Draft don't merge #104
Workflow file for this run
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| # 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() | |