lint vs. validate conflict: linter-recommended EDAM.TOPIC prefix fails validation but linter-disapproved EDAM_TOPIC works:

[cpauvert]

Describe the bug
Hello!
I have an issue with the prefix for the EDAM ontology when using meaning in an enum. I followed the the convention in biolink with EDAM_TOPIC but this raised issue with validation (details below)

TL;DR:

• with prefix EDAM_TOPIC: linkml-lint FAIL ; linkml-validate PASS
• with prefix EDAM.TOPIC: linkml-lint PASS ; linkml-validate FAIL

The linter has a default configuration with regards to prefixmaps.

Should I follow the convention in biolink with EDAM_TOPIC and ignore the lint?
because it seems that EDAM.TOPIC is converted to the python:

meaning=EDAM-TOPIC["3524"]

which causes a NameError: name 'EDAM' is not defined.

Best regards,

Details:

See more with prefix `EDAM_TOPIC`: linkml-lint FAIL ; linkml-validate PASS

https://github.com/FAIR-MI/miiid-schema/blob/410aeb29afd3e81961ecc45a534f59077b651222/src/miiid_schema/schema/miiid_schema.yaml#LL17

Linting

$ make lint
poetry run linkml-lint src/miiid_schema/schema/miiid_schema.yaml
/home/cpauvert/projects/linkml-projects/miiid-schema/src/miiid_schema/schema/miiid_schema.yaml
  warning  Schema maps prefix 'EDAM_TOPIC' to namespace 'http://edamontology.org/topic_' instead of using prefix 'EDAM.TOPIC'  (canonical_prefixes)

✖ Found 1 problem in 1 schema
make: *** [Makefile:119: lint] Error 1

Validation

linkml-validate -s src/miiid_schema/schema/miiid_schema.yaml -C IntermicrobialInteraction \
  src/data/examples/valid/IntermicrobialInteraction-pairwise.yaml 
# None

See more with prefix `EDAM.TOPIC`: linkml-lint PASS ; linkml-validate FAIL

https://github.com/FAIR-MI/miiid-schema/blob/26460cd64769ddb87ac4a2f471ef7bb2c0f07fdd/src/miiid_schema/schema/miiid_schema.yaml#L17

Linting

$ make lint
poetry run linkml-lint src/miiid_schema/schema/miiid_schema.yaml
✓ No problems found

Validation

linkml-validate -s src/miiid_schema/schema/miiid_schema.yaml -C IntermicrobialInteraction \
  src/data/examples/valid/IntermicrobialInteraction-pairwise.yaml 

ERROR:root:Error compiling generated python code: name 'EDAM' is not defined
Traceback (most recent call last):
  File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/bin/linkml-validate", line 8, in <module>
    sys.exit(cli())
  File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/lib/python3.9/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/lib/python3.9/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/lib/python3.9/site-packages/linkml/validators/jsonschemavalidator.py", line 135, in cli
    python_module = PythonGenerator(schema).compile_module()
  File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/lib/python3.9/site-packages/linkml/generators/pythongen.py", line 81, in compile_module
    raise e
  File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/lib/python3.9/site-packages/linkml/generators/pythongen.py", line 77, in compile_module
    return compile_python(pycode)
  File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/lib/python3.9/site-packages/linkml_runtime/utils/compile_python.py", line 47, in compile_python
    exec(spec, module.__dict__)
  File "test", line 169, in <module>
  File "test", line 176, in MethodType
NameError: name 'EDAM' is not defined

with one of the faulty line being probably:

simulation = PermissibleValue( text="simulation",                                                                                                                        
        description="Any type of biological computational model experiments", meaning=EDAM-TOPIC["3524"])     

[cpauvert]

This issues happened with linkml v1.5.5 and remains despite updating to 1.5.6.

[sierra-moxon]

Hi Charlie - thanks for the detailed issue; I’ll take a look.

[sierra-moxon]

@cpauvert - short answer, Biolink should be updated to use the edam.topic prefix following the conventions in bioregistry.io. but, this does mean linkml-validate will fail as you have demonstrated. I'm working on a couple of PRs to fix this behavior (see above).

[cpauvert]

Thanks @sierra-moxon for the heads-up, let me know how and when I should try out your edits!