diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py index b1915691407..fc5da2774f2 100644 --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -195,7 +195,6 @@ class GenomeDataProvider( BaseDataProvider ): except AttributeError: # FIXME: some data providers do not have a close function implemented. # Providers without a close function include: - # pysam Tabixfile # bx IntervalIndex pass @@ -346,13 +345,16 @@ class TabixDataProvider( FilterableMixin, GenomeDataProvider ): def open_data_file( self ): return ctabix.Tabixfile(self.dependencies['bgzip'].file_name, - index_filename=self.converted_dataset.file_name) + index=self.converted_dataset.file_name) def get_iterator( self, data_file, chrom, start, end, **kwargs ): - start, end = int(start), int(end) + # chrom must be a string, start/end integers. + # in previous versions of pysam, unicode was accepted for chrom, but not in 8.4 + chrom = str(chrom) + start = int(start) + end = int(end) if end >= (2 << 29): end = (2 << 29 - 1) # Tabix-enforced maximum - # Get iterator using either naming scheme. iterator = iter( [] ) if chrom in data_file.contigs: diff --git a/lib/galaxy/webapps/galaxy/api/quotas.py b/lib/galaxy/webapps/galaxy/api/quotas.py index 4a5ed045b3e..1403f09ab47 100644 --- a/lib/galaxy/webapps/galaxy/api/quotas.py +++ b/lib/galaxy/webapps/galaxy/api/quotas.py @@ -50,7 +50,7 @@ class QuotaAPIController( BaseAPIController, Admin, AdminActions, UsesQuotaMixin Displays information about a quota. """ quota = self.get_quota( trans, id, deleted=util.string_as_bool( deleted ) ) - return quota.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } ) + return quota.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'total_disk_usage': float } ) @web.expose_api @web.require_admin