details: http://www.bx.psu.edu/hg/galaxy/rev/7de8cf4f1581 changeset: 3379:7de8cf4f1581 user: Dan Blankenberg dan@bx.psu.edu date: Fri Feb 12 13:10:52 2010 -0500 description: Fix BAM groom_dataset_content and set_meta methods to respect exit codes.
diffstat:
lib/galaxy/datatypes/binary.py | 16 ++++++++++++---- 1 files changed, 12 insertions(+), 4 deletions(-)
diffs (40 lines):
diff -r 6d217bad7496 -r 7de8cf4f1581 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py Fri Feb 12 12:41:21 2010 -0500 +++ b/lib/galaxy/datatypes/binary.py Fri Feb 12 13:10:52 2010 -0500 @@ -70,12 +70,16 @@ samtools_created_sorted_file_name = "%s.bam" % tmp_sorted_dataset_file_name_prefix #samtools accepts a prefix, not a filename, it always adds .bam to the prefix command = "samtools sort %s %s" % ( file_name, tmp_sorted_dataset_file_name_prefix ) proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=open( stderr_name, 'wb' ) ) - proc.wait() + exit_code = proc.wait()
#Did sort succeed? stderr = open( stderr_name ).read().strip() if stderr: - raise Exception, "Error Grooming BAM file contents: %s" % stderr + if exit_code != 0: + shutil.rmtree( tmp_dir) #clean up + raise Exception, "Error Grooming BAM file contents: %s" % stderr + else: + print stderr
# Move samtools_created_sorted_file_name to our output dataset location shutil.move( samtools_created_sorted_file_name, file_name ) @@ -98,11 +102,15 @@ stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name command = 'samtools index %s %s' % ( dataset.file_name, index_file.file_name ) proc = subprocess.Popen( args=command, shell=True, stderr=open( stderr_name, 'wb' ) ) - proc.wait() + exit_code = proc.wait() #Did index succeed? stderr = open( stderr_name ).read().strip() if stderr: - raise Exception, "Error Setting BAM Metadata: %s" % stderr + if exit_code != 0: + os.unlink( stderr_name ) #clean up + raise Exception, "Error Grooming BAM file contents: %s" % stderr + else: + print stderr
dataset.metadata.bam_index = index_file