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Make the PubChem compound annotation test robust to outages #1111

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Merged
Zethson merged 1 commit into from
Sep 23, 2026
+10 −11
Merged

Make the PubChem compound annotation test robust to outages #1111

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21 changes: 10 additions & 11 deletions tests/metadata/test_compound.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,17 +42,16 @@ def adata() -> AnnData:

def test_compound_annotation(adata):
retries = 3
attempt = 0
while attempt < retries:
for attempt in range(retries):
try:
pt_compound.annotate_compounds(adata=adata, query_id="perturbation")
assert len(adata.obs.columns) == 5
pubchemid = [5328779, 9796068, 16124208, 5280343] * NUM_CELLS_PER_ID
assert pubchemid == list(adata.obs["pubchem_ID"])
return
except PubChemHTTPError:
annotated = pt_compound.annotate_compounds(adata=adata, query_id="perturbation", copy=True)
break
# pubchempy turns PubChem 404s into empty results, which surface as a ValueError for no matches
except (PubChemHTTPError, ValueError) as e:
if attempt == retries - 1:
# Should fail but it fails too often so we just let it pass
return
pytest.skip(f"PubChem unavailable: {e}")
time.sleep(10)
attempt += 1

assert len(annotated.obs.columns) == 5
pubchemid = [5328779, 9796068, 16124208, 5280343] * NUM_CELLS_PER_ID
assert pubchemid == list(annotated.obs["pubchem_ID"])
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