test_schematic_api.yml

# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help

# This workflow creates an instance of data curator app with schematic, then
# creates a flask server running schematic to test data curator's use of 
# schematic's REST API endpoints.
name: test-schematic-api

on:
  pull_request:
    branches:
      - main

jobs:
  test-schematic-rest-api:
    runs-on: ubuntu-latest
    # This image seems to be based on rocker/r-ver which in turn is based on debian
    container: rocker/rstudio
    env:
      # This should not be necessary for installing from public repo's however remotes::install_github() fails without it.
      GITHUB_PAT: ${{ secrets.REPO_PAT }}

    steps:
      - name: Install System Dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y pip python3.8-venv libcurl4-openssl-dev

      - uses: actions/checkout@v2

      - uses: r-lib/actions/setup-pandoc@v1

      - name: Create and Activate Python Virtual Environment
        shell: bash
        run: |
          python3 -m venv .venv
          chmod 755 .venv/bin/activate
          source .venv/bin/activate

      - name: Install R Packages Dependencies
        run: |
          R -f install-pkgs.R

      - name: Install Schematic
        shell: bash
        run: |
          source .venv/bin/activate
          # use 'poetry' to install schematic from the develop branch 
          pip3 install poetry
          git clone --single-branch --branch develop https://github.com/Sage-Bionetworks/schematic.git
          cd schematic
          poetry build
          pip3 install dist/schematicpy-1.0.0-py3-none-any.whl

      - name: Set Configurations for Schematic
        shell: bash
        run: |
          source .venv/bin/activate
          # download data model to the correct location
          R -e '
            config <- yaml::yaml.load_file(".github/schematic_config.yml");
            url  <- config$model$input$download_url;
            path <- config$model$input$location;
            system(sprintf("mkdir -p %s", dirname(path)));
            system(sprintf("wget %s -O %s", url, path));
          '
          # overwrite the config.yml in schematic
          mv -f .github/schematic_config.yml schematic/config.yml
          # write out configuration files using github secrets
          echo "${{ secrets.SCHEMATIC_SYNAPSE_CONFIG }}" > schematic/.synapseConfig
          echo "${{ secrets.SCHEMATIC_SERVICE_ACCT_CREDS }}" > schematic/schematic_service_account_creds.json
          echo "${{ secrets.SCHEMATIC_CREDS_PATH }}" > schematic/credentials.json
          echo "${{ secrets.SCHEMATIC_TOKEN_PICKLE }}" | base64 -d > schematic/token.pickle

      - name: Run schematic API service
        shell: bash
        run: |
          echo "SYNAPSE_PAT='${{ secrets.SYNAPSE_PAT }}'" > .Renviron
          source .venv/bin/activate
          cd schematic
          pip3 uninstall -y markupsafe
          pip3 install markupsafe==2.0.1
          python3 run_api.py &

      - name: Run tests
        shell: Rscript {0}
        run: |
          devtools::test()