Merge pull request #472 from bento-platform/chore/updates

chore: update dependencies and base images

.github/workflows/build.yml

@@ -20,7 +20,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           submodules: "recursive"
 

.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"

.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

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

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

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

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
 

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()

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

pyproject.toml

@@ -32,31 +32,32 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = "^3.10.0"
-bento-lib = {extras = ["django"], version = "^10.1.1"}
-Django = "^4.2.7"
+bento-lib = {extras = ["django"], version = "^11.3.0"}
+Django = "^4.2.9"
 django-autocomplete-light = "^3.9.4"
-django-cors-headers = "^3.13.0"
-django-filter = "^22.1"
+django-cors-headers = "^4.3.1"
+django-filter = "^23.5"
 djangorestframework = "^3.14.0"
 djangorestframework-camel-case = "^1.3.0"
-drf-spectacular = "^0.25.1"
+drf-spectacular = "^0.27.1"
 elasticsearch = "~7.8.0"
 fhirclient = "~3.2"
-jsonschema = {version = "~4.19.2", extras = ["format"]}
+jsonschema = {version = "~4.21.1", extras = ["format"]}
 psycopg2-binary = "~2.9.5"
 PyJWT = {extras = ["crypto"], version = "^2.6.0"}
 python-dateutil = "^2.8.2"
-python-dotenv = "^0.21.1"
+python-dotenv = "^1.0.1"
 rdflib = "^6.2.0"
 requests = "^2.31.0"
 rfc3987 = "^1.3.8"
 tabulate = "^0.9.0"
 uritemplate = "^4.1.1"
 pyhumps = "^3.8.0"
 adrf = "^0.1.1"
+referencing = "^0.32.1"
 
 [tool.poetry.group.dev.dependencies]
-coverage = "^6.5.0"
-flake8 = "^6.0.0"
-tox = "^4.2.8"
-debugpy = "^1.6.4"
+coverage = "^7.4.0"
+flake8 = "^7.0.0"
+tox = "^4.12.1"
+debugpy = "^1.6.7"