test-stack.yml

name: Test BEDBASE stack

on:
  workflow_dispatch:
    inputs:
      bedstat_branch:
        description: 'bedstat branch to checkout'
        required: true
        default: 'master'
      bedbuncher_branch:
        description: 'bedbuncher branch to checkout'
        required: true
        default: 'master'

jobs:
  pytest:
    strategy:
      matrix:
        os: [ubuntu-latest] # can't use macOS when using service containers or container jobs
        python-version: [3.6, 3.7, 3.8]
        r-version: [release]
    runs-on: ${{ matrix.os }}
    services:
        postgres:
          image: postgres
          env:
            POSTGRES_USER: postgres
            POSTGRES_PASSWORD: bedbasepassword
            POSTGRES_DB: postgres
          ports:
          - 5432:5432
          options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
    steps:
    - uses: actions/checkout@v2

    - name: Checkout bedstat@${{ github.event.inputs.bedstat_branch }}
      uses: actions/checkout@v2
      with:
        repository: databio/bedstat
        ref: ${{ github.event.inputs.bedstat_branch }}
        path: bedstat

    - name: Checkout bedbuncher@${{ github.event.inputs.bedbuncher_branch }}
      uses: actions/checkout@v2
      with:
        repository: databio/bedbuncher
        ref: ${{ github.event.inputs.bedbuncher_branch }}
        path: bedbuncher

    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install bedstat dependancies
      run: if [ -f bedstat/requirements/requirements-all.txt ]; then pip install -r bedstat/requirements/requirements-all.txt; fi

    - name: Install bedstat dev dependancies
      run: if [ -f bedstat/requirements/requirements-dev.txt ]; then pip install -r bedstat/requirements/requirements-dev.txt; fi

    - name: Install bedstat test dependancies
      run: if [ -f bedstat/requirements/requirements-test.txt ]; then pip install -r bedstat/requirements/requirements-test.txt; fi

    - name: Install bedbuncher dependancies
      run: if [ -f bedbuncher/requirements/requirements-all.txt ]; then pip install -r bedbuncher/requirements/requirements-all.txt; fi

    - name: Install bedbuncher dev dependancies
      run: if [ -f bedbuncher/requirements/requirements-dev.txt ]; then pip install -r bedbuncher/requirements/requirements-dev.txt; fi

    - name: Install bedbuncher test dependancies
      run: if [ -f bedbuncher/requirements/requirements-test.txt ]; then pip install -r bedbuncher/requirements/requirements-test.txt; fi

    - name: Install libcurl
      run: sudo apt-get install libcurl4-openssl-dev

    - name: Install libpng
      run: |
        sudo wget http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb
        sudo dpkg -i libpng12-0_1.2.54-1ubuntu1_amd64.deb

    - name: Compile and install IGD
      run: |
        git clone https://github.com/databio/IGD.git
        cd IGD
        make 
        cd ..
        echo "::add-path::$GITHUB_WORKSPACE/IGD/bin/"

    - name: Set up R ${{ matrix.r-version }}
      uses: r-lib/actions/setup-r@master
      with:
        r-version: ${{ matrix.r-version }}

    - name: Install R dependancies
      run: Rscript bedstat/scripts/installRdeps.R

    - name: Run bedstat pipeline
      run: looper run -p local ci/cfg/bedstat_config.yaml

    - name: Test plots exist
      run: |
        if ls $GITHUB_WORKSPACE/outputs/bedstat_output/*/test_hg38*.png 1> /dev/null 2>&1; then
          echo "SUCCESS";
        else
          echo "ERROR: files do not exist: $GITHUB_WORKSPACE/outputs/bedstat_output/*/test_hg38*.png";
          exit 1
        fi

    - name: Test metadata exist
      run: |
        if ls $GITHUB_WORKSPACE/outputs/bedstat_output/*/test_hg38*.json 1> /dev/null 2>&1; then
          echo "SUCCESS";
        else
          echo "ERROR: file does not exist: $GITHUB_WORKSPACE/outputs/bedstat_output/*/test_hg38.json";
          exit 1
        fi

    - name: Test records in bedfiles table
      run: python3 ci/scripts/count_records.py -t bedfiles -e 2

    - name: Run bedbuncher pipeline
      run: looper run -p local ci/cfg/bedbuncher_config.yaml

    - name: Test metadata exist
      run: |
        if ls $GITHUB_WORKSPACE/outputs/bedbuncher_output/*/bedbase_demo_bedset.json 1> /dev/null 2>&1; then
          echo "SUCCESS";
        else
          echo "ERROR: file does not exist: $GITHUB_WORKSPACE/outputs/bedbuncher_output/*/bedbase_demo_bedset.json";
          exit 1
        fi

    - name: Test igd archive exists
      run: |
        if ls $GITHUB_WORKSPACE/outputs/bedbuncher_output/*/bedbase_demo_bedset_igd.tar.gz 1> /dev/null 2>&1; then
          echo "SUCCESS";
        else
          echo "ERROR: file does not exist: $GITHUB_WORKSPACE/outputs/bedbuncher_output/*/bedbase_demo_bedset_igd.tar.gz";
          exit 1
        fi

    - name: Test PEP archive exists
      run: |
        if ls $GITHUB_WORKSPACE/outputs/bedbuncher_output/*/bedbase_demo_bedset_PEP.tar.gz 1> /dev/null 2>&1; then
          echo "SUCCESS";
        else
          echo "ERROR: file does not exist: $GITHUB_WORKSPACE/outputs/bedbuncher_output/*/bedbase_demo_bedset_PEP.tar.gz";
          exit 1
        fi

    - name: Test records in bedsets table
      run: python3 ci/scripts/count_records.py -t bedsets -e 1

    - name: Test records in bedset_bedfiles
      run: python3 ci/scripts/count_records.py -t bedset_bedfiles -e 2