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Misc workflow linting improvements #1437

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merged 2 commits into from
Mar 21, 2024
Merged

Misc workflow linting improvements #1437

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f244c1f
workflow lint: allow for nested assertions
bernt-matthias Mar 10, 2024
452f530
do not warn for missing input connections for inputs
bernt-matthias Mar 10, 2024
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18 changes: 12 additions & 6 deletions planemo/workflow_lint.py
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Original file line number Diff line number Diff line change
Expand Up @@ -220,13 +220,13 @@ def check_json_for_untyped_params(j):

# checks on individual steps
for step in steps.values():
print(step)
# disconnected inputs
for input in step.get("inputs", []):
if input.get("name") not in step.get("input_connections"): # TODO: check optional
lint_context.warn(
f"Input {input.get('name')} of workflow step {step.get('annotation') or step.get('id')} is disconnected."
)
if step.get("type") not in ["data_collection_input", "parameter_input"]:
for input in step.get("inputs", []):
if input.get("name") not in step.get("input_connections"): # TODO: check optional
lint_context.warn(
f"Input {input.get('name')} of workflow step {step.get('annotation') or step.get('id')} is disconnected."
)

# missing metadata
if not step.get("annotation"):
Expand Down Expand Up @@ -334,8 +334,14 @@ def _check_test_assertions(
assertions_valid = False
continue
signature = inspect.signature(function)
function_args = inspect.getfullargspec(function)
assertion_params = assertion_description["attributes"].copy()
if "verify_assertions_function" in function_args:
assertion_params["verify_assertions_function"] = asserts.verify_assertion(b"", [])
if "children" in function_args:
assertion_params["children"] = []
Comment on lines +339 to +342
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Any chance you could add a test for that ?

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Yes I should do this.

del assertion_params["that"]

try:
# try mapping the function with the attributes supplied and check for TypeError
signature.bind("", **assertion_params)
Expand Down