noctua-models/.github/workflows/check-models.yml at a7077dbf8eb3d7e62614c831fb59783452695e2b · geneontology/noctua-models · GitHub

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name: Check modified models

on:
  push:
    branches: [master]

jobs:
  check-models:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 2

      - name: Get modified model files
        id: changed
        run: |
          files=$(git diff --name-only --diff-filter=ACMR HEAD~1 HEAD -- 'models/*.ttl' | tr '\n' ' ')
          echo "files=$files" >> "$GITHUB_OUTPUT"

      - name: Set up Java
        if: steps.changed.outputs.files != ''
        uses: actions/setup-java@v4
        with:
          distribution: temurin
          java-version: '21'

      - name: Install Jena
        if: steps.changed.outputs.files != ''
        run: |
          wget -q https://archive.apache.org/dist/jena/binaries/apache-jena-6.0.0.tar.gz
          tar xzf apache-jena-6.0.0.tar.gz
          echo "$PWD/apache-jena-6.0.0/bin" >> "$GITHUB_PATH"

      - name: Run SPARQL checks
        if: steps.changed.outputs.files != ''
        env:
          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        run: |
          for model in ${{ steps.changed.outputs.files }}; do
            for query in sparql/*.rq; do
              query_name=$(basename "$query")

              # Run query on current version, stripping \r from CSV output
              csv_current=$(arq --data="$model" --query="$query" --results=csv 2>/dev/null | tr -d '\r')
              header=$(echo "$csv_current" | head -1)
              current_rows=$(echo "$csv_current" | tail -n +2 | grep -v '^$' || true)

              # Run query on previous version of model
              prev_ttl=$(mktemp --suffix=.ttl)
              if git show HEAD~1:"$model" > "$prev_ttl" 2>/dev/null; then
                prev_rows=$(arq --data="$prev_ttl" --query="$query" --results=csv 2>/dev/null | tr -d '\r' | tail -n +2 | grep -v '^$' || true)
              else
                prev_rows=""
              fi
              rm -f "$prev_ttl"

              # Find rows present in current but not in previous
              new_rows=$(comm -23 \
                <(echo "$current_rows" | grep -v '^$' | sort) \
                <(echo "$prev_rows" | grep -v '^$' | sort))

              if [ -n "$new_rows" ]; then
                md_table=$(printf '%s\n%s' "$header" "$new_rows" | awk -F',' '
                  NR==1 {
                    printf "| "
                    for (i=1; i<=NF; i++) printf "%s | ", $i
                    printf "\n| "
                    for (i=1; i<=NF; i++) printf "--- | "
                    printf "\n"
                  }
                  NR>1 {
                    printf "| "
                    for (i=1; i<=NF; i++) printf "%s | ", $i
                    printf "\n"
                  }
                ')

                title="Model check failed: ${query_name} on $(basename "$model")"
                body=$(cat <<EOF
          **Query:** \`${query_name}\`
          **Model:** \`${model}\`
          **Commit:** ${{ github.sha }}

          **New results:**

          ${md_table}
          EOF
                )
                gh issue create \
                  --title "$title" \
                  --body "$body" \
                  --assignee balhoff,kltm,vanaukenk,pgaudet
              fi
            done
          done