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feat!: change civic classification.primaryCode to use clinvar enum #455

Merged
merged 101 commits into from
Mar 7, 2025
Merged

feat!: change civic classification.primaryCode to use clinvar enum #455

merged 101 commits into from
Mar 7, 2025

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korikuzma
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close #452

  • Use ClinVar Submission clinicalImpactClassificationDescription enum

@korikuzma
wip: initial messy work
cc19f94
@korikuzma
wip: update normalizers
d0a26d6
@korikuzma
build: bump variation normalizer
2262bc5
@korikuzma
wip: add subptype to civic method
9ec5165
@korikuzma
wip: evidence level to vicc concept should include mappings
0ebb8a6
@korikuzma
wip: messy initial work for supporting civic assertions
42b4e6c
@korikuzma
wip
e1948ed
@korikuzma
wip
b477340
@korikuzma
revert strength (save for #419)
14a8cf5
@korikuzma
revert mane_genes (not needed anymore for varcat)
9390433
@korikuzma
fix tests
441283a
@korikuzma
bump cat_vrs
2d88fb6
@korikuzma
missed renames
d7420ae
@korikuzma
update ga4gh va spec imports
2553f46
@korikuzma
update coding
4633157
@korikuzma
use va spec gh
6a0ae3a
@korikuzma
Merge branch 'issue-415' into issue-240
c0a6cc4
@korikuzma
style: resolve ruff errors
65dc2a3
@korikuzma
Merge branch 'resolve-ruff' into issue-415
75931bb
@korikuzma
Merge branch 'issue-415' into issue-240
3fdcc58
@korikuzma
discard null variant
f81c98c
@korikuzma
fix ci
1d1c2bb
@korikuzma
Merge branch 'issue-415' into issue-240
62b564a
@korikuzma
strength is mappable concept, not coding
9e1596c
@korikuzma
Merge branch 'issue-415' into issue-240
3c1e1f5
@korikuzma
rm coding prefix
07c2bce
@korikuzma
Merge branch 'issue-415' into issue-240
e761a2f
@korikuzma
wip: update db
7c0db36
@korikuzma
wip: update query
e17272a
@korikuzma
fix transformer tests
00d369f
mcannon068nw
mcannon068nw previously approved these changes Feb 27, 2025
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@korikuzma korikuzma linked an issue Mar 4, 2025 that may be closed by this pull request
Change CIViC classification to match ClinVar enum #452
Closed
@korikuzma korikuzma marked this pull request as ready for review March 6, 2025 13:13
katiestahl
katiestahl previously approved these changes Mar 7, 2025
View reviewed changes
Base automatically changed from update-cache to staging March 7, 2025 19:16
@korikuzma korikuzma dismissed stale reviews from katiestahl and mcannon068nw March 7, 2025 19:16

The base branch was changed.

@korikuzma korikuzma merged commit add4368 into staging Mar 7, 2025
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@korikuzma korikuzma deleted the issue-452 branch March 7, 2025 19:16
@github-actions github-actions bot mentioned this pull request Mar 7, 2025
Closed
korikuzma added a commit that referenced this pull request Mar 9, 2025
@korikuzma
feat!: change civic classification.primaryCode to use clinvar enum (#…
4e435d2 
…455)

close #452

* Use ClinVar Submission `clinicalImpactClassificationDescription` enum
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@katiestahl katiestahl katiestahl left review comments

@mcannon068nw mcannon068nw Awaiting requested review from mcannon068nw

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Change CIViC classification to match ClinVar enum
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@korikuzma @katiestahl @mcannon068nw