distribute.yaml

name: Build and Publish
on:
  push:
    branches:
      - stable
      - master
    #      - stable-service-api
    paths-ignore:
      - '**/README.md'
      - 'sirius_doc/**/*'

jobs:
  distGUI:
    strategy:
      matrix:
        os: [ ubuntu-latest, windows-latest ]
#        os: [ ubuntu-latest, windows-latest, macos-latest ]
    runs-on: ${{ matrix.os }}
    env:
      GENERIC_INSTALLER_CERTIFICATE: ${{ secrets.GENERIC_INSTALLER_CERTIFICATE }}
      MACOS_APP_IDENTITY_ID: ${{ secrets.MACOS_APP_IDENTITY_ID }}
      MACOS_IDENTITY_ID: ${{ secrets.MACOS_IDENTITY_ID }}
      MACOS_APPLE_ID: ${{ secrets.MACOS_APPLE_ID }}
      MACOS_APPLE_ID_PW: ${{ secrets.MACOS_APPLE_ID_PW }}
      SIRIUS_USER: ${{ secrets.SIRIUS_USER }}
      SIRIUS_PW: ${{ secrets.SIRIUS_PW }}
    steps:
      - uses: actions/checkout@v3
        with:
          lfs: true
      - name: Git LFS Pull
        run: git lfs pull
      - name: Set up Zulu JDK-FX
        uses: actions/setup-java@v1
        with:
          java-version: '21' # The JDK version to make available on the path.
          java-package: jdk # (jre, jdk, or jdk+fx) - defaults to jdk
          architecture: x64 # (x64 or x86) - defaults to x64
      - name: Load Build properties
        uses: Reedyuk/read-properties@v1.0.1
        id: sirius_version
        with:
          path: './sirius_cli/src/main/resources/sirius_frontend.build.properties'
          property: 'de.unijena.bioinf.siriusFrontend.version'

      - if: ${{ (matrix.os == 'macos-latest') && (env.MACOS_APP_IDENTITY_ID != '') }}
        name: Import Apple APP Code-signing ID and p12
        uses: apple-actions/import-codesign-certs@v1
        with:
          keychain-password: ${{ secrets.MACOS_TMP_KEYCHAIN_PWD }}
          p12-file-base64: ${{ secrets.MACOS_APP_CERTIFICATE }}
          p12-password: ${{ secrets.MACOS_APP_CERTIFICATE_PWD }}

      - if: ${{ (matrix.os == 'macos-latest') && (env.MACOS_IDENTITY_ID != '') }}
        name: Import Apple Installer Code-signing ID and p12
        uses: apple-actions/import-codesign-certs@v1
        with:
          create-keychain: false
          keychain-password: ${{ secrets.MACOS_TMP_KEYCHAIN_PWD }}
          p12-file-base64: ${{ secrets.MACOS_CERTIFICATE }}
          p12-password: ${{ secrets.MACOS_CERTIFICATE_PWD }}

      - if: matrix.os == 'macos-latest'
        name: Check Identities
        run: /usr/bin/security find-identity

      #      - if: ${{ (matrix.os == 'windows-latest' ||  matrix.os == 'ubuntu-latest') && (env.GENERIC_INSTALLER_CERTIFICATE != '') }}
      #        name: Load generic installer codesign cert
      #        id: generic_codesign_cert
      #        uses: timheuer/base64-to-file@v1.1
      #        with:
      #          fileName: 'generic_installer_cert.p12'
      #          encodedString: ${{ env.GENERIC_INSTALLER_CERTIFICATE }}

      - name: Gradle Build
        uses: eskatos/gradle-command-action@v1
        env:
          WIN_INSTALLER_CERTIFICATE_FILE: ${{ steps.generic_codesign_cert.outputs.filePath }}
        with:
          gradle-version: 8.8
          build-root-directory: sirius_dist/sirius_gui_dist
          arguments: --stacktrace clean buildJpDists -P "build.sirius.native.openjfx.exclude=true" -P "build.sirius.starter.jdk.include=true" -P "de.unijena.bioinf.build.MACOS_APP_IDENTITY_ID=${{ secrets.MACOS_APP_IDENTITY_ID }}" -P "de.unijena.bioinf.build.MACOS_IDENTITY_ID=${{ secrets.MACOS_IDENTITY_ID }}" -P "de.unijena.bioinf.build.MACOS_APPLE_ID=${{ secrets.MACOS_APPLE_ID }}" -P "de.unijena.bioinf.build.MACOS_APPLE_ID_PW=${{ secrets.MACOS_APPLE_ID_PW }}" -P "de.unijena.bioinf.build.MACOS_TEAM_ID=${{ secrets.MACOS_TEAM_ID }}"

#      - name: Sirius Run
#        run: |
#          TEMP_ROOT="$(cd "$(dirname "sirius_cli")"; pwd -P)/$(basename "sirius_cli")"
#          TEMP_DIR="${TEMP_ROOT}/build/test/temp_results"
#          mkdir -p "${TEMP_DIR}" "${TEMP_DIR}/mgf_temp_output" "${TEMP_DIR}/mgf_temp_summary" "${TEMP_DIR}/ms_temp_output" "${TEMP_DIR}/ms_temp_summary" "${TEMP_DIR}/txt_temp_output" "${TEMP_DIR}/txt_temp_summary"
#          DEMO_DIR="$(cd "$(dirname "sirius_doc/manual/demo-data")"; pwd -P)/$(basename "sirius_doc/manual/demo-data")"
#          MGF_DATA="${DEMO_DIR}/mgf/laudanosine.mgf"
#          MS_DATA="${DEMO_DIR}/ms/Bicuculline.ms"
#          TXT_DATA_1="${DEMO_DIR}/txt/chelidonine_ms.txt"
#          TXT_DATA_2="${DEMO_DIR}/txt/chelidonine_msms1.txt,${DEMO_DIR}/txt/chelidonine_msms2.txt"
#          MGF_OUTPUT="${TEMP_DIR}/mgf_temp_output"
#          MGF_SUMMARY="${TEMP_DIR}/mgf_temp_summary"
#          MS_OUTPUT="${TEMP_DIR}/ms_temp_output"
#          MS_SUMMARY="${TEMP_DIR}/ms_temp_summary"
#          TXT_OUTPUT="${TEMP_DIR}/txt_temp_output"
#          TXT_SUMMARY="${TEMP_DIR}/txt_temp_summary"
#          case "$OSTYPE" in
#            darwin*) SIRIUS="./sirius_dist/sirius_gui_dist/build/distributions/sirius.app/Contents/MacOS/sirius" ;;
#            linux*) SIRIUS="./sirius_dist/sirius_gui_dist/build/distributions/sirius/bin/sirius" ;;
#            msys*) SIRIUS="./sirius_dist/sirius_gui_dist/build/distributions/sirius/sirius.exe" ;;
#            *) echo "Error: Could not find OS."; exit 1 ;;
#          esac
#          ${SIRIUS} login --show --user-env SIRIUS_USER --password-env SIRIUS_PW
#          ${SIRIUS} login --show --select-license ${{ env.GITHUB_REF_SLUG == 'stable' && secrets.SIRIUS_SUB || secrets.SIRIUS_SUB_DEV }}
#          ${SIRIUS} --input ${MGF_DATA} --output ${MGF_OUTPUT} formula -p orbitrap fingerprint structure compound-classes write-summaries --output ${MGF_SUMMARY}
#          ${SIRIUS} -1 ${TXT_DATA_1} -2 ${TXT_DATA_2} -z 354.134704589844 -o ${TXT_OUTPUT} formula -p orbitrap write-summaries --output ${TXT_SUMMARY}
#          ${SIRIUS} -o ${MS_OUTPUT} -i ${MS_DATA} --ignore-formula formula -p orbitrap -c 5 fingerprint structure compound-classes write-summaries --output ${MS_SUMMARY}
#        shell: bash
#
#      - name: Sirius MGF Test
#        run: |
#          RESULTS="sirius_cli/build/test/temp_results/"
#          OUTPUT="${RESULTS}mgf_temp_output/1_laudanosine_FEATURE_1/"
#          SUMMARY="${RESULTS}mgf_temp_summary/1_laudanosine_FEATURE_1/"
#          CANOPUS="${OUTPUT}canopus/"
#          CANOPUS_NPC="${OUTPUT}canopus_npc/"
#          FINGERPRINTS="${OUTPUT}fingerprints/"
#          FINGER_ID="${OUTPUT}fingerid/"
#          DIRS=(${SUMMARY} ${OUTPUT} ${CANOPUS} ${CANOPUS_NPC} ${FINGERPRINTS} ${FINGER_ID})
#          for DIR in "${DIRS[@]}" ; do
#            if [ -d "${DIR}" ]; then
#              echo "Found result directory ${DIR}..."
#              if [ "$(ls -A ${DIR})" ]; then
#                echo "${DIR} is not empty."
#              else
#                echo "Error: ${DIR} is empty."
#                exit 1
#              fi
#            else
#              echo "Error: result directory ${DIR} not found."
#              exit 1
#            fi
#          done
#        shell: bash
#
#      - name: Sirius MS Test
#        run: |
#          RESULTS="sirius_cli/build/test/temp_results/"
#          OUTPUT="${RESULTS}ms_temp_output/1_Bicuculline_Bicuculline/"
#          SUMMARY="${RESULTS}ms_temp_summary/1_Bicuculline_Bicuculline/"
#          CANOPUS="${OUTPUT}canopus/"
#          CANOPUS_NPC="${OUTPUT}canopus_npc/"
#          FINGERPRINTS="${OUTPUT}fingerprints/"
#          FINGER_ID="${OUTPUT}fingerid/"
#          echo "${FINGER_ID}"
#          DIRS=(${SUMMARY} ${OUTPUT} ${CANOPUS} ${CANOPUS_NPC} ${FINGERPRINTS} ${FINGER_ID})
#          echo "${DIRS}"
#          for DIR in "${DIRS[@]}" ; do
#            if [ -d "${DIR}" ]; then
#              echo "Found result directory ${DIR}..."
#              if [ "$(ls -A ${DIR})" ]; then
#                echo "${DIR} is not empty."
#              else
#                echo "Error: ${DIR} is empty."
#                exit 1
#              fi
#            else
#              echo "Error: result directory ${DIR} not found."
#              exit 1
#            fi
#          done
#        shell: bash
#
#      - name: Sirius TXT Test
#        run: |
#          RESULTS="sirius_cli/build/test/temp_results/"
#          SUMMARY="${RESULTS}txt_temp_summary/1_unknown_/"
#          if [ -d "${SUMMARY}" ]; then
#            echo "Found result directory ${SUMMARY}..."
#            if [ "$(ls -A ${SUMMARY})" ]; then
#              echo "${SUMMARY} is not empty."
#            else
#              echo "Error: ${SUMMARY} is empty."
#              exit 1
#            fi
#          else
#            echo "Error: result directory ${SUMMARY} not found."
#            exit 1
#          fi
#        shell: bash
#
#      - name: Sirius Run Cleanup
#        run: |
#          rm -r sirius_cli/build/test/temp_results
      - if: matrix.os == 'windows-latest'
        name: Azure Trusted Signing for Widows MSI
        uses: azure/trusted-signing-action@v0.3.16
        with:
          azure-tenant-id: ${{ secrets.AZURE_TENANT_ID }}
          azure-client-id: ${{ secrets.AZURE_CLIENT_ID }}
          azure-client-secret: ${{ secrets.AZURE_CLIENT_SECRET }}
          endpoint: ${{ secrets.AZURE_ENDPOINT }}
          code-signing-account-name: ${{ secrets.AZURE_CODE_SIGNING_NAME }}
          certificate-profile-name: ${{ secrets.AZURE_CERT_PROFILE_NAME }}

          # Sign all exes inside the folder
          files-folder: ./sirius_dist/sirius_gui_dist/build/jpDists/
          files-folder-filter: msi
          file-digest: SHA256

      - name: Upload Distributions
        uses: actions/upload-artifact@v4
        with:
          retention-days: 1
          name: "sirius-${{ steps.sirius_version.outputs.value }}-${{ runner.os }}-x86-64"
          path: |
            ./sirius_dist/sirius_gui_dist/build/jpDists/*.zip
            ./sirius_dist/sirius_gui_dist/build/jpDists/*.msi
            ./sirius_dist/sirius_gui_dist/build/jpDists/*.pkg
            ./sirius_dist/sirius_gui_dist/build/jpDists/*.deb
            ./sirius_dist/sirius_gui_dist/build/jpDists/*.sha256

#  dockergen:
#    needs: [ distGUI ]
#    uses: ./.github/workflows/dockergen.yaml
#    secrets: inherit

  release:
    needs: [distGUI]
#    needs: [ distCLI, distGUI]
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
        with:
          lfs: true
      - name: Git LFS Pull
        run: git lfs pull
      - name: Inject slug/short variables
        uses: rlespinasse/github-slug-action@v3.x
      - name: Load Build properties
        uses: Reedyuk/read-properties@v1.0.1
        id: sirius_version
        with:
          path: './sirius_cli/src/main/resources/sirius_frontend.build.properties'
          property: 'de.unijena.bioinf.siriusFrontend.version'
      - uses: actions/download-artifact@v4.1.7
        with:
          path: sirius_dist/build/tmp/artifacts/
      - name: Display downloaded artifact files
        run: ls -lah
        working-directory: sirius_dist/build/tmp/artifacts/
      - uses: ncipollo/release-action@v1
        with:
          artifacts: "sirius_dist/build/tmp/artifacts/*/*"
          body: |
            ### Prebuilt SIRIUS releases for all supported platforms. 
            
            Package names are made up as follows: `<App Name>-<Version>-<Operating System>-<Flavor>.<PackageType>`. Package types are either generic `.zip` archives or operating system specific installers (e.g. `.pkg` or `.msi`). The flavors describe builds with different features:
            * no _Flavor_ suffix represents for the standard SIRIUS package that contains the Graphical User Interface (GUI), the background service and the Command Line Tool (CLI)
            * [currently not available] `headless` represents a command line only version that does not contain GUI relevant packages. It is smaller and does not need any GUI libraries installed on the users system (good for servers). 
            
            See the [online documentation](https://v6.docs.sirius-ms.io/quick-start/) for details.
          
            Changelog can be found [here](https://v6.docs.sirius-ms.io/changelog/).
          name: "SIRIUS v${{ steps.sirius_version.outputs.value }}"
          tag: "v${{ steps.sirius_version.outputs.value }}"
          prerelease: ${{ endsWith(steps.sirius_version.outputs.value, '-SNAPSHOT') }}
          allowUpdates: ${{ endsWith(steps.sirius_version.outputs.value, '-SNAPSHOT') }}
          #draft: ${{ env.GITHUB_REF_SLUG == 'stable' && 'false' || 'true' }}
          draft: 'true'
          token: ${{ secrets.GITHUB_TOKEN }}

  trigger-client-api-build:
    needs: [ release ]
    runs-on: ubuntu-latest
    steps:
      - name: Trigger Actions on sirius-client-openAPI
        run: curl -X POST -H "Authorization:Bearer ${{ secrets.CLIENT_API_REPO_TOKEN }}" -H "Accept:application/vnd.github.v3+json" ${{ vars.CLIENT_API_REPO_URL }} -d '{"ref":"master"}'