shinyapps_deploy.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

name: shiny-deploy

on:
  push:
    branches:
      - main
      - develop*
      - include-setup
    tags:
      - v[0-9]+.[0-9]+.[0-9]+
    paths-ignore:
      - '.github/ISSUE_TEMPLATE/**'
      - '**/*.md'
      - '**/.gitignore'

jobs:
  shiny-deploy:
    runs-on: ubuntu-latest
    # This image seems to be based on rocker/r-ver which in turn is based on debian
    container: rocker/rstudio:4.1.2
    env:
      # This should not be necessary for installing from public repo's however remotes::install_github() fails without it.
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    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: |
          # has to activate each bash step
          source .venv/bin/activate
          # use 'poetry' to install schematic dev schematic
          # If commit is tagged for release or in main branch, install schematic from pypi
          if [[ $GITHUB_REF_NAME == v*.*.* ]] || [[ $GITHUB_REF_NAME == main ]]; then
            echo Installing pypi version of schematic
            git clone --single-branch --branch main https://github.com/Sage-Bionetworks/schematic.git
            cp schematic_config.yml schematic/config.yml
            cd schematic
            pip3 install schematicpy
          else
            pip3 install poetry
            echo Installing develop branch of schematic from github
            git clone --single-branch --branch develop https://github.com/Sage-Bionetworks/schematic.git
            cp schematic_config.yml schematic/config.yml
            cd schematic
            poetry build
            pip3 install dist/schematicpy-1.0.0-py3-none-any.whl
          fi

      - name: Set Configurations for Schematic
        shell: bash
        run: |
          # write out configuration files using github secrets
          echo "${{ secrets.SCHEMATIC_SYNAPSE_CONFIG }}" > .synapseConfig
          echo "${{ secrets.SCHEMATIC_CREDS_PATH }}" > credentials.json
          echo "${{ secrets.SCHEMATIC_TOKEN_PICKLE }}" | base64 -d > token.pickle

      - name: Save service account credentials for Schematic
        id: create-json
        uses: jsdaniell/create-json@1.1.2
        with:
          name: 'schematic_service_account_creds.json'
          json: ${{ secrets.SCHEMATIC_SERVICE_ACCT_CREDS }}

      - name: Set Configurations for Data Model
        shell: bash
        run: |
          source .venv/bin/activate
          # download the data models and create config.json
          python3 .github/config_schema.py \
            -c schematic_config.yml \
            --service_repo 'Sage-Bionetworks/schematic'

      - name: zip virtual env
        shell: bash
        # ShinyApps has a limit of 7000 files, far exceeded by the many Python dependencies
        # that this app' has.  As a workaround we zip the virtual environment and later
        # unzip it in 'global.R'
        run: |
          zip -rm .venv.zip .venv

      - name: Authorize and deploy app
        shell: Rscript {0}
        run: |
          # if there is a tag, 'refName' will be tag name
          repo <- Sys.getenv("GITHUB_REPOSITORY")
          appName <- "include-dcc-data-curator"
          refName <- Sys.getenv("GITHUB_REF_NAME")
          # if tag is v*.*.*, deploy to prod, if main to staging, otherwise to test
          if (grepl("v[0-9]+.[0-9]+.[0-9]+", refName)) {
            message("Deploying release version of app")
          } else if (refName == "main") {
            appName <- paste(appName, "staging", sep = "-")
            message("Deploying staging version of app")
          } else {
            appName <- paste(appName, "testing", sep = "-")
            message("Deploying testing version of app")
          }
          message(sprintf("Deploying to %s instance.", appName))
          rsConnectUser <- "${{ secrets.RSCONNECT_USER }}"
          rsConnectToken <- "${{ secrets.RSCONNECT_TOKEN }}"
          rsConnectSecret <- "${{ secrets.RSCONNECT_SECRET }}"
          # create config file
          config <- "CLIENT_ID: ${{ secrets.OAUTH_CLIENT_ID }}"
          config <- c(config, "CLIENT_SECRET: ${{ secrets.OAUTH_CLIENT_SECRET }}")
          appUrl <- sprintf("https://%s.shinyapps.io/%s", rsConnectUser, appName)
          config <- c(config, sprintf("APP_URL: %s", appUrl))
          configFileConn <- file("oauth_config.yml")
          tryCatch(
            writeLines(config, configFileConn),
            finally=close(configFileConn)
          )
          rsconnect::setAccountInfo(rsConnectUser, rsConnectToken, rsConnectSecret)
          rsconnect::deployApp(appName = appName)