fix n_fishers validation typo + fix mongodb column ordering + add exp… #18
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| name: Peskas Malawi Data Pipeline | |
| on: | |
| push: | |
| schedule: | |
| - cron: '0 0 */2 * *' | |
| env: | |
| MALAWI_SSF: ${{ secrets.MALAWI_SSF }} | |
| FISHERIES_ECAS: ${{ secrets.FISHERIES_ECAS }} | |
| FIELDDATAAPP_2024: ${{ secrets.FIELDDATAAPP_2024 }} | |
| FIELDDATAAPP_2024A: ${{ secrets.FIELDDATAAPP_2024A }} | |
| FIELDDATAAPP_2023F: ${{ secrets.FIELDDATAAPP_2023F }} | |
| KOBO_USERNAME: ${{ secrets.KOBO_USERNAME }} | |
| KOBO_PASSWORD: ${{ secrets.KOBO_PASSWORD }} | |
| PDS_TOKEN: ${{ secrets.PDS_TOKEN }} | |
| PDS_SECRET: ${{ secrets.PDS_SECRET }} | |
| MONGODB_CONNECTION_STRING: ${{ secrets.MONGODB_CONNECTION_STRING }} | |
| GCP_SA_KEY: ${{ secrets.GCP_SA_KEY }} | |
| GOOGLE_SHEET_ID: ${{ secrets.GOOGLE_SHEET_ID }} | |
| jobs: | |
| build-container: | |
| name: Build R container | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - 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-malawi | |
| dockerfile: Dockerfile.prod | |
| ingest-landings: | |
| name: Ingest Malawi SSF landings | |
| needs: build-container | |
| runs-on: ubuntu-latest | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.malawi.data.pipeline/r-runner-peskas-malawi | |
| 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_landings() | |
| run: Rscript -e 'peskas.malawi.data.pipeline::ingest_landings()' | |
| preprocess-landings: | |
| name: Preprocess Malawi SSF landings | |
| needs: ingest-landings | |
| runs-on: ubuntu-latest | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.malawi.data.pipeline/r-runner-peskas-malawi | |
| 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_landings() | |
| run: Rscript -e 'peskas.malawi.data.pipeline::preprocess_landings()' | |
| validate-landings: | |
| name: Validate Malawi SSF landings | |
| needs: preprocess-landings | |
| runs-on: ubuntu-latest | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.malawi.data.pipeline/r-runner-peskas-malawi | |
| 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: Validate landings | |
| run: Rscript -e 'peskas.malawi.data.pipeline::validate_landings()' | |
| export-landings: | |
| name: Export Malawi SSF landings | |
| needs: preprocess-landings | |
| runs-on: ubuntu-latest | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.malawi.data.pipeline/r-runner-peskas-malawi | |
| 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: Export landings | |
| run: Rscript -e 'peskas.malawi.data.pipeline::export_landings()' | |