def download(_, outputs, sample):
"""inputs (_) is None"""
msg_id = str(sample)
# e.g. sra
# test_data_downloaded_for_genesis/rsem_output/human/GSE24455/GSM602557/SRX029242/SRR070177/SRR070177.sra
sra, flag_file = outputs # the others are sra files
sra_outdir = os.path.dirname(sra)
if not os.path.exists(sra_outdir):
os.makedirs(sra_outdir)
# e.g. url_path:
# /sra/sra-instant/reads/ByExp/sra/SRX/SRX029/SRX029242
url_path = urlparse.urlparse(sample.url).path
sra_url_path = os.path.join(url_path, *sra.split('/')[-2:])
cmd = config['CMD_ASCP'].format(log_dir=sra_outdir,
url_path=sra_url_path,
output_dir=sra_outdir)
returncode = misc.execute(cmd, msg_id, flag_file, options.debug)
if returncode != 0 or returncode is None:
# try wget
# cmd template looks like this:
# wget ftp://ftp-trace.ncbi.nlm.nih.gov{url_path} -P {output_dir} -N
cmd = config['CMD_WGET'].format(url_path=sra_url_path,
output_dir=sra_outdir)
misc.execute(cmd, msg_id, flag_file, options.debug)
def test_execute_started_and_finished_successfully(self, mock_subprocess, mock_touch, L):
mock_subprocess.call.return_value = 0
self.assertEqual(misc.execute('some cmd', 'msg_id', 'some_flag.txt'), 0)
L.check(('rsempipeline.utils.misc', 'INFO', 'executing CMD: some cmd'),
('rsempipeline.utils.misc', 'INFO',
'msg_id: execution succeeded with a returncode of 0. CMD: "some cmd"'))
mock_touch.assert_called_with('some_flag.txt')
def test_execute_started_but_fail_to_finish(self, mock_subprocess, mock_touch, L):
mock_subprocess.call.return_value = 1
self.assertEqual(misc.execute('some cmd', 'msg_id'), 1)
L.check(('rsempipeline.utils.misc', 'INFO', 'executing CMD: some cmd'),
('rsempipeline.utils.misc', 'ERROR',
'msg_id: started, but failed to finish with a returncode of 1. CMD: "some cmd"'))
self.assertFalse(mock_touch.called)
def test_execute_fail_to_start(self, mock_subprocess, L):
mock_subprocess.call.side_effect = OSError('some err msg')
self.assertIsNone(misc.execute('some cmd', 'msg_id'))
L.check((
'rsempipeline.utils.misc', 'INFO', 'executing CMD: some cmd'
), ('rsempipeline.utils.misc', 'ERROR',
'msg_id: failed to start, raising OSError some err msg. CMD: "some cmd"'
))
def test_execute_started_but_fail_to_finish(self, mock_subprocess,
mock_touch, L):
mock_subprocess.call.return_value = 1
self.assertEqual(misc.execute('some cmd', 'msg_id'), 1)
L.check((
'rsempipeline.utils.misc', 'INFO', 'executing CMD: some cmd'
), ('rsempipeline.utils.misc', 'ERROR',
'msg_id: started, but failed to finish with a returncode of 1. CMD: "some cmd"'
))
self.assertFalse(mock_touch.called)
def test_execute_started_and_finished_successfully(self, mock_subprocess,
mock_touch, L):
mock_subprocess.call.return_value = 0
self.assertEqual(misc.execute('some cmd', 'msg_id', 'some_flag.txt'),
0)
L.check((
'rsempipeline.utils.misc', 'INFO', 'executing CMD: some cmd'
), ('rsempipeline.utils.misc', 'INFO',
'msg_id: execution succeeded with a returncode of 0. CMD: "some cmd"'
))
mock_touch.assert_called_with('some_flag.txt')
def download(_, outputs, sample):
"""inputs (_) is None"""
msg_id = str(sample)
# e.g. sra
# test_data_downloaded_for_genesis/rsem_output/human/GSE24455/GSM602557/SRX029242/SRR070177/SRR070177.sra
sra, flag_file = outputs # the others are sra files
sra_outdir = os.path.dirname(sra)
if not os.path.exists(sra_outdir):
os.makedirs(sra_outdir)
# e.g. url_path:
# /sra/sra-instant/reads/ByExp/sra/SRX/SRX029/SRX029242
url_path = urlparse.urlparse(sample.url).path
sra_url_path = os.path.join(url_path, *sra.split('/')[-2:])
cmd = config['CMD_ASCP'].format(
log_dir=sra_outdir, url_path=sra_url_path, output_dir=sra_outdir)
returncode = misc.execute(cmd, msg_id, flag_file, options.debug)
if returncode != 0 or returncode is None:
# try wget
# cmd template looks like this:
# wget ftp://ftp-trace.ncbi.nlm.nih.gov{url_path} -P {output_dir} -N
cmd = config['CMD_WGET'].format(
url_path=sra_url_path, output_dir=sra_outdir)
misc.execute(cmd, msg_id, flag_file, options.debug)
def test_execute_fail_to_start(self, mock_subprocess, L):
mock_subprocess.call.side_effect = OSError('some err msg')
self.assertIsNone(misc.execute('some cmd', 'msg_id'))
L.check(('rsempipeline.utils.misc', 'INFO', 'executing CMD: some cmd'),
('rsempipeline.utils.misc', 'ERROR',
'msg_id: failed to start, raising OSError some err msg. CMD: "some cmd"'))