Merge pull request #486 from pepkit/dev_474

Dev 474
pepkit · Mar 21, 2024 · 8d57742 · 8d57742
2 parents db70fe7 + 32697a0
commit 8d57742
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diff --git a/looper/utils.py b/looper/utils.py
@@ -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

diff --git a/tests/test_comprehensive.py b/tests/test_comprehensive.py
@@ -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"""