From 50f1089c72ff46397e525d4aa99dc80569081509 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 9 Mar 2016 10:40:19 -0500 Subject: [PATCH 1/4] Slight tweaks to our tabix usage. This fixes trackster without more divergence in our version of pysam. --- lib/galaxy/visualization/data_providers/genome.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py index a4d0a9a0121..15325280e15 100644 --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -347,15 +347,15 @@ 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) if end >= (2 << 29): end = (2 << 29 - 1) # Tabix-enforced maximum - # Get iterator using either naming scheme. iterator = iter( [] ) + chrom = str(chrom) if chrom in data_file.contigs: iterator = data_file.fetch(reference=chrom, start=start, end=end) else: From c6f3e9b5b28268cba1ef8d7be5f1bed90b6ecc00 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 9 Mar 2016 10:52:31 -0500 Subject: [PATCH 2/4] Slight cleanup, remove outdated comment regarding tabixfile.close() --- lib/galaxy/visualization/data_providers/genome.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py index 15325280e15..2c2457915dd 100644 --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -196,7 +196,6 @@ 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 @@ -350,12 +349,14 @@ class TabixDataProvider( FilterableMixin, GenomeDataProvider ): 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 (not unicode), start/end integers. + 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( [] ) - chrom = str(chrom) if chrom in data_file.contigs: iterator = data_file.fetch(reference=chrom, start=start, end=end) else: From f0b7a34dd3ea5b3b10494c7e186fb10fda30441f Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 9 Mar 2016 11:07:12 -0500 Subject: [PATCH 3/4] Apply patch from Fabien Mareuil to resolve json serialization of Decimal error; for more see http://dev.list.galaxyproject.org/quota-api-error-td4669081.html --- lib/galaxy/webapps/galaxy/api/quotas.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From a351c75687921bb8d2487577c5c4c0a64bee5e5f Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Wed, 9 Mar 2016 11:31:18 -0500 Subject: [PATCH 4/4] Extra documentation for @mvdbeek --- lib/galaxy/visualization/data_providers/genome.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py index 2c2457915dd..c8763f099f2 100644 --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -349,7 +349,8 @@ class TabixDataProvider( FilterableMixin, GenomeDataProvider ): index=self.converted_dataset.file_name) def get_iterator( self, data_file, chrom, start, end, **kwargs ): - # chrom must be a string (not unicode), start/end integers. + # 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)