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Catch no subject error early #463

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merged 3 commits into from
Sep 22, 2020
Merged

Catch no subject error early #463

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389d6e4
catch no subject error early
36000 Sep 22, 2020
56b6528
add better message; add test
36000 Sep 22, 2020
40964b9
pep8
36000 Sep 22, 2020
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6 changes: 6 additions & 0 deletions AFQ/api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -388,6 +388,12 @@ def __init__(self,
json.dump(pipeline_description, outfile)

self.subjects = bids_layout.get(return_type='id', target='subject')
if not len(self.subjects):
raise ValueError(
"`bids_path` contains no subjects in derivatives folders."
+ " This could be caused by derivatives folders not following"
+ " the BIDS format.")

sessions = bids_layout.get(return_type='id', target='session')
if len(sessions):
self.sessions = sessions
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17 changes: 17 additions & 0 deletions AFQ/tests/test_api.py
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Expand Up @@ -180,6 +180,23 @@ def test_AFQ_custom_tract():


@pytest.mark.nightly2
def test_AFQ_no_derivs():
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Should this test really be marked as nightly? It probably runs pretty quickly (?)

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test_AFQ_init is also marked nightly. Initializing an afq object takes about a minute I think, and if we have a lot of these tests, they can add up. To reduce time to make afq object, see: #448

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OK - that makes sense. Merging!

"""
Test the initialization of the AFQ object
"""
bids_path = create_dummy_bids_path(1, 1)
os.remove(op.join(
bids_path, "derivatives", "dmriprep", "dataset_description.json"))
with pytest.raises(
ValueError,
match="`bids_path` contains no subjects in derivatives folders."
+ " This could be caused by derivatives folders not"
+ " following the BIDS format."):
my_afq = api.AFQ(bids_path,
dmriprep="synthetic")


@pytest.mark.nightly3
def test_AFQ_init():
"""
Test the initialization of the AFQ object
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