diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 19415c001..b2c9bf1ae 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -20,7 +20,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: submodules: "recursive" diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 26f7185eb..19c3028af 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -10,7 +10,7 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - uses: actions/setup-python@v4 + - uses: actions/setup-python@v5 name: Set up Python with: python-version: "3.10" diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 8427518fc..80182732f 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -34,7 +34,7 @@ jobs: with: submodules: true - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - name: Install Poetry diff --git a/bento.Dockerfile b/bento.Dockerfile index e27b833d0..07fc3b218 100644 --- a/bento.Dockerfile +++ b/bento.Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.10.20 +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.01.01 SHELL ["/bin/bash", "-c"] @@ -7,7 +7,7 @@ SHELL ["/bin/bash", "-c"] RUN apt-get update -y && \ apt-get install -y postgresql-client && \ rm -rf /var/lib/apt/lists/* && \ - pip install --no-cache-dir "uvicorn[standard]==0.23.2" + pip install --no-cache-dir "uvicorn[standard]==0.27.0" # Backwards-compatible with old BentoV2 container layout WORKDIR /app diff --git a/bento.dev.Dockerfile b/bento.dev.Dockerfile index e5a1ce36f..46d73f855 100644 --- a/bento.dev.Dockerfile +++ b/bento.dev.Dockerfile @@ -1,4 +1,4 @@ -FROM ghcr.io/bento-platform/bento_base_image:python-debian-2023.10.20 +FROM ghcr.io/bento-platform/bento_base_image:python-debian-2024.01.01 LABEL org.opencontainers.image.description="Local development image for Katsu." LABEL devcontainer.metadata='[{ \ @@ -18,7 +18,7 @@ SHELL ["/bin/bash", "-c"] RUN apt-get update -y && \ apt-get install -y postgresql-client && \ rm -rf /var/lib/apt/lists/* && \ - pip install --no-cache-dir "uvicorn[standard]==0.23.2" + pip install --no-cache-dir "uvicorn[standard]==0.27.0" # Backwards-compatible with old BentoV2 container layout WORKDIR /app diff --git a/chord_metadata_service/metadata/service_info.py b/chord_metadata_service/metadata/service_info.py index c68b0d1fc..d4dbcf42e 100644 --- a/chord_metadata_service/metadata/service_info.py +++ b/chord_metadata_service/metadata/service_info.py @@ -1,6 +1,8 @@ from django.conf import settings -from bento_lib.service_info import SERVICE_ORGANIZATION_C3G, GA4GHServiceInfo, build_service_info +from bento_lib.service_info.constants import SERVICE_ORGANIZATION_C3G +from bento_lib.service_info.types import GA4GHServiceInfo +from bento_lib.service_info.helpers import build_service_info from .. import __version__ from ..logger import logger diff --git a/chord_metadata_service/metadata/settings.py b/chord_metadata_service/metadata/settings.py index af1c992fb..b3b241a6a 100644 --- a/chord_metadata_service/metadata/settings.py +++ b/chord_metadata_service/metadata/settings.py @@ -16,7 +16,7 @@ import json from os.path import exists -from bento_lib.service_info import GA4GHServiceType +from bento_lib.service_info.types import GA4GHServiceType from urllib.parse import quote, urlparse from dotenv import load_dotenv diff --git a/chord_metadata_service/phenopackets/schemas.py b/chord_metadata_service/phenopackets/schemas.py index 51be759b9..2d73b1296 100644 --- a/chord_metadata_service/phenopackets/schemas.py +++ b/chord_metadata_service/phenopackets/schemas.py @@ -2,6 +2,7 @@ import json from pathlib import Path from referencing import Registry, Resource +from referencing.jsonschema import DRAFT7 from chord_metadata_service.patients.schemas import INDIVIDUAL_SCHEMA from chord_metadata_service.resources.schemas import RESOURCE_SCHEMA from chord_metadata_service.restapi.schemas import ( @@ -658,7 +659,7 @@ "required": ["id", "meta_data"], }, descriptions.PHENOPACKET) -VRS_REF_RESOURCE = Resource.from_contents(contents=vrs_schema_definitions, default_specification=DRAFT_07) +VRS_REF_RESOURCE = Resource.from_contents(contents=vrs_schema_definitions, default_specification=DRAFT7) VRS_REF_REGISTRY = VRS_REF_RESOURCE @ Registry() resolver = VRS_REF_REGISTRY.resolver() diff --git a/docs/requirements.txt b/docs/requirements.txt index dd79b53d3..257637723 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -3,7 +3,7 @@ asgiref==3.6.0 Babel==2.12.1 certifi==2023.7.22 charset-normalizer==3.1.0 -Django==4.2.7 +Django==4.2.9 docutils==0.16 idna==3.4 imagesize==1.4.1 diff --git a/poetry.lock b/poetry.lock index 23903b429..b32c517ed 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,20 +1,21 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. [[package]] name = "adrf" -version = "0.1.2" +version = "0.1.3" description = "Async support for Django REST framework" optional = false python-versions = ">=3.8" files = [ - {file = "adrf-0.1.2-py3-none-any.whl", hash = "sha256:a33f8f51f0f80072ffb2af061df1fb119bc00adaa720a2972049d4aa33155337"}, - {file = "adrf-0.1.2.tar.gz", hash = "sha256:ce7160878ba27999d333752941cde0687c1a205fc26fa0eda1bad3924958dc69"}, + {file = "adrf-0.1.3-py3-none-any.whl", hash = "sha256:b848cab61d645e969261edf3fa1072411f8bfa84283fcbddd6a42b1f3ef57ce6"}, + {file = "adrf-0.1.3.tar.gz", hash = "sha256:f76e0ff59af5359bbdd5087fae13f3ab152b6aaebb59350d5aea5e88ea588d7d"}, ] [package.dependencies] async-property = ">=0.2.2" django = ">=4.1" djangorestframework = ">=3.14.0" +isort = "5.12.0" [[package]] name = "aiohttp" @@ -197,48 +198,50 @@ files = [ [[package]] name = "attrs" -version = "23.1.0" +version = "23.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - 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