import.yaml

name: import data

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

jobs:
  biotools:
    runs-on: ubuntu-latest
    outputs:
      commit_hash: ${{ steps.commit-and-push-biotools.outputs.commit_hash }}
    steps:
    - name: checkout contents repository
      uses: actions/checkout@v4
      with:
        ref: ${{ github.ref }}
    - name: delete previous import branch
      run: |
        branch_name="biotools-import-branch"
        # Check if the branch exists on the remote repository
        if git rev-parse --verify --quiet "origin/$branch_name"; then
          # The branch exists, so it can be safely deleted
          git push origin --delete "$branch_name"
          echo "Branch $branch_name has been deleted."
        else
          # The branch does not exist
          echo "Branch $branch_name does not exist on the remote repository."
        fi
    - name: Create and checkout feature branch
      run: git checkout -b biotools-import-branch
    - name: import bio.tools data from server
      uses: research-software-ecosystem/utils/biotools-import@main
      with:
        repo-user: ${{ secrets.GITHUB_USER }}
        repo-token: ${{ secrets.GITHUB_TOKEN }}
    - name: Commit and Push Changes
      id: commit-and-push-biotools
      uses: stefanzweifel/git-auto-commit-action@v5
      with:
        commit_user_name: Tools Platform Ecosystem bot
        commit_user_email: tpe-bot@github.com
        commit_author: Tools Platform Ecosystem bot <tpe-bot@github.com>
        commit_message: import bio.tools data
        branch: biotools-import-branch
        create_branch: true
  openebench:
    runs-on: ubuntu-latest
    outputs:
      commit_hash: ${{ steps.commit-and-push-openebench.outputs.commit_hash }}
    steps:
    - name: checkout contents repository
      uses: actions/checkout@v4
      with:
        ref: ${{ github.ref }}
    - name: delete previous import branch
      run:  |
        branch_name="openebench-import-branch"
        # Check if the branch exists on the remote repository
        if git rev-parse --verify --quiet "origin/$branch_name"; then
          # The branch exists, so it can be safely deleted
          git push origin --delete "$branch_name"
          echo "Branch $branch_name has been deleted."
        else
          # The branch does not exist
          echo "Branch $branch_name does not exist on the remote repository."
        fi
    - name: Create and checkout feature branch
      run: git checkout -b openebench-import-branch
    - name: import OpenEBench data from server
      uses: research-software-ecosystem/utils/openebench-import@main
      with:
        repo-user: ${{ secrets.GITHUB_USER }}
        repo-token: ${{ secrets.GITHUB_TOKEN }}
    - name: Commit and Push Changes
      id: commit-and-push-openebench
      uses: stefanzweifel/git-auto-commit-action@v5
      with:
        commit_user_name: Tools Platform Ecosystem bot
        commit_user_email: tpe-bot@github.com
        commit_author: Tools Platform Ecosystem bot <tpe-bot@github.com>
        commit_message: import OpenEBench data
        branch: openebench-import-branch
        create_branch: true
  bioconda:
    runs-on: ubuntu-latest
    outputs:
      commit_hash: ${{ steps.commit-and-push-bioconda.outputs.commit_hash }}
    steps:
    - name: checkout contents repository
      uses: actions/checkout@v4
      with:
        ref: ${{ github.ref }}
    - name: delete previous import branch
      run:  |
        branch_name="bioconda-import-branch"
        # Check if the branch exists on the remote repository
        if git rev-parse --verify --quiet "origin/$branch_name"; then
          # The branch exists, so it can be safely deleted
          git push origin --delete "$branch_name"
          echo "Branch $branch_name has been deleted."
        else
          # The branch does not exist
          echo "Branch $branch_name does not exist on the remote repository."
        fi
    - name: Create and checkout feature branch
      run: git checkout -b bioconda-import-branch
    - name: import bioconda data from server
      uses: research-software-ecosystem/utils/bioconda-import@main
      with:
        repo-user: ${{ secrets.GITHUB_USER }}
        repo-token: ${{ secrets.GITHUB_TOKEN }}
    - name: Commit and Push Changes
      id: commit-and-push-bioconda
      uses: stefanzweifel/git-auto-commit-action@v5
      with:
        commit_user_name: Tools Platform Ecosystem bot
        commit_user_email: tpe-bot@github.com
        commit_author: Tools Platform Ecosystem bot <tpe-bot@github.com>
        commit_message: import bioconda data
        branch: bioconda-import-branch
        create_branch: true
  biii:
    runs-on: ubuntu-latest
    outputs:
      commit_hash: ${{ steps.commit-and-push-biii.outputs.commit_hash }}
    steps:
    - name: checkout contents repository
      uses: actions/checkout@v4
      with:
        ref: ${{ github.ref }}
    - name: delete previous import branch
      run:  |
        branch_name="biii-import-branch"
        # Check if the branch exists on the remote repository
        if git rev-parse --verify --quiet "origin/$branch_name"; then
          # The branch exists, so it can be safely deleted
          git push origin --delete "$branch_name"
          echo "Branch $branch_name has been deleted."
        else
          # The branch does not exist
          echo "Branch $branch_name does not exist on the remote repository."
        fi
    - name: Create and checkout feature branch
      run: git checkout -b biii-import-branch
    - name: import biii data from server
      uses: research-software-ecosystem/utils/biii-import@main
      with:
        repo-user: ${{ secrets.GITHUB_USER }}
        repo-token: ${{ secrets.GITHUB_TOKEN }}
    - name: Commit and Push Changes
      id: commit-and-push-biii
      uses: stefanzweifel/git-auto-commit-action@v5
      with:
        commit_user_name: Tools Platform Ecosystem bot
        commit_user_email: tpe-bot@github.com
        commit_author: Tools Platform Ecosystem bot <tpe-bot@github.com>
        branch: biii-import-branch
        create_branch: true
  biocontainers:
    runs-on: ubuntu-latest
    outputs:
      commit_hash: ${{ steps.commit-and-push-biocontainers.outputs.commit_hash }}
    steps:
    - name: checkout contents repository
      uses: actions/checkout@v4
      with:
        ref: ${{ github.ref }}
    - name: delete previous import branch
      run: |
        branch_name="biocontainers-import-branch"
        # Check if the branch exists on the remote repository
        if git rev-parse --verify --quiet "origin/$branch_name"; then
          # The branch exists, so it can be safely deleted
          git push origin --delete "$branch_name"
          echo "Branch $branch_name has been deleted."
        else
          # The branch does not exist
          echo "Branch $branch_name does not exist on the remote repository."
        fi
    - name: Create and checkout feature branch
      run: git checkout -b biocontainers-import-branch
    - name: import biocontainers data from server
      uses: research-software-ecosystem/utils/biocontainers-import@main
      with:
        repo-user: ${{ secrets.GITHUB_USER }}
        repo-token: ${{ secrets.GITHUB_TOKEN }}
    - name: Commit and Push Changes
      id: commit-and-push-biocontainers
      uses: stefanzweifel/git-auto-commit-action@v5
      with:
        commit_user_name: Tools Platform Ecosystem bot
        commit_user_email: tpe-bot@github.com
        commit_author: Tools Platform Ecosystem bot <tpe-bot@github.com>
        commit_message: import biocontainers data
        branch: biocontainers-import-branch
        create_branch: true
  galaxytool:
    runs-on: ubuntu-latest
    outputs:
      commit_hash: ${{ steps.commit-and-push-galaxytool.outputs.commit_hash }}
    steps:
    - name: checkout contents repository
      uses: actions/checkout@v4
      with:
        ref: ${{ github.ref }}
    - name: delete previous import branch
      run: |
        branch_name="galaxytool-import-branch"
        # Check if the branch exists on the remote repository
        if git rev-parse --verify --quiet "origin/$branch_name"; then
          # The branch exists, so it can be safely deleted
          git push origin --delete "$branch_name"
          echo "Branch $branch_name has been deleted."
        else
          # The branch does not exist
          echo "Branch $branch_name does not exist on the remote repository."
        fi
    - name: Create and checkout feature branch
      run: git checkout -b galaxytool-import-branch
    - name: import galaxy tool data from server
      uses: research-software-ecosystem/utils/galaxytool-import@main
      with:
        repo-user: ${{ secrets.GITHUB_USER }}
        repo-token: ${{ secrets.GITHUB_TOKEN }}
    - name: Commit and Push Changes
      id: commit-and-push-galaxytool
      uses: stefanzweifel/git-auto-commit-action@v5
      with:
        commit_user_name: Tools Platform Ecosystem bot
        commit_user_email: tpe-bot@github.com
        commit_author: Tools Platform Ecosystem bot <tpe-bot@github.com>
        commit_message: import galaxy tools data
        branch: galaxytool-import-branch
        create_branch: true
  debian-med:
    runs-on: ubuntu-latest
    outputs:
      commit_hash: ${{ steps.commit-and-push-debianmed.outputs.commit_hash }}
    steps:
    - name: checkout contents repository
      uses: actions/checkout@v4
      with:
        ref: ${{ github.ref }}
    - name: delete previous import branch
      run: |
        branch_name="debianmed-import-branch"
        # Check if the branch exists on the remote repository
        if git rev-parse --verify --quiet "origin/$branch_name"; then
          # The branch exists, so it can be safely deleted
          git push origin --delete "$branch_name"
          echo "Branch $branch_name has been deleted."
        else
          # The branch does not exist
          echo "Branch $branch_name does not exist on the remote repository."
        fi
    - name: Create and checkout feature branch
      run: git checkout -b debianmed-import-branch
    - name: import Debian Med data
      uses: research-software-ecosystem/utils/debian-med-import@main
      with:
        repo-user: ${{ secrets.GITHUB_USER }}
        repo-token: ${{ secrets.GITHUB_TOKEN }}
    - name: Commit and Push Changes
      id: commit-and-push-debianmed
      uses: stefanzweifel/git-auto-commit-action@v5
      with:
        commit_user_name: Tools Platform Ecosystem bot
        commit_user_email: tpe-bot@github.com
        commit_author: Tools Platform Ecosystem bot <tpe-bot@github.com>
        commit_message: import Debian Med tools data
        branch: debianmed-import-branch
        create_branch: true
  bioconductor:
    runs-on: ubuntu-latest
    outputs:
      commit_hash: ${{ steps.commit-and-push-bioconductor.outputs.commit_hash }}
    steps:
    - name: checkout contents repository
      uses: actions/checkout@v4
      with:
        ref: ${{ github.ref }}
    - name: delete previous import branch
      run: |
        branch_name="bioconductor-import-branch"
        # Check if the branch exists on the remote repository
        if git rev-parse --verify --quiet "origin/$branch_name"; then
          # The branch exists, so it can be safely deleted
          git push origin --delete "$branch_name"
          echo "Branch $branch_name has been deleted."
        else
          # The branch does not exist
          echo "Branch $branch_name does not exist on the remote repository."
        fi
    - name: Create and checkout feature branch
      run: git checkout -b bioconductor-import-branch
    - name: import BioConductor data
      uses: research-software-ecosystem/utils/bioconductor-import@main
      with:
        repo-user: ${{ secrets.GITHUB_USER }}
        repo-token: ${{ secrets.GITHUB_TOKEN }}
    - name: Commit and Push Changes
      id: commit-and-push-bioconductor
      uses: stefanzweifel/git-auto-commit-action@v5
      with:
        commit_user_name: Tools Platform Ecosystem bot
        commit_user_email: tpe-bot@github.com
        commit_author: Tools Platform Ecosystem bot <tpe-bot@github.com>
        commit_message: import BioConductor tools data
        branch: bioconductor-import-branch
        create_branch: true
  merge:
    runs-on: ubuntu-latest
    needs:
      - biotools
      - openebench
      - bioconda
      - biii
      - biocontainers
      - galaxytool
      - debian-med
      - bioconductor
    if: always()
    steps:
      - name: Checkout Repository
        uses: actions/checkout@v4
      - name: Merge feature branches
        run: |
          git config --local user.email "tpe-bot@github.com"
          git config --local user.name "Tools Platform Ecosystem bot"
          merge_branch_if_exists() {
            local branch_name="$1"
            # Check if the branch exists on the remote repository
            if git ls-remote --exit-code --heads origin "$branch_name" &>/dev/null; then
              # The branch exists on the remote, so it can be safely merged
              git fetch origin "$branch_name"
              git merge "origin/$branch_name"
              echo "Merged $branch_name into the current branch."
            else
              # The branch does not exist on the remote
              echo "Branch $branch_name does not exist on the remote repository."
            fi
          }
          merge_branch_if_exists "biotools-import-branch"
          merge_branch_if_exists "openebench-import-branch"
          merge_branch_if_exists "bioconda-import-branch"
          merge_branch_if_exists "biii-import-branch"
          merge_branch_if_exists "biocontainers-import-branch"
          merge_branch_if_exists "galaxytool-import-branch"
          merge_branch_if_exists "debianmed-import-branch"
          merge_branch_if_exists "bioconductor-import-branch"
          git push origin master
  clean-branches:
    runs-on: ubuntu-latest
    needs:
      - merge
    if: always()
    steps:
      - name: Checkout Repository
        uses: actions/checkout@v4
      - name: Delete feature branches
        run: |
          git config --local user.email "tpe-bot@github.com"
          git config --local user.name "Tools Platform Ecosystem bot"
          delete_branch_if_exists() {
            local branch_name="$1"
            # Check if the branch exists on the remote repository
            if git ls-remote --exit-code --heads origin "$branch_name" &>/dev/null; then
              # The branch exists on the remote, so it can be deleted
              git push origin --delete "$branch_name"
              echo "Deleted $branch_name into the current branch."
            else
              # The branch does not exist on the remote
              echo "Branch $branch_name does not exist on the remote repository."
            fi
          }
          delete_branch_if_exists "biotools-import-branch"
          delete_branch_if_exists "openebench-import-branch"
          delete_branch_if_exists "bioconda-import-branch"
          delete_branch_if_exists "biii-import-branch"
          delete_branch_if_exists "biocontainers-import-branch"
          delete_branch_if_exists "galaxytool-import-branch"
          delete_branch_if_exists "debianmed-import-branch"
          delete_branch_if_exists "bioconductor-import-branch"