test_releases.yml

name: Check and test upstream releases or updates

on:
  workflow_dispatch:
  push:
  pull_request: # tests whether it is working on PR
     paths:
     - '.github/workflows/test_releases.yml'
  schedule:
    - cron: "0 0 1,15 * *"  # Run the workflow on the 1st and 15th day of each month
permissions:
  contents: write
  pages: write
  id-token: write
  issues: write
jobs:
                          ################################ChEBI###########################
  check_new_data_chebi:
    runs-on: ubuntu-22.04
    name: Check ChEBI
    outputs:
      RELEASE_NUMBER: ${{ steps.check_download.outputs.RELEASE_NUMBER }}
      CURRENT_RELEASE_NUMBER: ${{ steps.check_download.outputs.CURRENT_RELEASE_NUMBER }}
      NEW_RELEASE: ${{ steps.check_download.outputs.NEW_RELEASE }}
      DATE_NEW: ${{ steps.check_download.outputs.DATE_NEW }}
      DATE_OLD: ${{ steps.check_download.outputs.DATE_OLD }}
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Check release date
        id: check_download
        run: bash scripts/check_release_date.sh chebi
  test_sdf_processing_chebi:
    name: Test and diff ChEBI
    if: needs.check_new_data.outputs.NEW_RELEASE
    needs: check_new_data_chebi
    env:
      RELEASE_NUMBER: ${{ needs.check_new_data_chebi.outputs.RELEASE_NUMBER }}
      DATE_OLD: ${{ needs.check_new_data_chebi.outputs.DATE_OLD }}
      DATE_NEW: ${{ needs.check_new_data_chebi.outputs.DATE_NEW }}
      CURRENT_RELEASE_NUMBER: ${{ needs.check_new_data_chebi.outputs.CURRENT_RELEASE_NUMBER }}
    runs-on: ubuntu-22.04
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
      - name: Install R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: '4.1' # Specify the R version
          include-recommended: true    
      - name: Set up Java
        uses: actions/setup-java@v4
        with:
          java-version: '11'
          distribution: 'temurin'
      - name: Download and test new release data
        run: bash scripts/test_new_release.sh chebi
      - name: Diff ChEBI
        if:
          ${{ env.FAILED == 'false' }}
        run: bash scripts/diff_release.sh chebi
        
      - name: 'Upload ChEBI artifact'
        uses: actions/upload-artifact@v4
        with:
          name: chebi_processed
          path: datasources/chebi/recentData/*

      - uses: JasonEtco/create-an-issue@v2
        if: ${{ env.COUNT != 0 }}
        name: Post issue about ChEBI update availability
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          SOURCE: ChEBI
        with:
          filename: .github/ISSUE_TEMPLATE/ISSUE_UPDATE.md   
          update_existing: true
          
      - uses: JasonEtco/create-an-issue@v2
        name: Post issue about ChEBI failing test
        if: ${{ env.FAILED == 'true' }}
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          SOURCE: ChEBI
        with:
          filename: .github/ISSUE_TEMPLATE/ISSUE_FAIL.md
          update_existing: true
  
                          ################################HGNC###########################
  check_new_data_hgnc:
    runs-on: ubuntu-22.04
    name: Check HGNC
    outputs:
      COMPLETE_NEW: ${{ steps.check_download.outputs.COMPLETE_NEW }}
      WITHDRAWN_NEW: ${{ steps.check_download.outputs.WITHDRAWN_NEW }}
      DATE_NEW: ${{ steps.check_download.outputs.DATE_NEW }}
      DATE_OLD: ${{ steps.check_download.outputs.DATE_OLD }}
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Check release date
        id: check_download
        run: bash scripts/check_release_date.sh hgnc
  test_processing_hgnc:
    name: Test and diff HGNC
    needs: check_new_data_hgnc
    env:
      DATE_OLD: ${{ needs.check_new_data_hgnc.outputs.DATE_OLD }}
      DATE_NEW: ${{ needs.check_new_data_hgnc.outputs.DATE_NEW }}
      COMPLETE_NEW: ${{ needs.check_new_data_hgnc.outputs.COMPLETE_NEW }}
      WITHDRAWN_NEW: ${{ needs.check_new_data_hgnc.outputs.WITHDRAWN_NEW }}
    runs-on: ubuntu-22.04
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
      - name: Install R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: '4.1' # Specify the R version
          include-recommended: true    
      - name: Set up Java
        uses: actions/setup-java@v4
        with:
          java-version: '11'
          distribution: 'temurin'
      - name: Download and test new release data
        run: bash scripts/test_new_release.sh hgnc
      - name: Diff HGNC
        if:
          ${{ env.FAILED == 'false' }}
        run: bash scripts/diff_release.sh hgnc
        
      - name: 'Upload HGNC artifact'
        uses: actions/upload-artifact@v4
        with:
          name: hgnc_processed
          path: datasources/hgnc/recentData/*
          
      - uses: JasonEtco/create-an-issue@v2
        if: ${{ env.COUNT != 0 }}
        name: Post issue about HGNC update availability
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          SOURCE: HGNC
        with:
          filename: .github/ISSUE_TEMPLATE/ISSUE_UPDATE.md   
          update_existing: true
       
      - uses: JasonEtco/create-an-issue@v2
        name: Post issue about HGNC failing test
        if: ${{ env.FAILED == 'true' }}
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          SOURCE: HGNC
        with:
          filename: .github/ISSUE_TEMPLATE/ISSUE_FAIL.md
          update_existing: true
                          ################################HMDB###########################
  check_new_data_hmdb:
    runs-on: ubuntu-22.04
    name: Check HMDB
    outputs:
      DATE_NEW: ${{ steps.check_new_data_hmdb.outputs.DATE_NEW }}
      DATE_OLD: ${{ steps.check_new_data_hmdb.outputs.DATE_OLD }}
      NEW_RELEASE: ${{ steps.check_new_data_hmdb.outputs.NEW_RELEASE }}
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Check release date
        id: check_download
        run: bash scripts/check_release_date.sh hmdb
  test_processing_hmdb:
    name: Test and diff HMDB
    needs: check_new_data_hmdb
    env:
      DATE_OLD: ${{ needs.check_download.outputs.DATE_OLD }}
      DATE_NEW: ${{ needs.check_download.outputs.DATE_NEW }}
    runs-on: ubuntu-22.04
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
      - name: Install R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: '4.1' # Specify the R version
          include-recommended: true    
      - name: Set up Java
        uses: actions/setup-java@v4
        with:
          java-version: '11'
          distribution: 'temurin'
      - name: Download and test new release data
        run: bash scripts/test_new_release.sh hmdb
      - name: Diff HMDB
        if:
          ${{ env.FAILED == 'false' }}
        run: bash scripts/diff_release.sh hmdb
      - name: 'Upload HMDB artifact'
        uses: actions/upload-artifact@v4
        with:
          name: hmdb_processed
          path: datasources/hgnc/recentData/*
      - uses: JasonEtco/create-an-issue@v2
        if: ${{ env.COUNT != 0 }}
        name: Post issue about HGNC update availability
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          SOURCE: HMDB
        with:
          filename: .github/ISSUE_TEMPLATE/ISSUE_UPDATE.md   
          update_existing: true
   
      - uses: JasonEtco/create-an-issue@v2
        name: Post issue about HGNC failing test
        if: ${{ env.FAILED == 'true' }}
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          SOURCE: HMDB
        with:
          filename: .github/ISSUE_TEMPLATE/ISSUE_FAIL.md
          update_existing: true
                          ################################NCBI###########################
  check_new_data_ncbi:
    runs-on: ubuntu-22.04
    name: Check NCBI
    outputs:
      DATE_NEW: ${{ steps.check_download.outputs.DATE_NEW }}
      DATE_OLD: ${{ steps.check_download.outputs.DATE_OLD }}
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Check release date
        id: check_download
        run: bash scripts/check_release_date.sh ncbi
  test_processing_ncbi:
    name: Test and diff NCBI
    needs: check_new_data_ncbi
    env:
      DATE_OLD: ${{ needs.check_new_data_ncbi.outputs.DATE_OLD }}
      DATE_NEW: ${{ needs.check_new_data_ncbi.outputs.DATE_NEW }}
    runs-on: ubuntu-22.04
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
      - name: Install R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: '4.1' # Specify the R version
          include-recommended: true    
      - name: Set up Java
        uses: actions/setup-java@v4
        with:
          java-version: '11'
          distribution: 'temurin'
      - name: Download and test new release data
        run: |
          echo New date $DATE_NEW
          bash scripts/test_new_release.sh ncbi
      - name: Diff NCBI
        if:
          ${{ env.FAILED == 'false' }}
        run: bash scripts/diff_release.sh ncbi

      - name: 'Upload NCBI artifact'
        uses: actions/upload-artifact@v4
        with:
          name: ncbi_processed
          path: datasources/ncbi/recentData/*

      - uses: JasonEtco/create-an-issue@v2
        if: ${{ env.COUNT != 0 }}
        name: Post issue about NCBI update availability
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          SOURCE: NCBI
        with:
          filename: .github/ISSUE_TEMPLATE/ISSUE_UPDATE.md   
          update_existing: true
       
      - uses: JasonEtco/create-an-issue@v2
        name: Post issue about NCBI failing test
        if: ${{ env.FAILED == 'true' }}
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          SOURCE: NCBI
        with:
          filename: .github/ISSUE_TEMPLATE/ISSUE_FAIL.md
          update_existing: true
                          ##############################UNIPROT#########################
  check_new_data_uniprot:
    runs-on: ubuntu-22.04
    name: Check UniProt
    outputs:
      UNIPROT_SPROT_NEW: ${{ steps.check_download.outputs.UNIPROT_SPROT_NEW }}
      SEC_AC_NEW: ${{ steps.check_download.outputs.SEC_AC_NEW }}
      DELAC_SP_NEW: ${{ steps.check_download.outputs.DELAC_SP_NEW }}
      DATE_NEW: ${{ steps.check_download.outputs.DATE_NEW }}
      DATE_OLD: ${{ steps.check_download.outputs.DATE_OLD }}
    steps:
      - name: Checkout
        uses: actions/checkout@v4
      - name: Check release date
        id: check_download
        run: bash scripts/check_release_date.sh uniprot
  test_processing_uniprot:
    name: Test and diff UniProt
    needs: check_new_data_uniprot
    env:
      DATE_OLD: ${{ needs.check_new_data_uniprot.outputs.DATE_OLD }}
      DATE_NEW: ${{ needs.check_new_data_uniprot.outputs.DATE_NEW }}
    runs-on: ubuntu-22.04
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4
      - name: Install R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: '4.1' # Specify the R version
          include-recommended: true    
      - name: Set up Java
        uses: actions/setup-java@v4
        with:
          java-version: '11'
          distribution: 'temurin'
      - name: Download and test new release data
        run: bash scripts/test_new_release.sh uniprot
      - name: Diff UniProt
        if:
          ${{ env.FAILED == 'false' }}
        run: bash scripts/diff_release.sh uniprot

      - name: 'Upload UNIPROT artifact'
        uses: actions/upload-artifact@v4
        with:
          name: uniprot_processed
          path: datasources/uniprot/recentData/*

      - uses: JasonEtco/create-an-issue@v2
        if: ${{ env.COUNT != 0 }}
        name: Post issue about UniProt update availability
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          SOURCE: UniProt
        with:
          filename: .github/ISSUE_TEMPLATE/ISSUE_UPDATE.md   
          update_existing: true
       
      - uses: JasonEtco/create-an-issue@v2
        name: Post issue about UniProt failing test
        if: ${{ env.FAILED == 'true' }}
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          SOURCE: UniProt
        with:
          filename: .github/ISSUE_TEMPLATE/ISSUE_FAIL.md
          update_existing: true
  #trigger-docker-update:
  #  runs-on: ubuntu-22.04
  #  steps:
  #    - name: Checkout
  #      uses: actions/checkout@v4
  #    - name: Trigger docker release
  #      uses: peter-evans/repository-dispatch@v3
  #      with:
  #        token: ${{ secrets.pat_external_workflow }}
  #        repository: sec2pri/omicsFixID
  #        event-type: update-event