Merge pull request #93 from HopkinsIDD/main-check-fix #83
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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: ${{ runner.os }}-r- | ||
| - name: Install gh package | ||
| run: Rscript -e 'install.packages("gh")' | ||
| - name: Install here package | ||
| run: Rscript -e 'install.packages("here")' | ||
| - name: Install readr package | ||
| run: Rscript -e 'install.packages("readr")' | ||
| - name: Install lubridate package | ||
| run: Rscript -e 'install.packages("lubridate")' | ||
| - name: Install ggridges package | ||
| run: Rscript -e 'install.packages("ggridges")' | ||
| - name: Install forcats package | ||
| run: Rscript -e 'install.packages("forcats")' | ||
| - name: Install arrow package | ||
| run: Rscript -e 'install.packages("arrow")' | ||
| - name: Install dplyr package | ||
| run: Rscript -e 'install.packages("dplyr")' | ||
| - name: Install jsonlite package | ||
| run: Rscript -e 'install.packages("jsonlite")' | ||
| - name: Install purrr package | ||
| run: Rscript -e 'install.packages("purrr")' | ||
| - name: Install hubViz | ||
| run: | | ||
| Rscript -e 'install.packages("remotes")' | ||
| Rscript -e 'remotes::install_github("hubverse-org/hubVis")' | ||
| - name: Install hubUtils | ||
| run: | | ||
| Rscript -e 'remotes::install_github("kjsato/hubUtils@main-mr_schema", upgrade = "never")' | ||
| - name: Install hubEnsembles | ||
| run: | | ||
| Rscript -e 'remotes::install_github("hubverse-org/hubEnsembles")' | ||
| - name: Install hubData | ||
| run: | | ||
| Rscript -e 'remotes::install_github("kjsato/hubData@main-mr_schema", upgrade = "never")' | ||
| - name: Check if RETRO files are present | ||
| id: check_files | ||
| run: | | ||
| echo 'retro='$(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 -v '.*-RETRO.*\.\(csv\|parquet\)' | grep -c .) >> $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 ${{ github.event | ||
| .pull_request.user.login }} in #${{ 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 ${{ github.event | ||
| .pull_request.user.login }} in #${{ github.event.pull_request.number }}" | ||
| git push | ||
| echo "RSV data uploaded"; | ||
| else | ||
| echo "no upload"; | ||
| fi | ||
| shell: bash | ||
