isatab.validate does not return a failure of rule 1003 during validation
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 48
- Forks
- 42
- PR merge metrics
- No merged PRs in 30d
Description
In isatools 12.2, isatab.validate doesn't return a failure of rule 1003 in the validator_errors object.
Notably, isatab.py check_samples_not_declared_in_study_used_in_assay only writes an error to the logger and does not add the failure of this rule to validator_errors object.
A member of our team mentioned that this rule previously prevented isa-tools from processing the metadata, but its seems to have been changed and now will let isa-tools process the metadata while being in violation of this rule.
Is this the expected that moving forward that we should process the metadata while having a sample in the assay file that is not in the sample file, or should this condition cause the processor to fail?
Contributor guide
No contributing guide indexed for this repository
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 in isatab.py, reading isatab.validate and check_samples_not_declared_in_study_used_in_assay; trace how rule 1003 failures are represented in validator_errors versus the logger. Confirm the intended behavior for an undeclared assay sample and verify that the chosen behavior is consistently reflected in the validation result.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- testing-qa
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100