Use LinkML to parse and validate NEAT YAML files

Knowledge-Graph-Hub / neat-ml

Network Embedding All the Things

BSD 3-Clause "New" or "Revised" License

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Use LinkML to parse and validate NEAT YAML files #52

Closed justaddcoffee closed 2 years ago

justaddcoffee commented 2 years ago

We should consider using LinkML to validate our NEAT YAML files. Right now we are using some simple procedural code within the YamlHelper class to do this, but LinkML would provide a more sophisticated and thorough check of the YAML.

On the other hand, this would take some time to implement, and might increase the complexity of debugging NEAT YAML validation.

Just making this ticket to discuss

caufieldjh commented 2 years ago

Now implemented in https://github.com/Knowledge-Graph-Hub/NEAT_schema - thanks @hrshdhgd !

Will just need a validation function for NEAT - can run during pre run checks.

justaddcoffee commented 2 years ago

Nice! Thanks @hrshdhgd

caufieldjh commented 2 years ago

Tasks:

[ ] Convert yaml helper to use new neat_schema
[ ] Implement LinkML-driven validation of input config files (primarily just using imported linkml and neat_schema, then use JsonSchemaValidator)
[ ] Translate test yamls to neat_schema
[ ] Add new test(s) for input validation
[ ] Update existing tests (some may be rendered obsolete by new validation)