Linting a module with faulty ontology entry results in unspecific error message
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- Dominant language
- Python
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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
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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