Peskas Timor Data Pipeline #2078
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| name: Peskas Timor Data Pipeline | |
| on: | |
| push: | |
| schedule: | |
| - cron: '0 0 */2 * *' | |
| env: | |
| KOBO_PASSWORD: ${{ secrets.KOBO_PASSWORD }} | |
| KOBO_USERNAME: ${{ secrets.KOBO_USERNAME }} | |
| KOBO_PESKAS1: ${{ secrets.KOBO_PESKAS1 }} | |
| KOBO_PESKAS2: ${{ secrets.KOBO_PESKAS2 }} | |
| KOBO_PESKAS3: ${{ secrets.KOBO_PESKAS3 }} | |
| GCP_SA_KEY: ${{ secrets.PESKAS_DATAINGESTION_GCS_KEY }} | |
| AIRTABLE_KEY: ${{ secrets.AIRTABLE_KEY }} | |
| PDS_TOKEN: ${{ secrets.PESKAS_PDS_TOKEN }} | |
| PDS_SECRET: ${{ secrets.PESKAS_PDS_SECRET }} | |
| VALID_SHEET_ID: ${{ secrets.VALID_SHEET_ID }} | |
| GOOGLE_SHEET_ID: ${{ secrets.GOOGLE_SHEET_ID }} | |
| 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-timor | |
| dockerfile: Dockerfile.prod | |
| ingest-preprocess-metadata-tables: | |
| name: Ingest metadata tables | |
| needs: build-container | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.timor.data.pipeline/r-runner-peskas-timor | |
| 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_metadata_tables() | |
| run: Rscript -e 'peskas.timor.data.pipeline::ingest_metadata_tables()' | |
| - name: Call preprocess_metadata_tables() | |
| run: Rscript -e 'peskas.timor.data.pipeline::preprocess_metadata_tables()' | |
| - name: Call ingest_rfish_table() | |
| continue-on-error: true | |
| run: Rscript -e 'peskas.timor.data.pipeline::ingest_rfish_table()' | |
| ingest-preprocess-landings-v1-v3: | |
| name: Ingest and preprocess legacy and ongoing landings | |
| needs: build-container | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.timor.data.pipeline/r-runner-peskas-timor | |
| 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.timor.data.pipeline::ingest_landings_v1v3()' | |
| - name: Call preprocess_legacy_landings() | |
| run: Rscript -e 'peskas.timor.data.pipeline::preprocess_legacy_landings()' | |
| - name: Call preprocess_updated_landings() | |
| run: Rscript -e 'peskas.timor.data.pipeline::preprocess_updated_landings()' | |
| ingest-preprocess-v2-landings-step1: | |
| name: "Ingest-process landings 1/2" | |
| needs: build-container | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.timor.data.pipeline/r-runner-peskas-timor | |
| 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_v2() | |
| run: Rscript -e 'peskas.timor.data.pipeline::ingest_landings_v2()' | |
| - name: Call preprocess_landings_step_1() | |
| run: Rscript -e 'peskas.timor.data.pipeline::preprocess_landings_step_1()' | |
| ingest-preprocess-v2-landings-step2: | |
| name: "Ingest-process landings 2/2" | |
| needs: ingest-preprocess-v2-landings-step1 | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.timor.data.pipeline/r-runner-peskas-timor | |
| 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_step_2() | |
| run: Rscript -e 'peskas.timor.data.pipeline::preprocess_landings_step_2()' | |
| merge-landings: | |
| name: Merge landings | |
| needs: [ingest-preprocess-v2-landings-step2, ingest-preprocess-landings-v1-v3, ingest-preprocess-metadata-tables] | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.timor.data.pipeline/r-runner-peskas-timor | |
| 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 merge_landings() | |
| run: Rscript -e 'peskas.timor.data.pipeline::merge_landings()' | |
| - name: Call calculate_weights() | |
| run: Rscript -e 'peskas.timor.data.pipeline::calculate_weights()' | |
| validate-landings: | |
| name: Validate landings | |
| needs: [merge-landings] | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.timor.data.pipeline/r-runner-peskas-timor | |
| 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.timor.data.pipeline::validate_landings()' | |
| - name: Test validated landings | |
| run: Rscript -e 'tinytest::run_test_file(system.file("tinytest/test_validated_landings.R", package = "peskas.timor.data.pipeline"))' | |
| ingest-pds-data: | |
| name: Ingest pds data | |
| needs: build-container | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.timor.data.pipeline/r-runner-peskas-timor | |
| 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_pds_trips() | |
| run: Rscript -e 'peskas.timor.data.pipeline::ingest_pds_trips()' | |
| - name: Call ingest_pds_tracks() | |
| run: Rscript -e 'peskas.timor.data.pipeline::ingest_pds_tracks()' | |
| preprocess-pds-data: | |
| name: Preprocess pds data | |
| needs: [ingest-pds-data] | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.timor.data.pipeline/r-runner-peskas-timor | |
| 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_pds_trips() | |
| run: Rscript -e 'peskas.timor.data.pipeline::preprocess_pds_trips()' | |
| - name: Call preprocess_pds_tracks() | |
| run: Rscript -e 'peskas.timor.data.pipeline::preprocess_pds_tracks()' | |
| validate-pds-data: | |
| name: Validate pds data | |
| needs: preprocess-pds-data | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.timor.data.pipeline/r-runner-peskas-timor | |
| 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 validate_pds_trips() | |
| run: Rscript -e 'peskas.timor.data.pipeline::validate_pds_trips()' | |
| - name: Test validated PDS trips | |
| run: Rscript -e 'tinytest::run_test_file(system.file("tinytest/test_validated_pds_trips.R", package = "peskas.timor.data.pipeline"))' | |
| merge-trips: | |
| name: Merge trips | |
| needs: [validate-landings, validate-pds-data] | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.timor.data.pipeline/r-runner-peskas-timor | |
| 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 merge_trips() | |
| run: Rscript -e 'peskas.timor.data.pipeline::merge_trips()' | |
| - name: Test merged_trips | |
| run: Rscript -e 'tinytest::run_test_file(system.file("tinytest/test_merged_trips.R", package = "peskas.timor.data.pipeline"))' | |
| model-indicators: | |
| name: Estimate fishery indicators | |
| needs: [merge-trips] | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.timor.data.pipeline/r-runner-peskas-timor | |
| 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 estimate_fishery_indicators() | |
| run: Rscript -e 'peskas.timor.data.pipeline::estimate_fishery_indicators()' | |
| export-trips: | |
| name: Export trips | |
| needs: [merge-trips, model-indicators] | |
| runs-on: ubuntu-20.04 | |
| container: | |
| image: docker.pkg.github.com/worldfishcenter/peskas.timor.data.pipeline/r-runner-peskas-timor | |
| 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 format_public_data() | |
| run: Rscript -e 'peskas.timor.data.pipeline::format_public_data()' | |
| - name: Test public data | |
| run: Rscript -e 'tinytest::run_test_file(system.file("tinytest/test_public_data.R", package = "peskas.timor.data.pipeline"))' | |
| - name: Generate and upload enumerators report | |
| run: Rscript -e 'source(system.file("report/generate_enumerators_report.R", package = "peskas.timor.data.pipeline"))' |