ci-lint-validate-convert.yml

name: Make JSON-LD and Build Dependencies Table

on:
  pull_request:
    branches: 'main'
    paths: 'HTAN.model.csv'
  release:
    types: [published]
  workflow_dispatch:

concurrency:
  group: ${{ github.workflow }}-${{ github.ref_type }}-${{ github.sha }}
  cancel-in-progress: true

env:
  SCHEMATIC_VERSION: '24.2.1'
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

jobs:
  lint:
    name: Lint CSV
    if: always()
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: csvlinter
      uses: kcheriyath/csvlinter@V0.6.0
      with:
        find_pattern: "*.csv"

  validate:
    name: Validate CSV
    if: always()
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: '3.10'
      - name: Install IPython
        run: |
          pip install ipython==8.18.1    
      - name: Install Schematic
        run: |
          pip install schematicpy==$SCHEMATIC_VERSION
      - name: Convert CSV schema
        run: |
          schematic schema convert .github/CSV.model.csv
      - name: Validate data model CSV
        run: |
          schematic model -c .github/CSV_schematic_config.yml validate -mp HTAN.model.csv -dt "DataModel" |
            grep "Your manifest has been validated successfully. There are no errors in your manifest, and it can be submitted without any modifications."

  convert:
    name: Convert CSV to JSON-LD
    needs:
      - lint
      - validate
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: '3.10'
      - name: Install IPython
        run: |
          pip install ipython==8.18.1
      - name: Install Schematic
        run: |
          pip install schematicpy==$SCHEMATIC_VERSION
      - name: Convert .csv to .jsonld
        run: |
          schematic schema convert HTAN.model.csv
      - name: Set up Git user
        run: |
          git config --local user.name "github-actions[bot]"
          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
      - name: Fetch PR details
        if: github.event_name == 'pull_request'
        uses: r-lib/actions/pr-fetch@v2
        with:
          repo-token: ${{ secrets.GITHUB_TOKEN }}
      - name: Commit the changes
        run: |
          git add HTAN.model.jsonld
          git commit -m "GitHub Action: convert *.model.csv to *.model.jsonld" || echo "No changes to commit"
      - name: Push changes back to PR
        if: github.event_name == 'pull_request'
        uses: r-lib/actions/pr-push@v2
        with:
          repo-token: ${{ secrets.GITHUB_TOKEN }}

  build-dependencies:
    name: Build Dependencies Table
    needs: convert
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v2

      - name: Fetch latest changes
        run: git pull origin main

      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: 3.8

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install requests pandas

      - name: Fetch attribute table
        run: |
          python - <<EOF
          import requests
          import pandas as pd

          url = "https://schematic.api.sagebionetworks.org/v1/ui/"  # Endpoint URL
          if "${{ github.event_name }}" == "pull_request":
              jsonld_url = "https://raw.githubusercontent.com/${{ github.repository }}/pull/${{ github.event.pull_request.number }}/head/HTAN.model.jsonld"
          else:
              jsonld_url = "https://raw.githubusercontent.com/${{ github.repository }}/main/HTAN.model.jsonld"
          
          response = requests.get(jsonld_url)
          response.raise_for_status()
          model_jsonld = response.json()

          response = requests.post(url, json=model_jsonld)
          response.raise_for_status()
          attribute_table = response.json()  # Adjust this line based on the actual response format

          df = pd.DataFrame(attribute_table)
          
          df.to_csv('HTAN.dependencies.csv', index=False)
          EOF

      - name: Commit changes
        run: |
          git config --global user.name "github-actions[bot]"
          git config --global user.email "github-actions[bot]@users.noreply.github.com"
          git add HTAN.dependencies.csv
          git commit -m "Update HTAN.dependencies.csv with the latest attribute table"

      - name: Create Pull Request
        if: github.event_name == 'pull_request'
        uses: r-lib/actions/pr-push@v2
        with:
          repo-token: ${{ secrets.GITHUB_TOKEN }}
      
      - name: Create Pull Request
        if: github.event_name != 'pull_request'
        uses: peter-evans/create-pull-request@v3
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          commit-message: "Update HTAN.dependencies.csv"
          branch: update-attribute-table
          title: "Update HTAN.dependencies.csv"
          body: "This PR updates HTAN.dependencies.csv with the latest attribute table."