Dev #3860
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Dev #3860
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hanars
commented
Feb 6, 2024
hanars
commented
- All unit test are passing and coverage has not substantively dropped
- No new dependency vulnerabilities have been introduced
- Any changes to the docker image have been vetted for potential vulnerabilities
- If any python requirements are updated, they are noted and here and will be updated before deploying:
- bump cryptography
- Any database migrations are noted here, and will be run before deploying:
- All major changes are recorded in the changelog, and the changelog has been updated to reflect the latest release
- Any new endpoints are explicitly tested to ensure they are only accessible to correctly permissioned users
- No secrets have been committed
- Any changes to environment variables or secrets are noted here, and will properly configured before deploying:
add help label for variant id in variant lookup
Enable build 37 for hail backend
explicitly set spark driver memory
…iant-lookup-genotypes
parse env var to int
add env variable to hail search tests
The following vulnerabilities are fixed by pinning transitive dependencies: - https://snyk.io/vuln/SNYK-PYTHON-CRYPTOGRAPHY-6050294 - https://snyk.io/vuln/SNYK-PYTHON-CRYPTOGRAPHY-6126975
Use variant lookup page for all-project single variant search
Bumps [aiohttp](https://github.com/aio-libs/aiohttp) from 3.9.0 to 3.9.2. - [Release notes](https://github.com/aio-libs/aiohttp/releases) - [Changelog](https://github.com/aio-libs/aiohttp/blob/master/CHANGES.rst) - [Commits](aio-libs/aiohttp@v3.9.0...v3.9.2) --- updated-dependencies: - dependency-name: aiohttp dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]>
…ch/aiohttp-3.9.2 Bump aiohttp from 3.9.0 to 3.9.2 in /hail_search
properly handle 37 variant ids
configure hail backend extraJavaOptions
…7ede7438ef3ba23a2 [Snyk] Security upgrade cryptography from 41.0.6 to 42.0.0
refactor variant lookup aggregation
do not load project tables with no queried variants
add caching for variant lookup
The original code here does a next(iter(<dictionary>)) which has an indeterministic order, so this occasionally returns the variantTag for an AIP variant, which gets transformed with a different key, causing this test to intermittently fail. For this reason, we'll hard select the the variant VT1726961_2103343353_r0390_100 to look at the keys for.
Bumps [cryptography](https://github.com/pyca/cryptography) from 41.0.6 to 42.0.0. - [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst) - [Commits](pyca/cryptography@41.0.6...42.0.0) --- updated-dependencies: - dependency-name: cryptography dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]>
…t to default (cherry picked from commit 9d8ad2a)
…phy-42.0.0 Bump cryptography from 41.0.6 to 42.0.0
Update indeterministic assertion in test_json_for_saved_variants_with_tags
…anscript feat: Clearly show when variant transcript is not Canonical nor MANE
bpblanken
approved these changes
Feb 6, 2024
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