def test_all_separate_no_sdc(anatomical_pipeline, tmpdir):
all_separate_no_sdc_opts = get_default_cli_args()
all_separate_no_sdc_opts.work_dir = tmpdir
all_separate_no_sdc_opts.ignore = []
all_separate_no_sdc_opts.output_dir = op.join(tmpdir, "all_separate_no_sdc")
all_separate_no_sdc_opts.combine_all_dwis = False
all_separate_no_sdc_opts.anat_only = False
all_separate_no_sdc_opts.prefer_dedicated_fmaps = True
#assert link_anatomicals(tmpdir)
with mock.patch.object(
argparse.ArgumentParser, 'parse_args', return_value=all_separate_no_sdc_opts):
with pytest.raises(SystemExit):
cli_main()
def test_preproc_plus_controllability(bids_singlescan_data, tmpdir):
preproc_plus_controllability = get_default_cli_args()
preproc_plus_controllability.bids_dir = WORKING_SINGLE_DIR + "/DSCSDSI"
preproc_plus_controllability.work_dir = tmpdir
preproc_plus_controllability.recon_only = False
preproc_plus_controllability.output_dir = op.join(tmpdir,
"preproc_control")
preproc_plus_controllability.recon_spec = pkgrf(
"qsiprep", "data/pipelines/controllability.json")
with mock.patch.object(argparse.ArgumentParser,
'parse_args',
return_value=preproc_plus_controllability):
with pytest.raises(SystemExit):
cli_main()
def anatomical_pipeline(bids_data):
"""Download data and run the anatomical preprocessing."""
anat_only_opts = get_default_cli_args()
anat_only_opts.anat_only = True
anat_only_opts.output_dir = op.join(WORKING_DIR, "anat_only_output")
if RUN_ANAT:
with mock.patch.object(
argparse.ArgumentParser, 'parse_args', return_value=anat_only_opts):
with pytest.raises(SystemExit):
cli_main()
else:
status = os.system('curl -sSL {} | tar xvfJ - -C {}'.format(
URL_PREFIX + ANAT_URL, WORKING_DIR))
assert status == 0
wd_files = os.listdir(WORKING_DIR)
assert 'qsiprep_wf' in wd_files