1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/85d76cb4761f/
changeset: r5436:85d76cb4761f
user: kanwei
date: 2011-04-19 20:45:55
summary: trackster: use simple hash to calculate unique ID for tabix
affected #: 1 file (25 bytes)
--- a/lib/galaxy/visualization/tracks/data_providers.py Tue Apr 19 14:20:11 2011 -0400
+++ b/lib/galaxy/visualization/tracks/data_providers.py Tue Apr 19 14:45:55 2011 -0400
@@ -620,7 +620,8 @@
# BED dataset.
feature = line.split()
length = len(feature)
- payload = [ feature[1]+"-"+feature[2]+":"+str(count), int(feature[1]), int(feature[2]) ]
+ # Unique id is just a hash of the line
+ payload = [ hash(line), int(feature[1]), int(feature[2]) ]
if no_detail:
results.append( payload )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/a8f476227efe/
changeset: r5435:a8f476227efe
user: kanwei
date: 2011-04-19 20:20:11
summary: trackster: don't show tile if no tile (fixes ReferenceTrack)
affected #: 1 file (113 bytes)
--- a/static/scripts/trackster.js Tue Apr 19 11:49:18 2011 -0400
+++ b/static/scripts/trackster.js Tue Apr 19 14:20:11 2011 -0400
@@ -1856,6 +1856,10 @@
// console.log( "draw_and_show_tile", resolution, tile_index, w_scale );
var tile = track.draw_tile(result, resolution, tile_index, w_scale, seq_data);
track.tile_cache.set(key, tile);
+ // Don't show if no tile
+ if (tile === undefined) {
+ return;
+ }
track.show_tile(tile, parent_element, tile_low, w_scale);
drawn_tiles[drawn_tiles.length] = tile;
};
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/c1aeb2f33b4a/
changeset: r5433:c1aeb2f33b4a
user: greg
date: 2011-04-19 16:20:01
summary: Improved exception handling in the tool shed.
affected #: 2 files (89 bytes)
--- a/lib/galaxy/webapps/community/controllers/upload.py Tue Apr 19 09:44:28 2011 -0400
+++ b/lib/galaxy/webapps/community/controllers/upload.py Tue Apr 19 10:20:01 2011 -0400
@@ -51,7 +51,7 @@
try:
uploaded_file = urllib2.urlopen( url_paste )
except ( ValueError, urllib2.HTTPError ), e:
- message = 'An error occurred trying to retrieve the URL entered on the upload form: %s' % e
+ message = 'An error occurred trying to retrieve the URL entered on the upload form: %s' % str( e )
status = 'error'
except urllib2.URLError, e:
message = 'An error occurred trying to retrieve the URL entered on the upload form: %s' % e.reason
--- a/lib/galaxy/webapps/community/datatypes/__init__.py Tue Apr 19 09:44:28 2011 -0400
+++ b/lib/galaxy/webapps/community/datatypes/__init__.py Tue Apr 19 10:20:01 2011 -0400
@@ -65,8 +65,8 @@
# xml_files and tool_tags will only be received if we're called from the ToolSuite.verify() method.
try:
tar = tarfile.open( f.name )
- except tarfile.ReadError:
- raise DatatypeVerificationError( 'The archive is not a readable tar file.' )
+ except tarfile.ReadError, e:
+ raise DatatypeVerificationError( 'Error reading the archive, problem: %s' % str( e ) )
if not xml_files:
# Make sure we're not uploading a tool suite
if filter( lambda x: x.lower().find( 'suite_config.xml' ) >= 0, tar.getnames() ):
@@ -78,9 +78,8 @@
try:
tree = ElementTree.parse( tar.extractfile( xml_file ) )
root = tree.getroot()
- except:
- log.exception( 'fail:' )
- continue
+ except Exception, e:
+ raise DatatypeVerificationError( 'Error parsing file "%s", problem: %s' % ( str( xml_file ), str( e ) ) )
if root.tag == 'tool':
if 'id' not in root.keys():
raise DatatypeVerificationError( "Tool xml file (%s) does not include the required 'id' attribute in the <tool> tag" % str( xml_file ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/91d49371fd1e/
changeset: r5432:91d49371fd1e
user: james_taylor
date: 2011-04-19 15:44:28
summary: trackster: for line painter, determine min and max from data if not provided (not actually used for trackster)
affected #: 1 file (537 bytes)
--- a/static/scripts/trackster.js Tue Apr 19 08:24:57 2011 -0400
+++ b/static/scripts/trackster.js Tue Apr 19 09:44:28 2011 -0400
@@ -2864,6 +2864,20 @@
var LinePainter = function( data, view_start, view_end, prefs, mode ) {
Painter.call( this, data, view_start, view_end, prefs, mode );
+ if ( this.prefs.min_value === undefined ) {
+ var min_value = Infinity;
+ for (var i = 0, len = this.data.length; i < len; i++) {
+ min_value = Math.min( min_value, this.data[i][1] );
+ }
+ this.prefs.min_value = min_value;
+ }
+ if ( this.prefs.max_value === undefined ) {
+ var max_value = -Infinity;
+ for (var i = 0, len = this.data.length; i < len; i++) {
+ max_value = Math.max( max_value, this.data[i][1] );
+ }
+ this.prefs.max_value = max_value;
+ }
};
LinePainter.prototype.default_prefs = { min_value: undefined, max_value: undefined, mode: "Histogram", color: "#000", overflow_color: "#F66" };
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.