active_update_truth_weekly.yml

name: (Active) Update JHU, NY Times, USAFacts truth data weekly
on:
  workflow_dispatch:
    inputs: 
      skip_zoltar_upload:
        description: 'true/false indicating whether to skip Zoltar upload'
        required: false
        default: 'false'
  schedule:
    - cron: '0 16 * * 0'

jobs:
  upload_zoltar:
    if: github.repository_owner == 'reichlab'
    runs-on: ubuntu-latest
    strategy:
      matrix:
        node-version: [10.2]

    steps:
    # - run: sudo apt-get remove ghc-** azure-cli firefox google-cloud-sdk google-chrome-stable hhvm dotnet-sdk-** dotnet-runtime-** moby-** adoptopenjdk-** mongodb-org-** mysql-**
    # - run: sudo apt-get autoremove
    - name: Free disk space
      run: |
          df --human-readable
          sudo apt clean
          docker rmi $(docker image ls --all --quiet)
          rm --recursive --force "$AGENT_TOOLSDIRECTORY"
          
    - name: Maximize build space
      uses: easimon/maximize-build-space@v4
      with:
        root-reserve-mb: 4096
        swap-size-mb: 4096
        remove-dotnet: 'true'
        remove-android: 'true'
        remove-haskell: 'true'
        
    - name: Check space available
      run: df --human-readable
      
    - name: Checkout covid19-forecast-hub repo
      uses: actions/checkout@v3
      with:
        lfs: true
        path: covid19-forecast-hub
    
    - name: Checkout LFS objects
      run: git lfs checkout
      working-directory: ./covid19-forecast-hub  
        
    - name: Setup GitHub Action for R language
      uses: r-lib/actions/setup-r@v2
      with:
        use-public-rspm: true

    - name: Install system dependencies
      run: sudo apt-get install libudunits2-dev libcurl4-openssl-dev libgdal-dev
      
    - name: Checkout covidData
      uses: actions/checkout@v3
      with:
        repository: reichlab/covidData
        token: ${{secrets.GH_TOKEN}}
        path: covidData
        
    - name: Setup Python
      uses: actions/setup-python@v2
      with:
        python-version: '3.x' # Version range or exact version of a Python version to use, using SemVer's version range syntax
        architecture: 'x64' # optional x64 or x86. Defaults to x64 if not specified
    
    - name: Install python dependencies 
      run: pip3 install -r visualization/requirements.txt
      working-directory: ./covid19-forecast-hub
      
    - name: Install R dependencies (for covidData + covidHubUtils)
      working-directory: ./covid19-forecast-hub
      run: Rscript code/R_scripts/install_dependencies.R
      env:
        GITHUB_PAT: ${{ secrets.GH_TOKEN }}

    - run: mkdir ./covidData/data-raw/JHU/
    
    - name: Install covidData
      run: make recent_data
      working-directory: ./covidData/code/data-processing
      
    - name: Generate truth csv files (NYTimes, JHU, Hospitalization, Zoltar)
      run: Rscript ./covid19-forecast-hub/code/R_scripts/generate_truth_csvs.R
      
    - name: Push generated files to GitHub
      run: bash ./travis/push-gh.sh
      working-directory: ./covid19-forecast-hub
      env:
        GH_TOKEN: ${{secrets.GH_TOKEN}}
        
    - name: Push Zoltar truth to Zoltar
      run: python3 ./code/zoltar_scripts/upload_truth_to_zoltar.py
      working-directory: ./covid19-forecast-hub
      env:
        Z_USERNAME: ${{ secrets.Z_USERNAME }}
        Z_PASSWORD: ${{ secrets.Z_PASSWORD }}
      
    - name: Check space available after update
      run: df --human-readable