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Add support for MOA prognostic data #408

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korikuzma opened this issue Dec 10, 2024 · 1 comment
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Add support for MOA prognostic data #408

korikuzma opened this issue Dec 10, 2024 · 1 comment
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enhancement New feature or request priority:high High priority

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Currently only MOA therapeutic response assertion data is captured. Now that we have VA-Spec model for prognostic data, we should add the ability to 1) harvest prognostic data 2) transform harvested data to prognostic VA-Spec model 3) load transformed data into db

This is needed for VarCat + ClinVar Submission.
@korikuzma korikuzma added enhancement New feature or request priority:high High priority labels Dec 10, 2024
@korikuzma korikuzma self-assigned this Dec 10, 2024
This was referenced Dec 12, 2024
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korikuzma added a commit that referenced this issue Dec 18, 2024
@korikuzma
feat!: add support for moa prognostic assertions (#411)
7d72c99 
close #408 

Note: This work revealed a bug with uniqueness constraints (#409). This
will be addressed in a separate PR. This PR focuses on changes to the
harvester + transformer: `python3 -m pytest tests/unit/harvesters
tests/unit/transformers`

* Harvester output changed
  * Therapy fields are now nested inside `therapy` key
  * Remove `clinical_significance` and retain original values from MOA
  * `source_ids` -> `source_id` since we only store one ID
* `MoaTransformer` now supports MOA prognostic assertions
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Closed by #411.

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