build: upgrade FOCA (#64)

.github/workflows/main.yml

@@ -1,43 +1,86 @@
----
-name: Test with docker compose
+name: proWES checks
+
 on:
   push:
     branches: [ dev ]
   pull_request:
     branches: [ dev ]
 
+
 jobs:
-  build:
+  lint:
+    name: Run linting
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install requirements
+        run: |
+          pip install -r requirements_dev.txt
+          pip install .
+      - name: Lint with Flake8
+        run: flake8
+  test:
+    name: Run tests
     runs-on: ubuntu-latest
     env:
-      PROBE_ENDPOINT: localhost:8080/ga4gh/wes/v1/ui/
-    strategy:
-      fail-fast: true
-      matrix:
-        python-version: ["3.7", "3.8","3.9", "3.10"]
-
+      PROBE_ENDPOINT: localhost:8090/ga4gh/wes/v1/service-info
+    permissions:
+      contents: read
+      packages: write
     steps:
-    - uses: actions/checkout@v2
-    - name: Install dependencies
-      run: pip install docker-compose
-    - name: Create data directories
-      run: mkdir -p ${HOME}/data/{db,output,tmp}
-    - name: Docker compose up
-      run: docker-compose up -d
-    - name: Sleep 30
-      run: sleep 30
-    - name: PROBE
-      run: echo "${PROBE_ENDPOINT}"
-    - name: Test
-      run: |
-        test $( \
-          curl \
-           -sL \
-           -v \
-           -o /dev/null \
-           -w '%{http_code}' \
-           -X GET \
-           --header 'Accept: application/json' \
-           "${PROBE_ENDPOINT}" \
-          ) == '200' || exit 1
-
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Deploy app
+        run: docker-compose up -d --build
+      - name: Wait for app startup
+        run: sleep 20
+      - name: Probe endpoint
+        run: |
+          test $( \
+            curl \
+             -sL \
+             -v \
+             -o /dev/null \
+             -w '%{http_code}' \
+             -X GET \
+             --header 'Accept: application/json' \
+             "${PROBE_ENDPOINT}" \
+            ) == '200' || exit 1
+  publish:
+    name: Build and publish app image
+    runs-on: ubuntu-latest
+    if: ${{ github.event_name == 'push' }}
+    needs: [lint, test]
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Generate tag
+        run: |
+          echo "TAG=$(date '+%Y%m%d')" >> $GITHUB_ENV
+      - name: Build and publish image
+        id: docker
+        uses: philips-software/[email protected]
+        with:
+          dockerfile: .
+          image-name: "prowes"
+          tags: "latest ${{ env.TAG }}"
+          push-branches: "${{ github.event.repository.default_branch }}"
+        env:
+          REGISTRY_USERNAME: ${{ secrets.DOCKERHUB_LOGIN }}
+          REGISTRY_TOKEN: "${{ secrets.DOCKERHUB_TOKEN }}"
+          DOCKER_ORGANIZATION: ${{ secrets.DOCKERHUB_ORG }}
+          GITHUB_ORGANIZATION: ${{ github.repository_owner }}
+      - name: Verify that image was pushed
+        run: |
+          echo "Push indicator: ${{ steps.docker.outputs.push-indicator }}"
+          echo "# Set to 'true' if image was pushed, empty string otherwise"
+          test "${{ steps.docker.outputs.push-indicator }}" == "true"

Dockerfile

@@ -1,43 +1,24 @@
 ##### BASE IMAGE #####
-FROM elixircloud/foca:20220524-py3.7
+FROM elixircloud/foca:20230818-py3.10
 
 ##### METADATA #####
-LABEL base.image="elixircloud/foca:20220524-py3.7"
-LABEL version="2.0"
+LABEL version="3.0"
 LABEL software="proWES"
-LABEL software.version="0.15.0"
-LABEL software.description="Flask microservice implementing the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification."
+LABEL software.description="Flask microservice implementing the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification as a proxy for middleware injection (e.g., workflow distribution logic)."
 LABEL software.website="https://github.com/elixir-europe/proWES"
 LABEL software.documentation="https://github.com/elixir-europe/proWES"
-LABEL software.license="https://github.com/elixir-europe/proWES/blob/master/LICENSE"
-LABEL software.tags="General"
-LABEL maintainer="[email protected]"
-LABEL maintainer.organisation="Biozentrum, University of Basel"
-LABEL maintainer.location="Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland"
-LABEL maintainer.lab="ELIXIR Cloud & AAI"
-LABEL maintainer.license="https://spdx.org/licenses/Apache-2.0"
+LABEL software.license="https://spdx.org/licenses/Apache-2.0"
+LABEL maintainer="[email protected]"
+LABEL maintainer.organisation="ELIXIR Cloud & AAI"
 
 # Python UserID workaround for OpenShift/K8S
 ENV LOGNAME=ipython
 ENV USER=ipython
 
-## Set working directory
 WORKDIR /app
+COPY ./ .
+RUN pip install -e .
 
-## Copy Python requirements
-COPY ./requirements.txt /app/requirements.txt
-COPY ./requirements_dev.txt /app/requirements_dev.txt
-
-## Install Python dependencies
-RUN cd /app \
-  && pip install -r requirements.txt \
-  && pip install -r requirements_dev.txt \
-  && cd /
-
-## Copy remaining app files
-COPY ./ /app
-
-## Install app
-RUN cd /app \
-  && python setup.py develop \
-  && cd /
+## Add permissions for storing updated API specification
+## (required by FOCA)
+RUN chmod -R a+rwx /app/pro_wes/api

docker-compose.yaml

@@ -10,7 +10,7 @@ services:
     links:
       - mongodb
       - rabbitmq
-    command: bash -c "cd /app/pro_wes; celery -A worker worker -E --loglevel=info"
+    command: bash -c "cd /app/pro_wes; celery -A celery_worker worker -E --loglevel=info"
     volumes:
       - ${PROWES_DATA_DIR:-../data/pro_wes}:/data
 
@@ -23,8 +23,6 @@ services:
     links:
       - mongodb
     command: bash -c "cd /app/pro_wes; gunicorn -c gunicorn.py wsgi:app"
-    volumes:
-      - ${PROWES_DATA_DIR:-../data/pro_wes}:/data
     ports:
       - "8090:8080"
 
@@ -53,4 +51,3 @@ services:
     command: flower --broker=amqp://guest:guest@rabbitmq:5672// --port=5555
     ports:
       - "5565:5555"
-

pro_wes/__init__.py

@@ -1 +1 @@
-__version__ = '0.17.0'
+"""proWES app package root."""

pro_wes/app.py

@@ -13,7 +13,7 @@
 def init_app() -> App:
     foca = Foca(
         config_file=Path(__file__).resolve().parent / "config.yaml",
-        custom_config_model='pro_wes.config_models.CustomConfig',
+        custom_config_model="pro_wes.config_models.CustomConfig",
     )
     app = foca.create_app()
     with app.app.app_context():
@@ -31,6 +31,6 @@ def run_app(app: App) -> None:
     app.run(port=app.port)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     app = init_app()
     run_app(app)

pro_wes/celery_worker.py

@@ -0,0 +1,12 @@
+"""Celery worker entry point."""
+
+from pathlib import Path
+
+from celery import Celery
+from foca import Foca  # type: ignore
+
+foca = Foca(
+    config_file=Path(__file__).resolve().parent / "config.yaml",
+    custom_config_model="pro_wes.config_models.CustomConfig",
+)
+celery: Celery = foca.create_celery_app()

pro_wes/client_wes.py

@@ -19,7 +19,7 @@
 )
 
 
-class WesClient():
+class WesClient:
     """Client to communicate with GA4GH WES API.
 
     Arguments:
@@ -39,6 +39,7 @@ class WesClient():
         token: Bearer token for gaining access to WES endpoints.
         session: Client server session.
     """
+
     def __init__(
         self,
         host: str,
@@ -123,9 +124,7 @@ def post_run(
         try:
             RunRequest(**form_data)
         except Exception as exc:
-            raise ValueError(
-                f"invalid form data: {form_data}"
-            ) from exc
+            raise ValueError(f"invalid form data: {form_data}") from exc
         try:
             response_unvalidated = self.session.post(
                 url,
@@ -320,7 +319,7 @@ def set_token(
 
     def set_headers(
         self,
-        content_accept: str = 'application/json',
+        content_accept: str = "application/json",
         content_type: Optional[str] = None,
     ) -> None:
         """Set session headers.
@@ -330,8 +329,8 @@ def set_headers(
             content_type: Type of content sent with the request.
         """
         headers = {}
-        headers['Accept'] = content_accept
+        headers["Accept"] = content_accept
         if content_type is not None:
-            headers['Content-Type'] = content_type
-        headers['Authorization'] = f"Bearer {self.token}"
+            headers["Content-Type"] = content_type
+        headers["Authorization"] = f"Bearer {self.token}"
         self.session.headers.update(headers)