automatic_rdata_update.yml

name: Update database collections

on:
  workflow_dispatch:
  schedule:
  - cron: "0 0 15 * *"

concurrency:
  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
  cancel-in-progress: true 

jobs:
  download-and-build:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v2
        with:
          submodules: true
          fetch-depth: 0
          ref: main
      - name: Fetch GMT files
        id: gmts
        run: |
          sudo apt-get update
          sudo apt-get install libcurl4-openssl-dev 
          shiny_run/scripts/fetch_gmts.sh     
        
      - name: Setup R
        uses: r-lib/actions/setup-r@v2

      - name: Install packages
        run: |
          install.packages(c("dplyr","magrittr","httr","jsonlite","BiocManager"))
          BiocManager::install("rWikiPathways", ask = FALSE)
        shell: Rscript {0}
        
      - name: Build database
        run: |
          Rscript -e "source('shiny_run/scripts/build_db_ghaction.R')"

      - name: Rotate and commit
        run: |
          git config --global user.name 'GitHub Action'
          git config --global user.email 'action@github.com'
          if [ "$(ls -A shiny_run/databases/temp)" ]; then
            git rm -f shiny_run/databases/archive/*.RData
            mkdir shiny_run/databases/archive
            git mv -f shiny_run/databases/*.RData shiny_run/databases/archive/
            mv shiny_run/databases/temp/*.RData shiny_run/databases/
            git add -f shiny_run/databases/*.RData
            git commit -m 'Update RData database collections'
            git push
          else 
            echo "No new RData files"
          fi