data-pipeline.yaml

name: Peskas Zanzibar Data Pipeline

on:
  push:
  schedule:
    - cron:  '0 0 */2 * *'

env:
  WCS_SURVEYS_ID: ${{ secrets.WCS_SURVEYS_ID }}
  WCS_SURVEYS_UNAME: ${{ secrets.WCS_SURVEYS_UNAME }}
  WCS_SURVEYS_PSSW: ${{ secrets.WCS_SURVEYS_PSSW }}
  GCP_SA_KEY: ${{ secrets.PESKAS_DATAINGESTION_GCS_KEY }}
jobs:
  build-container:
    name: Build R container
    runs-on: ubuntu-20.04
    steps:
      - name: Checkout repository
        uses: actions/checkout@v2
      - name: Build image with cache
        id: build-docker
        uses: whoan/docker-build-with-cache-action@v5
        with:
          username: $GITHUB_ACTOR
          password: "${{ secrets.GITHUB_TOKEN }}"
          registry: docker.pkg.github.com
          image_name: r-runner-peskas-zanzibar
          dockerfile: Dockerfile.prod

  ingest-wcs-surveys:
    name: Ingest WCS kobo surveys
    needs: build-container
    runs-on: ubuntu-20.04
    container:
      image: docker.pkg.github.com/worldfishcenter/peskas.zanzibar.data.pipeline/r-runner-peskas-zanzibar
      credentials:
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}
    steps:
      - name: Set env to production
        if: endsWith(github.ref, '/main')
        run: echo "R_CONFIG_ACTIVE=production" >> $GITHUB_ENV
      - name: Call ingest_wcs_surveys()
        run: Rscript -e 'peskas.zanzibar.data.pipeline::ingest_wcs_surveys()'

  preprocess-wcs-surveys:
    name: Preprocess WCS kobo surveys
    needs: ingest-wcs-surveys
    runs-on: ubuntu-20.04
    container:
      image: docker.pkg.github.com/worldfishcenter/peskas.zanzibar.data.pipeline/r-runner-peskas-zanzibar
      credentials:
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}
    steps:
      - name: Set env to production
        if: endsWith(github.ref, '/main')
        run: echo "R_CONFIG_ACTIVE=production" >> $GITHUB_ENV
      - name: Call preprocess_wcs_surveys()
        run: Rscript -e 'peskas.zanzibar.data.pipeline::preprocess_wcs_surveys()'