8000 GKS support · Issue #154 · griffithlab/civicpy · GitHub
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ahwagner opened this issue Dec 13, 2024 · 5 comments · Fixed by #160
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GKS support #154

ahwagner opened this issue Dec 13, 2024 · 5 comments · Fixed by #160
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@korikuzma

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@ahwagner
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Prerequisites:

We will want to be able to emit GKS-compliant representations of CIViC data (VA-spec + Cat-VRS) directly from CIViCpy.
@korikuzma
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korikuzma commented Mar 14, 2025 •
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@ahwagner and I talked - we'd like to move the current CIViC Transformer in MetaKB, which takes CIViC data and transforms it to GKS representations, to civicpy.

This will create a dependency on our GKS Python reference implementations (VRS/Cat-VRS/VA-Spec Python), which we may want to separate as optional dependencies.

@korikuzma korikuzma self-assigned this Mar 14, 2025
@ahwagner
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ahwagner commented Apr 9, 2025

Hey @susannasiebert, do you think it makes the most sense to implement the GKS transformers in the export module, or would you recommend we place this somewhere else? Also, we are thinking about converting the module to a package, with separated modules for VCF and for GKS. Would like to get your thoughts on this as well.

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Clarifying question:

converting the module to a package, with separated modules for VCF and for GKS

Are you saying to make a separate python package that deals with exporting CIViC data in several formats? That seems a bit overkill to me.

A few thoughts:

  • The VcfWriter class basically is our implementation of a VCF parser/writer. Converting a Variant to VCF format is partially done in here and partially done by methods in the Variant class.
    • We should consider refactoring this class to use existing VCF parsers (I personally like VCFpy) instead of reinventing the wheel
    • If we want to start having "transformers" then I think the logic for transforming a CIViC variant to a VCF record (e.g., a vcfpy.Record object if we use existing parsers) should be moved outside of the Variant class as well, in some sort of VCF transformer module.
  • I think reorganizing/renaming the existing exports module makes sense. Maybe renaming exports to vcf_writer would clarify things and then have a new module for the GKS transformer and the VCF transformer. These could possible be reorganized under a exports/exporters/transformers subfolder. I'm not really clear on what the output type of the GKS transformer is, though.

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Latest work for clinvar-this is on issue-4: https://github.com/clingen-data-model/clinvar-this/tree/issue-4

@susannasiebert susannasiebert mentioned this issue Apr 14, 2025
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feat: add exporter for CIViC Assertions to GKS JSON griffithlab/civicpy
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