Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

When using semsimiam implementation, opaque errors are omitted if no predicates are passed` #641

Open
cmungall opened this issue Aug 21, 2023 · 0 comments

Comments

@cmungall
Copy link
Collaborator

runoak --stacktrace -i semsimian:sqlite:obo:phenio -v termset-similarity MP:0010771 MP:0002169 MP:0005391 MP:0005389 MP:0005367 @ HP:0004325 HP:0000093 MP:0006144 HP:0001254 HP:0001217 HP:0001222 HP:0001248 HP:0001263 HP:0001279

gives

  File "/Users/cjm/repos/ontology-access-kit/src/oaklib/implementations/semsimian/semsimian_implementation.py", line 237, in termset_pairwise_similarity
    semsimian = self._get_semsimian_object(
  File "/Users/cjm/repos/ontology-access-kit/src/oaklib/implementations/semsimian/semsimian_implementation.py", line 88, in _get_semsimian_object
    predicates = tuple(sorted(predicates))
TypeError: 'NoneType' object is not iterable

Minimally it should check for this condition and throw a NotImplemented error with a message explaining that predicates must be selected

or better: semsimian should simply accept empty predicates, meaning use all predicates

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant