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feat!: add support for transforming concepts that fail to normalize #427

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@korikuzma korikuzma commented Jan 31, 2025

close #417

  • This adds support for transforming concepts (such as gene, variant, disease, and therapy) that fail to normalize.
    • Since this work is mainly needed for ClinVar Submission work, this is only focused on adding support in CDM files generated by the Transformers. The database will NOT load statements that fail to normalize concepts, and therefore the QueryHandler is unable to search on these non-normalizable concepts. This will require more thought on the search algorithm (exact match? Something else?)
    • Concepts that fail to normalize will have the following Extension: {"name": "vicc_normalizer_failure", "value": True}
      • Since MOA does not have record IDs for some objects, the IDs used in these cases will be f"moa.{therapy|disease|gene}:{name}", where name is the MOA label for the concept where whitespace characters are replaced with underscores.

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@korikuzma korikuzma added enhancement New feature or request priority:medium Medium priority labels Jan 31, 2025
@korikuzma korikuzma self-assigned this Jan 31, 2025
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Need to look this over before requesting review

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