From 6635e2abdab677c6ea4f61a085ad7e8c1530a5b1 Mon Sep 17 00:00:00 2001 From: Joshua Teves Date: Fri, 8 Nov 2019 12:41:56 -0500 Subject: [PATCH] Prevents shell expansion in API (#431) --- tedana/tests/test_integration.py | 5 ++++- tedana/workflows/tedana.py | 2 ++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/tedana/tests/test_integration.py b/tedana/tests/test_integration.py index 80ce4e2c6..c5b46603c 100644 --- a/tedana/tests/test_integration.py +++ b/tedana/tests/test_integration.py @@ -81,8 +81,11 @@ def test_integration_five_echo(skip_integration): # download data and run the test download_test_data('https://osf.io/9c42e/download', os.path.dirname(out_dir)) + prepend = '/tmp/data/five-echo/p06.SBJ01_S09_Task11_e' + suffix = '.sm.nii.gz' + datalist = [prepend + str(i+1) + suffix for i in range(5)] tedana_workflow( - data='/tmp/data/five-echo/p06.SBJ01_S09_Task11_e[1,2,3,4,5].sm.nii.gz', + data=datalist, tes=[15.4, 29.7, 44.0, 58.3, 72.6], out_dir=out_dir, debug=True, verbose=True) diff --git a/tedana/workflows/tedana.py b/tedana/workflows/tedana.py index c93dd7f55..1c4d849b3 100644 --- a/tedana/workflows/tedana.py +++ b/tedana/workflows/tedana.py @@ -366,6 +366,8 @@ def tedana_workflow(data, tes, mask=None, mixm=None, ctab=None, manacc=None, # coerce data to samples x echos x time array if isinstance(data, str): + if not op.exists(data): + raise ValueError('Zcat file {} does not exist'.format(data)) data = [data] LGR.info('Loading input data: {}'.format([f for f in data]))