fix jre extraction #565
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| name: Build and Publish | |
| on: | |
| push: | |
| branches: | |
| - stable | |
| - stable-codesign | |
| - master | |
| # - stable-service-api | |
| paths-ignore: | |
| - '**/README.md' | |
| - 'sirius_doc/**/*' | |
| jobs: | |
| distGUI: | |
| strategy: | |
| matrix: | |
| os: [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: ${{ secrets.AZURE_CERT_PROFILE_NAME }} | |
| # Sign all exes inside the folder | |
| files-folder: ./sirius_dist/sirius_gui_dist/build/jpDists/ | |
| files-folder-filter: msi | |
| file-digest: SHA256 | |
| - name: Upload Distributions | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| retention-days: 1 | |
| name: "sirius-${{ 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@v2 | |
| 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) and the Command Line Tool (CLI) | |
| * `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). | |
| * `service` like standard but additionally contains the experimental _service mode_ of SIRIUS which allows to start SIRIUS as a background service that can be queried form scripting languages or as part of workflows. See the [online documentation](https://v6.docs.sirius-ms.io/quick-start/#background-service---generic-sirius-api) 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' }} | |
| 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"}' |