def test_download_samples_second(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
mem = '100MB'
d.download_sample = MagicMock()
d.download_samples(samples, index=1)
d.download_sample.assert_called_once_with('ASDURF', 'SRX5322424', True,
None, mem)
def test_download_samples(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
mem = '100MB'
d.download_sample = MagicMock()
d.download_samples(samples)
d.download_sample.assert_any_call('POLR2A', 'SRR8518913', True, None, mem)
d.download_sample.assert_any_call('ASDURF', 'SRX5322424', True, None, mem)
d.download_sample.assert_any_call('POLR1C', 'SRR8518915', True, None, mem)
def test_download_sample_slow_singleend(testdir, mock_testclass):
srr = 'SRR8518913'
mem = '100MB'
threads = 1
subprocess.run = MagicMock(side_effect=create_file(srr + '_1.fastq'))
d.download_sample('POLR2A', srr, False, threads, mem)
subprocess.run.assert_called_with(['fastq-dump', '--split-files', srr],
check=True)
assert os.path.exists('POLR2A_1.fastq')
def test_download_samples_allslow(testdir, mock_testclass):
samples = Path(__file__).parent.joinpath('samples.txt')
mem = '200MB'
threads = 2
d.download_sample = MagicMock()
d.download_samples(samples, False, threads, mem)
d.download_sample.assert_any_call('POLR2A', 'SRR8518913', False, threads,
mem)
d.download_sample.assert_any_call('ASDURF', 'SRX5322424', False, threads,
mem)
d.download_sample.assert_any_call('POLR1C', 'SRR8518915', False, threads,
mem)
def test_download_sample_failed(testdir, mock_testclass):
srr = 'SRR8518913'
mem = '100MB'
threads = 1
subprocess.run = MagicMock(side_effect=subprocess.CalledProcessError(
'Could not download file', ['test']))
with pytest.raises(subprocess.CalledProcessError):
d.download_sample('POLR2A', srr, True, threads, mem)
subprocess.run.assert_called_with([
'fasterq-dump', '--split-files', '--threads',
str(threads), '--mem', mem, srr
],
check=True)
assert not os.path.exists('POLR2A_1.fastq')
assert not os.path.exists('POLR2A_2.fastq')