tool_list_conversion.yml

name: Validation of the tools and page metadata
on:
  pull_request:
    branches: [ master, main ]
  schedule:
    - cron:  '0 13 * * 1'
  workflow_dispatch:

jobs:
  validation:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.8]
    steps:
      - name: Checkout
        uses: actions/checkout@v3
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install ruamel.yaml requests python-frontmatter
      - name: Run tool table 2 yaml
        run: | 
          python var/tools_validator.py
  
  registry-lookup:
    if: |
        github.repository_owner == 'elixir-europe' &&  github.event_name != 'pull_request'
  
    runs-on: ubuntu-latest

    strategy:
      matrix:
        python-version: [3.8]

    steps:
      - name: Checkout
        uses: actions/checkout@v3

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install ruamel.yaml requests python-frontmatter

      - name: Run regsitry lookup for the tools file
        run: | 
          python var/tools_validator.py --reg --username ${{ secrets.FAIRSHARING_USERNAME }} --password "${{ secrets.FAIRSHARING_PASSWORD }}"

      - name: Fetch country names with corresponding iso
        run: |
          python var/country_list.py

      - name: Show differences
        run: |
          git diff --stat

      - name: Create Pull Request
        id: cpr
        uses: peter-evans/create-pull-request@v3
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          commit-message: Update tool/resource_list.yaml
          title: 'Automatic tool/resource-list update'
          body: |
            This PR is automatically generated based on new links made between the tools and the registries: TeSS, Bio.tools and FAIRsharing.

            Please verify if these changes are valid.
          labels: |
            automatic PR
          reviewers: bedroesb
          branch: list_updates
          base: main

      - name: Check output
        run: |
          echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}"