python-package.yml

# This workflow will install Python dependencies, run tests and lint for Python scripts
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: Covid-19 DP submission CI

on:
  push:
    branches: [ main ]
  pull_request:
    branches: [ main ]

jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        java-version: [1.11]
        python-version: [3.8]
        vcf-validator-version: [0.9.4]
        mongo-version: [4.0.21]
    services:
      db:
        image: postgres
        env:
          POSTGRES_DB: postgres
          POSTGRES_USER: postgres
          POSTGRES_PASSWORD: postgres
        ports:
          - 5432:5432
      mongodb:
        image: mongo:${{ matrix.mongo-version }}
        ports:
          - 27017:27017
    steps:
    - uses: actions/checkout@v2
    - name: Setup Java JDK # Nextflow relies on JDK
      uses: actions/setup-java@v1.4.3
      # The Java version to make available on the path. Takes a whole or semver Java version, or 1.x syntax (e.g. 1.8 => Java 8.x). Early access versions can be specified in the form of e.g. 14-ea, 14.0.0-ea, or 14.0.0-ea.28
      with:
        java-version: ${{ matrix.java-version }}
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install flake8 pytest
        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
        python setup.py install
    - name: Set up Nextflow
      run: |
        sudo bash -c "export JAVA_CMD="$(which java)" && cd /usr/bin && (curl -s https://get.nextflow.io | bash) && chmod 755 nextflow"
        /usr/bin/nextflow -version
    - name: Set up VCF validator and assembly checker
      run: |
        sudo bash -c "cd /usr/bin && wget https://github.com/EBIvariation/vcf-validator/releases/download/v${{ matrix.vcf-validator-version }}/vcf_validator_linux && chmod 755 vcf_validator_linux"
        sudo bash -c "cd /usr/bin && wget https://github.com/EBIvariation/vcf-validator/releases/download/v${{ matrix.vcf-validator-version }}/vcf_assembly_checker_linux && chmod 755 vcf_assembly_checker_linux"
    - name: Set up BCFtools
      run: |
        sudo apt update
        sudo apt -y install maven samtools bcftools parallel libbz2-dev liblzma-dev
    - name: Set up ascp binary
    # Might need to periodically update this URL
      run: |
        curl https://d3gcli72yxqn2z.cloudfront.net/connect_latest/v4/bin/ibm-aspera-connect_4.1.3.93_linux.tar.gz -o ibm-aspera-connect.tar.gz
        tar xzvf ibm-aspera-connect.tar.gz
        ./ibm-aspera-connect_*_linux.sh
        chmod +x ~/.aspera/connect/bin/ascp; sudo ln -s ~/.aspera/connect/bin/ascp /usr/bin
    - name: Test with pytest
      env:
        EVA_STATS_DEV_PASSWORD: ${{ secrets.EVA_STATS_DEV_PASSWORD }}
      run: |
        export ASPERA_ID_DSA=~/.aspera/connect/etc/asperaweb_id_dsa.openssh
        PYTHONPATH=. pytest tests
    - name: Test bash script
      run: |
        tests/test_run_ingestion.sh