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Merged
hanars merged 5 commits into from
Sep 30, 2025
Merged

Dev #5058

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bb5acd9
clinvar xml release (#5050)
bpblanken Sep 29, 2025
b4eaff5
python 3.11
hanars Sep 29, 2025
d0660d0
Merge pull request #5051 from broadinstitute/python-11
hanars Sep 30, 2025
85c0991
update python version for runtime image
hanars Sep 30, 2025
60b1ae3
Merge pull request #5056 from broadinstitute/update-python-version-al…
hanars Sep 30, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/unit-tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.9, 3.11]
python-version: [3.11]

services:
# Label used to access the service container
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4 changes: 2 additions & 2 deletions deploy/docker/seqr/Dockerfile
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@@ -1,4 +1,4 @@
FROM python:3.9-slim-bullseye as build
FROM python:3.11-slim-bullseye as build

LABEL maintainer="Broad TGG"

Expand Down Expand Up @@ -50,7 +50,7 @@ COPY ./ui/ .

RUN npm run build

FROM python:3.9-slim-bullseye as runtime
FROM python:3.11-slim-bullseye as runtime

SHELL ["/bin/bash", "-o", "pipefail", "-c"]
RUN apt-get update && apt-get install -y --no-install-recommends \
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2 changes: 1 addition & 1 deletion seqr/management/commands/reload_clinvar_all_variants.py
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Expand Up @@ -52,7 +52,7 @@ def replace_spaces_with_underscores(value: Union[str, list[str], list[tuple[str,
'practice guideline': 4,
}
WEEKLY_XML_RELEASE = (
'https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarVCVRelease_00-latest.xml.gz'
'https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/weekly_release/ClinVarVCVRelease_00-latest_weekly.xml.gz'
)

def clinvar_run_sql(sql: str):
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