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feat!: update to vrs 2.0-alpha #512

Merged
merged 17 commits into from
Sep 18, 2023
Merged

feat!: update to vrs 2.0-alpha #512

merged 17 commits into from
Sep 18, 2023

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korikuzma
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@korikuzma korikuzma commented Sep 12, 2023 •
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close #476

Notes:

  • Remove ga4gh.vrsatile.pydantic dependency. Now uses VRS 2.0-alpha models from ga4gh.vrs
    • Remove VRSATILE and Value Object Descriptors. VRS 2.0-alpha models now include a lot of the VOD fields.
    • Text Variation was removed in VRS 2.0-alpha
  • Updates gene-normalizer + cool-seq-tool + pydantic (v2) versions
  • HGVS Dup Del Mode
    • Removed rse_expr and lse_exprmodes and added allele mode
    • Updated default characteristics
  • Includes fixes for VRS IDs changing in get_priority_translation (original PRs: fix: _get_priority_translation_result using wrong variable #504, 507)
  • Adds F401 (unused-import) to fixable by ruff
  • Sets response_model_exclude_none=True in FastAPI response
  • QueryHandler no longer accepts cool-seq-tool input parameters. Can set via environment variables.
  • Removes molecule_context from Classifications

@korikuzma
Merge branch 'refactor' into staging
aa44f26
@korikuzma
refactor: rm unused + add missing tests to normalize
90c014e
@korikuzma
cicd: pin pipenv version where --skip-lock exists
58b9bc3
@korikuzma
wip: initial work for 2.0-alpha
e3aa870
@korikuzma
wip: store progress
6908114
@korikuzma
wip: fix calculating repeat_subunit_length
9b3e916
@korikuzma
wip: storing progress
9f5f797
@korikuzma
fix: _get_priority_translation_result using wrong variable (#504)
60f0b80 
- Was using `translations` when it should have been using
  `preferred_translations`
@korikuzma
update vrs ids
14093f5
@korikuzma
Merge branch 'staging' into issue-476
7785355
@korikuzma
fix: still return a result for protein/cdna with no mane data found
c0c46a8 
* Originally done in #507
* Creates an enum for vrs sequence location accession status
* Fix getting priority translation result in `_get_priority_translation_result` when there are multiple translation results for a given ac status
@korikuzma
wip: update deps
1abbfe1
@korikuzma
update with 00b2d7c4e2ea9 from vrs-python
06a1adf
@korikuzma
update ga4gh.vrs version
f46a234
@korikuzma
bump version
01144ae
@korikuzma korikuzma added enhancement New feature or request priority:high High priority labels Sep 12, 2023
@korikuzma korikuzma self-assigned this Sep 12, 2023
@korikuzma korikuzma marked this pull request as ready for review September 12, 2023 18:32
@korikuzma korikuzma linked an issue Sep 12, 2023 that may be closed by this pull request
Update metaschema to use VRS 2.0-alpha changes #476
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jsstevenson
jsstevenson approved these changes Sep 12, 2023
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godspeed

@korikuzma korikuzma merged commit 97459df into staging Sep 18, 2023
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@korikuzma korikuzma deleted the issue-476 branch September 18, 2023 18:31
@github-actions github-actions bot mentioned this pull request Sep 18, 2023
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@korikuzma korikuzma mentioned this pull request Apr 4, 2024
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Update metaschema to use VRS 2.0-alpha changes
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