Diverse Validation enhancements #31
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RichardBruskiewich
commented
Aug 11, 2022
RichardBruskiewich
commented
- Node categories screened for deprecation, mixin and abstract nature
- Edge attribute_type_id screened for status as a biolink:association_slot etc. (issue Add Biolink Model validation depth to Edge attribute (constraint) validation #19)
… change since validation method doesn't yet exist in BMT! Just saving the intent for now...)
… change since validation method doesn't yet exist in BMT! Just saving the intent for now...)
…on' into issue-19-edge-attribute-validation
…olink_version parameter to be more explicitly Optional[str]
…ink validation of test input edges to check for deprecated classes
…input edge validation and also, reuse common code in graph validations; unit test messages fixed
…refix (already testing if it is a proper association_slot)
RichardBruskiewich
requested review from
edeutsch,
kennethmorton and
sierra-moxon
| else: | ||
| # TODO: attempt some deeper attribute validation here | ||
| for attribute in attributes: | ||
| attribute_type_id: str = attribute['attribute_type_id'] |
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is attribute.get('attribute_type_id', None) necessary here or can we assume this key exists due to prior validation?
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yes, good idea. I should also check for a non-None 'value' field as well.
| # | ||
| if not self.is_curie(attribute_type_id): | ||
| self.report_error( | ||
| f"Edge '{edge_id}' attribute_type_id '{str(attribute_type_id)}' is not a CURIE?" |
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I would say warning is probably more beneficial as attributes_types are not always well standardized.
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At the moment, all discrepancies are reported as 'error' but Eric has made the same point, and also, some normalization of errors into an index set of error codes (with parameters) is on the near term horizon, maybe over the next few days. Afterwards, it may be useful to decide which items are absolute errors, and which could be warnings or even info items.
…omponents; check for missing TRAPI Attribute 'attribute_type_id' and 'value' fields.
