nf-core / nf-core/tools

Linting a module with faulty ontology entry results in unspecific error message

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bug
Dominant language
Python
Stars
322
Forks
255
Avg merge
2d 3h
Merged PRs (30d)
5

Description

Description of the bug

Linting a module with the following 'fault' ontology string:

          ontologies:
            - http://edamontology.org/format_1975 # GFF3 format

(missing the edam: bit before the URL)

Gives an error of:

meta_yml_valid: The meta.yml of the module bakta/bakta is not valid: 'http://edamontology.org/format_1370' is not of type 'object'. Check the entry for hmms.

This error message is not useful in that it seems to have a generic error 'not of type 'object' , and the link to the meta_yml_valid check docs, the information there makes no reference to the specific 'rule' that has been invalidated.

At a minimum, this page should list all the specific checks this test is checking for, but also a specific error message when the ontology name prefix is missing would be helpful.

Command used and terminal output

System information

No response

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start at the meta_yml_valid check and reproduce the reported failure with an ontology URL missing its prefix. Trace how the validation error is converted into the current message; done means reporting the specific ontology-prefix problem and documenting the checks performed by meta_yml_valid.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
tooling
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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