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

[Galaxy] Exception if output is not annotated #194

Open
dsavchenko opened this issue Aug 16, 2024 · 1 comment
Open

[Galaxy] Exception if output is not annotated #194

dsavchenko opened this issue Aug 16, 2024 · 1 comment
Assignees
Labels

Comments

@dsavchenko
Copy link
Member

2024-08-16 14:35:54,553 ERROR cli  unexpected exception: Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/odabot/cli.py", line 868, in make_galaxy_tools
    to_galaxy(input_path=wf_repo_dir,
  File "/usr/local/lib/python3.9/site-packages/nb2workflow/galaxy.py", line 600, in to_galaxy
    script_str = _nb2script(nba, ontology_path)
  File "/usr/local/lib/python3.9/site-packages/nb2workflow/galaxy.py", line 203, in _nb2script
    outp = GalaxyOutput.from_inspect(vv, ontology_path=ontology_path, dprod=nba.name)
  File "/usr/local/lib/python3.9/site-packages/nb2workflow/galaxy.py", line 170, in from_inspect
    if onto.is_data_product(owl_uri, include_parameter_products=False):
  File "/usr/local/lib/python3.9/site-packages/oda_api/ontology_helper.py", line 404, in is_data_product
    if owl_uri.startswith("http"): owl_uri = f"<{owl_uri}>"
AttributeError: 'NoneType' object has no attribute 'startswith'
@dsavchenko dsavchenko self-assigned this Aug 16, 2024
@dsavchenko
Copy link
Member Author

Also, if something is annotated as data-product, but there is no oda-api - it will fail because there is no CustomJSONEncoder

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

No branches or pull requests

1 participant