From bb5acd9ebd57f32fcdb06afb3d6241849f572808 Mon Sep 17 00:00:00 2001 From: Benjamin Blankenmeister Date: Mon, 29 Sep 2025 16:20:33 -0400 Subject: [PATCH 1/3] clinvar xml release (#5050) --- seqr/management/commands/reload_clinvar_all_variants.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/seqr/management/commands/reload_clinvar_all_variants.py b/seqr/management/commands/reload_clinvar_all_variants.py index 3b05a63883..7d6137b6d3 100644 --- a/seqr/management/commands/reload_clinvar_all_variants.py +++ b/seqr/management/commands/reload_clinvar_all_variants.py @@ -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): From b4eaff5343c01da32065cf6f07fa4c7a2583f8f0 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Mon, 29 Sep 2025 16:42:59 -0400 Subject: [PATCH 2/3] python 3.11 --- .github/workflows/unit-tests.yml | 2 +- deploy/docker/seqr/Dockerfile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/unit-tests.yml index 71c309be6e..b4f1039abe 100644 --- a/.github/workflows/unit-tests.yml +++ b/.github/workflows/unit-tests.yml @@ -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 diff --git a/deploy/docker/seqr/Dockerfile b/deploy/docker/seqr/Dockerfile index d003ad1b41..c73e37199a 100644 --- a/deploy/docker/seqr/Dockerfile +++ b/deploy/docker/seqr/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.9-slim-bullseye as build +FROM python:3.11-slim-bullseye as build LABEL maintainer="Broad TGG" From 85c0991476eaf69f0f667e6943d74d51544b1636 Mon Sep 17 00:00:00 2001 From: Hana Snow Date: Tue, 30 Sep 2025 12:15:38 -0400 Subject: [PATCH 3/3] update python version for runtime image --- deploy/docker/seqr/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deploy/docker/seqr/Dockerfile b/deploy/docker/seqr/Dockerfile index c73e37199a..0b8cec3ccd 100644 --- a/deploy/docker/seqr/Dockerfile +++ b/deploy/docker/seqr/Dockerfile @@ -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 \