( "jquery", "jquery.event.drag", "jquery.mousewheel", "lrucache", "trackster" )}

<script type="text/javascript">

diff -r b25297e88f96 -r cb842f737d46 templates/tracks/new_browser.mako --- a/templates/tracks/new_browser.mako Tue Oct 06 21:25:01 2009 -0400 +++ b/templates/tracks/new_browser.mako Tue Oct 06 23:47:08 2009 -0400 @@ -11,39 +11,48 @@ </script> </%def>

-<div class="form"> - <div class="form-title">Select datasets to include in browser</div> - <div id="dbkey" class="form-body"> - <form id="form" method="POST"> - <div class="form-row"> - <label for="dbkey">Reference genome build (dbkey): </label> - <div class="form-row-input"> - <select name="dbkey" id="dbkey" refresh_on_change="true"> - %for tmp_dbkey in dbkey_set: - <option value="${tmp_dbkey}" - %if tmp_dbkey == dbkey: - selected="selected" - %endif - >${tmp_dbkey}</option> - %endfor - </select> +% if not converters: + <div class="errormessagelarge"> + There are no available converters needed for visualization. Please verify that your tool_conf.xml file contains + converters for datatypes (see tool_conf.xml.sample) for examples. + </div> + +% else: + <div class="form"> + <div class="form-title">Select datasets to include in browser</div> + + <div id="dbkey" class="form-body"> + <form id="form" method="POST"> + <div class="form-row"> + <label for="dbkey">Reference genome build (dbkey): </label> + <div class="form-row-input"> + <select name="dbkey" id="dbkey" refresh_on_change="true"> + %for tmp_dbkey in dbkey_set: + <option value="${tmp_dbkey}" + %if tmp_dbkey == dbkey: + selected="selected" + %endif + >${tmp_dbkey}</option> + %endfor + </select> + </div> + <div style="clear: both;"></div> </div> - <div style="clear: both;"></div> + <div class="form-row"> + <label for="dataset_ids">Datasets to include: </label> + %for dataset_id, (dataset_ext, dataset_name) in datasets.iteritems(): + <div> + <input type="checkbox" id="${dataset_id}" name="dataset_ids" value="${dataset_id}" /> + <label style="display:inline; font-weight: normal" for="${dataset_id}">[${dataset_ext}] ${dataset_name}</label> + </div> + %endfor + + <div style="clear: both;"></div> + </div> </div> <div class="form-row"> - <label for="dataset_ids">Datasets to include: </label> - %for dataset_id, (dataset_ext, dataset_name) in datasets.iteritems(): - <div> - <input type="checkbox" id="${dataset_id}" name="dataset_ids" value="${dataset_id}" /> - <label style="display:inline; font-weight: normal" for="${dataset_id}">[${dataset_ext}] ${dataset_name}</label> - </div> - %endfor - - <div style="clear: both;"></div> + <input type="submit" name="browse" value="Browse"/> </div> - </div> - <div class="form-row"> - <input type="submit" name="browse" value="Browse"/> - </div> - </form> -</div> + </form> + </div> +% endif