2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/853b1da64f4d/ changeset: 853b1da64f4d user: jgoecks date: 2013-01-27 21:19:27 summary: Cleanup and documentation for method that gets genome's chromosome information. affected #: 1 file diff -r f36d5d615dd4775d71ee778f500bd0c1d3fdf68e -r 853b1da64f4db37e93d1cbf43b6d0b5f45e63d38 lib/galaxy/visualization/genomes.py --- a/lib/galaxy/visualization/genomes.py +++ b/lib/galaxy/visualization/genomes.py @@ -215,8 +215,7 @@ dbkeys.extend( [ ( genome.description, genome.key ) for key, genome in self.genomes.items() if filter_fn( genome ) ] ) return dbkeys - #return [ (v, k) for k, v in trans.db_builds if ( ( k in self.genomes and self.genomes[ k ].len_file ) or k in user_keys ) ] - + def chroms( self, trans, dbkey=None, num=None, chrom=None, low=None ): """ @@ -256,15 +255,25 @@ genome = Genome( dbkey, dbkey_name, len_file=len_file, twobit_file=twobit_file ) - # Look in system builds. + # Look in history and system builds. if not genome: + # Look in history for chromosome len file. len_ds = trans.db_dataset_for( dbkey ) - if not len_ds: + if len_ds: + genome = Genome( dbkey, dbkey_name, len_file=len_ds.file_name ) + # Look in system builds. + elif dbkey in self.genomes: genome = self.genomes[ dbkey ] - else: - genome = Genome( dbkey, dbkey_name, len_file=len_ds.file_name ) + + # Set up return value or log exception if genome not found for key. + rval = None + if genome: + rval = genome.to_dict( num=num, chrom=chrom, low=low ) + else: + log.exception( 'genome not found for key %s' % dbkey ) - return genome.to_dict( num=num, chrom=chrom, low=low ) + return rval + def has_reference_data( self, trans, dbkey, dbkey_owner=None ): """ https://bitbucket.org/galaxy/galaxy-central/commits/18d528947af2/ changeset: 18d528947af2 user: jgoecks date: 2013-01-28 00:13:13 summary: Reinstate grid footer updates because they now work again with embedded grids. This also prevents spurious grid posts. affected #: 1 file diff -r 853b1da64f4db37e93d1cbf43b6d0b5f45e63d38 -r 18d528947af20aca02f105722a844d32f90fa0ec templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -569,7 +569,7 @@ $('#grid-table-body').html(parsed_response_text[0]); // FIXME: this does not work at all; what's needed is a function // that updates page links when number of pages changes. - //$('#grid-table-footer').html(parsed_response_text[1]); + $('#grid-table-footer').html(parsed_response_text[1]); // Trigger custom event to indicate grid body has changed. $('#grid-table-body').trigger('update'); 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.