MicrobiomeProfiler/.github/workflows/update_external_data.yml at devel · YuLab-SMU/MicrobiomeProfiler · GitHub

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name: Update External Data

on:
  schedule:
    - cron: "0 0 1 * *"
  workflow_dispatch:

jobs:
  update-external-data:
    runs-on: ubuntu-latest
    permissions:
      contents: write

    steps:
      - name: Checkout main branch
        uses: actions/checkout@v4
        with:
          path: repo

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: "release"
          use-public-rspm: true

      - name: Setup dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          working-directory: repo
          extra-packages: any::pkgload, any::jsonlite, any::digest, bioc::bugsigdbr

      - name: Build BugSigDB artifact
        working-directory: repo
        run: >
          Rscript -e 'source("data-raw/build_bugsigdb.R");
          build_bugsigdb_artifact(
            output_dir = "build/external-data/bugsigdb/current",
            base_url = "https://yulab-smu.github.io/MicrobiomeProfiler/datasets/bugsigdb/current"
          )'

      - name: Build eggNOG artifact
        working-directory: repo
        run: >
          Rscript -e 'source("data-raw/build_eggnog.R");
          build_eggnog_artifact(
            output_dir = "build/external-data/eggnog/current",
            base_url = "https://yulab-smu.github.io/MicrobiomeProfiler/datasets/eggnog/current"
          )'

      - name: Build Disbiome artifact
        id: build_disbiome
        continue-on-error: true
        working-directory: repo
        run: >
          Rscript -e 'source("data-raw/build_disbiome.R");
          build_disbiome_artifact(
            output_dir = "build/external-data/disbiome/current",
            base_url = "https://yulab-smu.github.io/MicrobiomeProfiler/datasets/disbiome/current",
            timeout = 600
          )'

      - name: Report partial dataset update
        if: always()
        run: |
          if [ "${{ steps.build_disbiome.outcome }}" != "success" ]; then
            echo "::warning::Disbiome artifact update failed; keeping the previously published gh-pages version."
          fi

      - name: Prepare gh-pages worktree
        working-directory: repo
        run: |
          rm -rf ../gh-pages
          if git ls-remote --exit-code --heads origin gh-pages; then
            git fetch origin gh-pages
            git worktree add -B gh-pages ../gh-pages origin/gh-pages
          else
            git worktree add --detach ../gh-pages
            cd ../gh-pages
            git checkout --orphan gh-pages
            git rm -rf . >/dev/null 2>&1 || true
          fi

      - name: Publish external data staging
        working-directory: repo
        run: >
          Rscript -e 'source("data-raw/publish_external_data.R");
          publish_external_data(
            source_root = "build/external-data",
            gh_pages_dir = "../gh-pages"
          )'

      - name: Commit and push gh-pages updates
        working-directory: gh-pages
        run: |
          git config --local user.name "github-actions[bot]"
          git config --local user.email "github-actions[bot]@users.noreply.github.com"
          git add datasets index.json latest.json
          if git diff --staged --quiet; then
            echo "No external data changes to publish"
          else
            git commit -m "chore: update external data artifacts"
            git push origin HEAD:gh-pages
          fi