Main pr4 #80
Workflow file for this run
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| name: After Validate Submission Workflow | |
| on: | |
| #workflow_run: | |
| # workflows: ["Hub Submission Validation (R)"] # The name of the workflow we want to trigger from | |
| # types: | |
| # - completed | |
| pull_request_target: | |
| types: | |
| - closed | |
| jobs: | |
| copy-files-to-rsv-data-repo: | |
| runs-on: ubuntu-latest | |
| # if: ${{ github.event.workflow_run.conclusion == 'success' }} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| if: github.event.pull_request.merged == true | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| install-r: false | |
| use-public-rspm: true | |
| - name: Get list of changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v44 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Print changed files | |
| run: | | |
| echo 'Changed files: ${{ steps.changed-files.outputs.added_files }}' | |
| echo 'Modified files: ${{ steps.changed-files.outputs.modified_files }}' | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev | |
| - name: Cache R packages | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ hashFiles('DESCRIPTION') }} | |
| restore-keys: ${{ runner.os }}-r- | |
| - name: Install gh package | |
| run: Rscript -e 'install.packages("gh")' | |
| - name: Install here package | |
| run: Rscript -e 'install.packages("here")' | |
| - name: Install readr package | |
| run: Rscript -e 'install.packages("readr")' | |
| - name: Install lubridate package | |
| run: Rscript -e 'install.packages("lubridate")' | |
| - name: Install ggridges package | |
| run: Rscript -e 'install.packages("ggridges")' | |
| - name: Install forcats package | |
| run: Rscript -e 'install.packages("forcats")' | |
| - name: Install arrow package | |
| run: Rscript -e 'install.packages("arrow")' | |
| - name: Install dplyr package | |
| run: Rscript -e 'install.packages("dplyr")' | |
| - name: Install jsonlite package | |
| run: Rscript -e 'install.packages("jsonlite")' | |
| - name: Install purrr package | |
| run: Rscript -e 'install.packages("purrr")' | |
| - name: Install hubViz | |
| run: | | |
| Rscript -e 'install.packages("remotes")' | |
| Rscript -e 'remotes::install_github("Infectious-Disease-Modeling-Hubs/hubVis")' | |
| - name: Install hubUtils | |
| run: | | |
| Rscript -e 'remotes::install_github("kjsato/hubUtils@enhancement/v3-utils", upgrade = "never")' | |
| - name: Install hubEnsembles | |
| run: | | |
| Rscript -e 'remotes::install_github("Infectious-Disease-Modeling-Hubs/hubEnsembles")' | |
| - name: Install hubData | |
| run: | | |
| Rscript -e 'remotes::install_github("kjsato/hubData@feature/handle-samples", upgrade = "never")' | |
| - name: Check if RETRO files are present | |
| id: check_files | |
| run: | | |
| echo 'retro='$(echo '${{ steps.changed-files.outputs.added_files }} ${{ steps.changed-files.outputs.modified_files }}' | tr ' ' '\n' | grep 'model-output' | grep '.*-RETRO.*\.\(csv\|parquet\)'| grep -v '\.github/') >> $GITHUB_ENV | |
| echo 'conventional='$(echo '${{ steps.changed-files.outputs.added_files }} ${{ steps.changed-files.outputs.modified_files }}' | tr ' ' '\n' | grep -v '\.github/' | grep -c -v '.*-RETRO.*\.\(csv\|parquet\)') >> $GITHUB_ENV | |
| - name: Run R script | |
| run: | | |
| cd ./scripts | |
| Rscript ensemble.R | |
| if: ${{ env.conventional != '0' }} | |
| - name: Run retro_ensemble.R | |
| run: | | |
| cd ./scripts | |
| for file in $(echo '${{ steps.changed-files.outputs.added_files }} ${{ steps.changed-files.outputs.modified_files }}' | tr ' ' '\n' | grep 'model-output' | grep '.*-RETRO.*\.\(csv\|parquet\)'| grep -v '\.github/'); do | |
| echo "Processing file: $file" | |
| Rscript retro_ensemble.R $file | |
| done | |
| if: ${{ env.retro != '0' }} | |
| - name: Commit and push new files to root repository | |
| run: | | |
| git config user.name "github-actions[bot]" | |
| git config user.email "41898282+github-actions[bot]@users.noreply.github.com" | |
| if [ -n "$(git status --porcelain)" ]; then | |
| git add model-output/hub-ensemble/* | |
| git commit -m "Upload new files to RSV data repo by ${GITHUB_ACTOR} in #${{ github.event.pull_request.number }}" | |
| git push | |
| echo "Data for hub-ensemble uploaded to root repo"; | |
| else | |
| echo "no upload for root repo"; | |
| fi | |
| shell: bash | |
| - name: Checkout and push to another repository | |
| uses: actions/checkout@v2 | |
| with: | |
| repository: HopkinsIDD/rsv-forecast-hub_data | |
| #repository: kjsato/rsv-forecast-hub_data | |
| token: ${{ secrets.KJ3_PATC }} | |
| path: ./rsv-forecast-hub_data | |
| fetch-depth: 2 | |
| ref: main | |
| - name: Copy new files | |
| run: | | |
| for FILE in model-output/**/* model-metadata/*; do | |
| if [ -f "$FILE" ]; then | |
| mkdir -p ./rsv-forecast-hub_data/$(dirname $FILE) | |
| cp $FILE ./rsv-forecast-hub_data/$FILE | |
| fi | |
| done | |
| - name: Commit and push new files | |
| run: | | |
| cd ./rsv-forecast-hub_data | |
| git config user.name "github-actions[bot]" | |
| git config user.email "41898282+github-actions[bot]@users.noreply.github.com" | |
| git pull origin main | |
| if [ -n "$(git status --porcelain)" ]; then | |
| git add . | |
| git commit -m "Upload new files to RSV data repo by ${GITHUB_ACTOR} in #${{ github.event.pull_request.number }}" | |
| git push | |
| echo "RSV data uploaded"; | |
| else | |
| echo "no upload"; | |
| fi | |
| shell: bash |