[Auto-generated] Check & update dependencies (pyproject.toml)

.github/utils/run_with_coverage.py

@@ -11,7 +11,7 @@
 
 from coverage import Coverage
 
-cov = Coverage(data_file=".coverage.docker", config_file="pyproject.toml")
+cov = Coverage(data_file="/app/.coverage.docker", config_file="/app/pyproject.toml")
 cov.start()
 
 from entities_service.main import APP  # noqa: F401, E402

.github/workflows/ci_tests.yml

@@ -54,7 +54,7 @@ jobs:
       ENTITIES_SERVICE_CA_FILE: docker_security/test-ca.pem
       # These are used in the Dockerfile as well as in pytest
       ENTITIES_SERVICE_HOST: localhost
-      ENTITIES_SERVICE_PORT: 8000
+      ENTITIES_SERVICE_PORT: 7000
 
     steps:
       - name: Checkout ${{ github.repository }}
@@ -83,15 +83,41 @@ jobs:
             --volume "${{ github.workspace }}/docker_security:/mongo_tls" \
             mongo:8 \
             --tlsMode allowTLS --tlsCertificateKeyFile /mongo_tls/test-server1.pem --tlsCAFile /mongo_tls/test-ca.pem
-          sleep 10  # Wait for the database to start
+
+          # Health check
+          tmp_file=.dockerPs
+          while ! docker exec mongo mongosh --eval "db.runCommand('ping').ok" mongodb://root:root@localhost:27017/?authSource=admin --quiet ; do
+            docker ps -a > $tmp_file
+            grep -E "^.*mongo .* Exited .*$" $tmp_file && exited=yes && break
+            sleep 3
+          done
+          rm -f $tmp_file
+
+          # Write logs
+          docker logs mongo
+
+          if [ -n "$exited" ]; then
+            exit 1
+          fi
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
 
       - name: Build Docker image
-        run: |
-          docker build \
-            --pull \
-            --tag entities-service \
-            --target ${{ matrix.docker_target }} \
-            .
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          target: ${{ matrix.docker_target }}
+          load: true
+          tags: entities-service
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          provenance: false
+          build-args: |
+            CI=1
 
       - name: Install test dependencies
         run: |
@@ -106,20 +132,37 @@ jobs:
           touch -a logs/entities_service.log
 
           # Run the service in the background
-          docker run --rm -d \
+          docker run -d \
             --env ENTITIES_SERVICE_MONGO_URI \
             --env ENTITIES_SERVICE_X509_CERTIFICATE_FILE \
             --env ENTITIES_SERVICE_CA_FILE \
-            --env PORT=${ENTITIES_SERVICE_PORT} \
-            --env RUN_TIME=60 \
-            --env STOP_TIME=3 \
             --name "entities-service" \
             --network "host" \
             --volume "${PWD}:/app" \
-            --entrypoint "./.github/utils/coverage_entrypoint.sh" \
+            --user "$(id -u):$(id -g)" \
+            --init \
+            --entrypoint "gunicorn" \
             entities-service \
-            ${{ matrix.docker_target }}
-          sleep 5  # Wait for the service to start
+            --bind="0.0.0.0:${ENTITIES_SERVICE_PORT}" --workers=1 --worker-class="uvicorn.workers.UvicornWorker" --log-level="debug" --pythonpath=".github/utils" run_with_coverage:APP
+
+          # Install requirements for health check
+          sudo apt-get update && sudo apt-get install -y --no-install-recommends -fqqy curl
+
+          # Health check
+          tmp_file=.dockerPs
+          while ! curl -sf http://localhost:${ENTITIES_SERVICE_PORT}/openapi.json >> /dev/null ; do
+            docker ps -a > $tmp_file
+            grep -E "^.*entities-service .* Exited .*$" $tmp_file && exited=yes && break
+            sleep 1
+          done
+          rm -f $tmp_file
+
+          # Write logs
+          docker logs entities-service
+
+          if [ -n "$exited" ]; then
+            exit 1
+          fi
 
       - name: Run tests
         run: |
@@ -137,20 +180,30 @@ jobs:
 
       - name: Collect coverage
         run: |
-          # We have mapped the current working directory with the service's working
-          # directory in Docker. This means that we can, first of all, stop the service
-          # via a file touch, and then collect the coverage data from the service.
-          #
-          # See the .github/utils/coverage_entrypoint.sh file for more details on the
-          # stopping mechanism.
-          touch stop_gunicorn
+          # We can stop the service via a SIGINT signal.
+          # Since we map the current directory to /app in the container, the coverage file will be
+          # available in the current working directory.
+          docker kill --signal=SIGTERM entities-service
 
-          sleep 3  # Wait for the service to stop
+          # Wait for the coverage file to be written and the service to stop
+          sleep 10
 
-          mv .coverage .coverage.pytest
-          coverage combine --data-file=.coverage.final --rcfile=pyproject.toml .coverage.pytest .coverage.docker
-          coverage xml --data-file=.coverage.final --rcfile=pyproject.toml -o coverage.xml
-          coverage report --data-file=.coverage.final --rcfile=pyproject.toml --show-missing --skip-covered --skip-empty
+          # Combine the coverage data from pytest and the service
+          {
+            mv .coverage .coverage.pytest &&
+            coverage combine --data-file=.coverage.final --rcfile=pyproject.toml .coverage.pytest .coverage.docker &&
+            coverage xml --data-file=.coverage.final --rcfile=pyproject.toml -o coverage.xml &&
+            coverage report --data-file=.coverage.final --rcfile=pyproject.toml --show-missing --skip-covered --skip-empty
+          } || {
+            echo "Failed to collect coverage data." &&
+            echo "Here's the Docker logs for the service:" &&
+            docker logs entities-service &&
+
+            echo -e "\nAnd the service log:" &&
+            cat logs/entities_service.log &&
+
+            exit 1
+          }
 
       - name: Upload coverage
         if: github.repository_owner == 'SINTEF'
@@ -165,6 +218,14 @@ jobs:
           OS: ubuntu-latest
           PYTHON: '3.10'
 
+      - name: Clean up Docker
+        if: always()
+        run: |
+          docker stop entities-service ||:
+          docker rm entities-service ||:
+          docker stop mongo ||:
+          docker rm mongo ||:
+
   pytest:
     runs-on: ubuntu-latest
 

Dockerfile

@@ -1,7 +1,16 @@
-FROM python:3.10 as base
+FROM python:3.10 AS base
 
+# Prevent writing .pyc files on the import of source modules.
+# Set unbuffered mode to ensure logging outputs.
+# Ignore root user actions for pip.
+ENV PYTHONDONTWRITEBYTECODE=1
+ENV PYTHONUNBUFFERED=1
+ENV PIP_ROOT_USER_ACTION=ignore
+
+# Set the working directory
 WORKDIR /app
 
+# Copy the source code
 COPY entities_service entities_service/
 COPY pyproject.toml LICENSE README.md ./
 
@@ -10,27 +19,26 @@ RUN python -m pip install -U pip && \
   pip install -U setuptools wheel && \
   pip install -U -e .[server]
 
+EXPOSE 7000
+ENTRYPOINT [ "gunicorn", "entities_service.main:APP", "--bind=0.0.0.0:7000", "--workers=1", "--worker-class=entities_service.uvicorn.UvicornWorker" ]
+
+ARG CI=0
+RUN --mount=type=bind,source=.github/utils/requirements.txt,target=/tmp/requirements_ci.txt \
+  if [ "$CI" = "1" ]; then pip install -U -r /tmp/requirements_ci.txt; fi
+
 ## DEVELOPMENT target
-FROM base as development
+FROM base AS development
 
 # Copy over the self-signed certificates for development
 COPY docker_security docker_security/
 
-ENV PORT=80
-EXPOSE ${PORT}
-
 # Set debug mode, since we're running in development mode
 ENV ENTITIES_SERVICE_DEBUG=1
 
-ENTRYPOINT gunicorn --bind "0.0.0.0:${PORT}" --log-level debug --workers 1 --worker-class entities_service.uvicorn.UvicornWorker --reload entities_service.main:APP
+CMD [ "--log-level=debug", "--reload" ]
 
 ## PRODUCTION target
-FROM base as production
-
-ENV PORT=80
-EXPOSE ${PORT}
+FROM base AS production
 
 # Force debug mode to be off, since we're running in production mode
 ENV ENTITIES_SERVICE_DEBUG=0
-
-ENTRYPOINT gunicorn --bind "0.0.0.0:${PORT}" --workers 1 --worker-class entities_service.uvicorn.UvicornWorker entities_service.main:APP

README.md

@@ -52,10 +52,10 @@ ENTITIES_SERVICE_MONGO_PASSWORD=<your MongoDB Atlas user's password with read-on
 Run the service:
 
 ```shell
-uvicorn entities_service.main:APP --host localhost --port 8000 --no-server-header --header "Server:EntitiesService"
+uvicorn entities_service.main:APP --host localhost --port 7000 --no-server-header --header "Server:EntitiesService"
 ```
 
-Finally, go to [localhost:8000/docs](http://localhost:8000/docs) and try out retrieving an entity.
+Finally, go to [localhost:7000/docs](http://localhost:7000/docs) and try out retrieving an entity.
 
 `--log-level debug` can be added to the `uvicorn` command to get more verbose logging.
 `--reload` can be added to the `uvicorn` command to enable auto-reloading of the service when any files are changed.
@@ -102,13 +102,13 @@ docker run --rm -d \
   --env "ENTITIES_SERVICE_CA_FILE=docker_security/test-ca.pem" \
   --name "entities-service" \
   -u "${id -ur}:${id -gr}" \
-  -p "8000:80" \
+  -p "7000:7000" \
   entities-service
 ```
 
 Now, fill up the MongoDB with valid entities at the `entities_service` database in the `entities` collection.
 
-Then go to [localhost:8000/docs](http://localhost:8000/docs) and try out retrieving an entity.
+Then go to [localhost:7000/docs](http://localhost:7000/docs) and try out retrieving an entity.
 
 ---
 
@@ -129,8 +129,6 @@ By default the `development` target will be built, to change this, set the `ENTI
 ENTITIES_SERVICE_DOCKER_TARGET=production docker compose --env-file=.env up --build
 ```
 
-Furthermore, the used `localhost` port can be changed via the `PORT` environment variable.
-
 The `--env-file` argument is optional, but if used, it should point to a file containing the environment variables needed by the service.
 See the section on [using a file for environment variables](#using-a-file-for-environment-variables) for more information.
 
@@ -239,13 +237,13 @@ To test uploading entities using the CLI, one must note that validation of the e
 The validation that is most tricky when testing locally is the namespace validation, as the service will validate the namespace against the `ENTITIES_SERVICE_BASE_URL` environment variable set when starting the service, which defaults to `http://onto-ns.com/meta`.
 However, if using this namespace in the CLI, the CLI will connect to the publicly running service at `http://onto-ns.com/meta`, which will not work when testing locally.
 
-So to make all this work together, one should start the service with the `ENTITIES_SERVICE_BASE_URL` environment variable set to `http://localhost:8000` (which is done through the locally available environment variable `ENTITIES_SERVICE_HOST`), and then use the CLI to upload entities to the service running at `http://localhost:8000`.
+So to make all this work together, one should start the service with the `ENTITIES_SERVICE_BASE_URL` environment variable set to `http://localhost:7000` (which is done through the locally available environment variable `ENTITIES_SERVICE_HOST`), and then use the CLI to upload entities to the service running at `http://localhost:7000`.
 
 In practice, this will look like this:
 
 ```shell
 # Set the relevant environment variables
-export ENTITIES_SERVICE_BASE_URL=http://localhost:8000
+export ENTITIES_SERVICE_BASE_URL=http://localhost:7000
 export ENTITIES_SERVICE_HOST=${ENTITIES_SERVICE_BASE_URL}
 
 # Start the service
@@ -255,7 +253,7 @@ docker compose up -d
 entities-service upload my_entities.yaml --format=yaml
 ```
 
-The `my_entities.yaml` file should contain one or more entities with `uri` values of the form `http://localhost:8000/...`.
+The `my_entities.yaml` file should contain one or more entities with `uri` values of the form `http://localhost:7000/...`.
 
 ### Extra pytest markers
 

docker-compose.yml → compose.yml

@@ -6,7 +6,7 @@ services:
       context: "."
       target: "${ENTITIES_SERVICE_DOCKER_TARGET:-development}"
     ports:
-      - "${ENTITIES_SERVICE_PORT:-8000}:80"
+      - "${ENTITIES_SERVICE_PORT:-7000}:7000"
     environment:
       ENTITIES_SERVICE_BASE_URL: "${ENTITIES_SERVICE_HOST:-http://onto-ns.com/meta}"
       ENTITIES_SERVICE_BACKEND: mongodb
@@ -28,14 +28,9 @@ services:
     image: mongo:8
     restart: always
     ports:
-      - "${MONGO_PORT:-27017}:27017"
-    environment:
-      IN_DOCKER: "true"
-      HOST_USER: "${USER}"
+      - "27017:27017"
     networks:
       - entities_service_net
-    expose:
-      - 27017
     volumes:
       - "./.github/docker_init/create_x509_user.js:/docker-entrypoint-initdb.d/0_create_x509_user.js"
       - "./docker_security:/mongo_tls"

docs/example/dlite_example.ipynb

@@ -13,7 +13,7 @@
     "  - Local `entities_service` package.\n",
     "  - `requests`\n",
     "  - `DLite-Python`\n",
-    "- Running Entities Service at `http://localhost:8000` setup to connect to SOFT Cluster on MongoDB Atlas."
+    "- Running Entities Service at `http://localhost:7000` setup to connect to SOFT Cluster on MongoDB Atlas."
    ]
   },
   {

docs/example/dlite_example.py

@@ -5,7 +5,7 @@
 
 
 def get_instance(uri: str) -> Instance:
-    uri = uri.replace("http://onto-ns.com/meta", "http://localhost:8000")
+    uri = uri.replace("http://onto-ns.com/meta", "http://localhost:7000")
     response = requests.get(uri)
     if not response.ok:
         error_message = (

pyproject.toml

@@ -47,28 +47,27 @@ dependencies = [
     "pydantic-settings ~=2.6",
     "pymongo ~=4.10",
     "python-dotenv ~=1.0",
-    "uvicorn >=0.24.0,<1",
+    "uvicorn ~=0.32.0",
 ]
 
 [project.optional-dependencies]
 cli = [
     "httpx-auth ~=0.22.0",
     "pyyaml ~=6.0",
-    "typer[all] >=0.9.0,<1",
+    "typer[all] ~=0.12.5",
 ]
 testing = [
     "cryptography ~=43.0",
     "dlite-python ~=0.5.23",
     "mongomock ~=4.2",
-    "numpy <2",  # requirement for DLite v0.5.16, which does not support NumPy v2
     "pytest ~=8.3",
     "pytest-asyncio ~=0.24.0",
-    "pytest-cov ~=5.0",
-    "pytest-httpx ~=0.32.0",
+    "pytest-cov ~=6.0",
+    "pytest-httpx ~=0.33.0",
     "entities-service[cli]",
 ]
 server = [
-    "gunicorn >=21.2.0,<24",
+    "gunicorn ~=23.0.0",
 ]
 dev = [
     "pre-commit ~=4.0",