refactor: upgrade FOCA & major app rewrite (#248)

Co-authored-by: Alex Kanitz <alexander.kanitz@alumni.ethz.ch>
Co-authored-by: Alex Kanitz <alexander.kanitz@unibas.ch>

.github/workflows/checks.yml

@@ -0,0 +1,75 @@
+name: cwl-WES checks
+
+on:
+  push:
+    branches: [dev]
+  pull_request:
+    branches: [dev]
+
+jobs:
+  lint:
+    name: Run linting
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.7"
+      - name: Install requirements
+        run: |
+          pip install .
+          pip install -r requirements_dev.txt
+      - name: Lint with Flake8
+        run: flake8 cwl_wes/ setup.py
+      - name: Lint with Pylint
+        run: pylint cwl_wes/ setup.py
+  test:
+    name: Run tests
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+      - name: Deploy app
+        run: docker-compose up -d --build
+      - name: Wait for app startup
+        shell: bash
+        run: sleep 20
+      - name: Run integration tests
+        shell: bash
+        run: bash tests/integration_tests.sh
+      - name: Tear down app
+        run: docker-compose down
+  publish:
+    name: Build and publish app image
+    runs-on: ubuntu-latest
+    if: ${{ github.event_name == 'push' }}
+    needs: [lint, test]
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+      - name: Generate tag
+        run: |
+          echo "TAG=$(date '+%Y%m%d')" >> $GITHUB_ENV
+      - name: Build and publish image
+        id: docker
+        uses: philips-software/docker-ci-scripts@v5.0.0
+        with:
+          dockerfile: .
+          image-name: "cwl-wes"
+          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

@@ -1,51 +1,24 @@
-##### BASE IMAGE #####
-FROM python:3.7-slim-stretch
+FROM elixircloud/foca:20221110-py3.7
 
-##### METADATA #####
-LABEL base.image="python:3.6-slim-stretch"
-LABEL version="1.1"
+LABEL version="2.0"
 LABEL software="cwl-WES"
-LABEL software.version="1.0"
-LABEL software.description="Flask microservice implementing the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification."
+LABEL software.description="Trigger CWL workflows via GA4GH WES and TES"
 LABEL software.website="https://github.com/elixir-cloud-aai/cwl-WES"
 LABEL software.documentation="https://github.com/elixir-cloud-aai/cwl-WES"
-LABEL software.license="https://github.com/elixir-cloud-aai/cwl-WES/blob/master/LICENSE"
-LABEL software.tags="General"
-LABEL maintainer="alexander.kanitz@alumni.ethz.ch"
-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="cloud-service@elixir-europe.org"
+LABEL maintainer.organisation="ELIXIR Cloud & AAI"
 
 # Python UserID workaround for OpenShift/K8S
 ENV LOGNAME=ipython
 ENV USER=ipython
-ENV HOME=/tmp/user
 
-# Install general dependencies
-RUN apt-get update && apt-get install -y nodejs openssl git build-essential python3-dev curl jq
-
-## Set working directory
 WORKDIR /app
-
-## Copy Python requirements
 COPY ./requirements.txt /app/requirements.txt
+RUN pip install -r requirements.txt
+COPY ./ .
+RUN pip install -e .
 
-## Install Python dependencies
-RUN cd /app \
-  && pip install -r requirements.txt \
-  && cd /app/src/cwl-tes \
-  && python setup.py develop \
-  && cd / \
-  && mkdir -p /tmp/user
-
-## Copy remaining app files
-COPY ./ /app
-
-## Install app & set write permissions for specs directory
-RUN cd /app \
-  && python setup.py develop \
-  && cd / \
-  && chmod g+w /app/cwl_wes/api/ \
-  && chmod g+w -R /tmp/user
-
+## Add permissions for storing updated API specification
+## (required by FOCA)
+RUN chmod -R a+rwx /app/cwl_wes/api

README.md

@@ -87,7 +87,7 @@ cd app
 * Via the **app configuration file**
 
   ```bash
-  vi cwl_wes/config/app_config.yaml
+  vi cwl_wes/config.yaml
   ```
 
 * Via **environment variables**
@@ -253,7 +253,7 @@ question etc.
 [badge-url-ci]: <https://travis-ci.com/elixir-cloud-aai/cwl-WES>
 [badge-url-health]: <https://csc-wes.rahtiapp.fi/ga4gh/wes/v1/ui/>
 [badge-url-license]: <http://www.apache.org/licenses/LICENSE-2.0>
-[config-app]: cwl_wes/config/app_config.yaml
+[config-app]: cwl_wes/config.yaml
 [docs-kubernetes]: deployment/README.md
 [elixir-aai]: https://perun.elixir-czech.cz/
 [elixir-user-group-apply]: https://perun.elixir-czech.cz/fed/registrar/?vo=elixir&group=ECP_CLN:OSS

cwl_wes/__init__.py

@@ -1 +1 @@
-__version__ = '0.15.0'
+"""cwl-WES package."""