Migrate sssom validation to new LinkML validation framework #532
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matentzn
changed the title
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@pkalita-lbl Thanks a ton for your help, I made issues for everything and will resume work here once they are resolved. Thank you! |
Using the latest version of LinkML to get latest validator features.
In this commit we 1. Add a new parameter, fail_on_error, to all validation methods (if true, throws and exception when errors are encountered) 2. We generate ValidationResult instances fall all custom checks (reusing the LinkML validation framework) 3. Add a few missing docstrings 4. Add a new validation check, check_strict_curie_format, which looks for curies with a | character in it
Previously I used dataclasses. asdict to turn a dataclass instance to a dictionary to pass to the validation framework. @pkalita-lbl explained to me why this was not a good idea (essentially, dataclass instances dont look like what the validation framework expects), and recommended the use of linkml_runtime.dumpers.json_dumper instead. Tests work fine!
.. to ensure that it recognises the argument fail_on_error.
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@hrshdhgd I assigned this to you for review. I think it is done, but I am a bit scared of how the changes will impact people relying on validation downstream, so I prefer to have your eyes on it. Thank you! Ideally this should be a careful review beyond "lgtm" as I feel I cant afford messing this up! |
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@hrshdhgd just to be sure I need a positive approval from you for this PR, and real certainty that all is understood and correct. Can you comment on the exact pieces of code you have questions about? |
That is exactly what I'm trying to do as per my previous comment. |
I hope this PR is only affecting the |
Blocked by:
Note to future self, only thing that stands in the way of this PR now is #2164, if that is dealt with
print_linkml_report(report, False)to print_linkml_report(report, fail_on_error)