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Fix inconsistency with resolving pipeline interfaces depending on single vs a list of interfaces #486

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merged 2 commits into from
Mar 21, 2024
Merged

Fix inconsistency with resolving pipeline interfaces depending on single vs a list of interfaces #486

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fd588e7
Fix for #474
donaldcampbelljr Mar 21, 2024
32697a0
add test skipping for pephub test
donaldcampbelljr Mar 21, 2024
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3 changes: 3 additions & 0 deletions looper/utils.py
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Expand Up @@ -560,6 +560,9 @@ def read_looper_config_file(looper_config_path: str) -> dict:

# Expand paths in case ENV variables are used
for k, v in return_dict.items():
if k == SAMPLE_PL_ARG or k == PROJECT_PL_ARG:
# Pipeline interfaces are resolved at a later point. Do it there only to maintain consistency. #474
pass
if isinstance(v, str):
v = expandpath(v)
# TODO this is messy because is_pephub_registry needs to fail on anything NOT a pephub registry path
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1 change: 1 addition & 0 deletions tests/test_comprehensive.py
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Expand Up @@ -148,6 +148,7 @@ def test_comprehensive_looper_pipestat(prep_temp_pep_pipestat):
retrieved_result = psm.retrieve_one(record_identifier="frog_2")


@pytest.mark.skipif(not is_connected(), reason="This test needs internet access.")
def test_comprehensive_looper_pephub(prep_temp_pep_pephub):
"""Basic test to determine if Looper can run a PEP from PEPHub"""

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