Merge branch 'refs/heads/master' into stable

sirius-ms · Jul 21, 2024 · b004470 · b004470
2 parents 8db78ca + ebbeff0
commit b004470
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diff --git a/.github/workflows/distribute.yaml b/.github/workflows/distribute.yaml
@@ -29,7 +29,7 @@ jobs:
 #      - name: Set up Zulu JDK
 #        uses: actions/setup-java@v1
 #        with:
-#          java-version: '17' # The JDK version to make available on the path.
+#          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
@@ -73,7 +73,7 @@ jobs:
 #        env:
 #          WIN_INSTALLER_CERTIFICATE_FILE: ${{ steps.generic_codesign_cert.outputs.filePath }}
 #        with:
-#          gradle-version: 7.6
+#          gradle-version: 8.8
 #          build-root-directory: sirius_dist/sirius_cli_single_os
 #          arguments: clean publishSiriusPublicationToMavenLocal -P "build.sirius.starter.jdk.include=true" -P "de.unijena.bioinf.build.MACOS_APP_IDENTITY_ID=${{ 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=${{ secrets.MACOS_APPLE_ID_PW }}" -P "de.unijena.bioinf.build.WIN_INSTALLER_CERTIFICATE_FILE=${{ steps.generic_codesign_cert.outputs.filePath }}"  -P "de.unijena.bioinf.build.WIN_INSTALLER_CERTIFICATE_PW=${{ secrets.GENERIC_INSTALLER_CERTIFICATE_PW }}" -P "de.unijena.bioinf.build.WIN_INSTALLER_CERTIFICATE_TIMESTAMP_URL=${{ secrets.GENERIC_INSTALLER_CERTIFICATE_TIMESTAMP_URL }}"
 #
@@ -208,13 +208,15 @@ jobs:
       SIRIUS_USER: ${{ secrets.SIRIUS_USER }}
       SIRIUS_PW: ${{ secrets.SIRIUS_PW }}
     steps:
-      - uses: actions/checkout@v2
+      - 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: '17' # The JDK version to make available on the path.
+          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
@@ -258,9 +260,9 @@ jobs:
         env:
           WIN_INSTALLER_CERTIFICATE_FILE: ${{ steps.generic_codesign_cert.outputs.filePath }}
         with:
-          gradle-version: 7.6
+          gradle-version: 8.8
           build-root-directory: sirius_dist/sirius_gui_dist
-          arguments: clean publishSiriusPublicationToMavenLocal  -P "build.sirius.native.openjfx.exclude=true" -P "build.sirius.starter.jdk.include=true" -P "de.unijena.bioinf.build.MACOS_APP_IDENTITY_ID=${{ 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=${{ secrets.MACOS_APPLE_ID_PW }}" -P "de.unijena.bioinf.build.WIN_INSTALLER_CERTIFICATE_FILE=${{ steps.generic_codesign_cert.outputs.filePath }}"  -P "de.unijena.bioinf.build.WIN_INSTALLER_CERTIFICATE_PW=${{ secrets.GENERIC_INSTALLER_CERTIFICATE_PW }}" -P "de.unijena.bioinf.build.WIN_INSTALLER_CERTIFICATE_TIMESTAMP_URL=${{ secrets.GENERIC_INSTALLER_CERTIFICATE_TIMESTAMP_URL }}"
+          arguments: --stacktrace clean publishSiriusPublicationToMavenLocal  -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.WIN_INSTALLER_CERTIFICATE_FILE=${{ steps.generic_codesign_cert.outputs.filePath }}"  -P "de.unijena.bioinf.build.WIN_INSTALLER_CERTIFICATE_PW=${{ secrets.GENERIC_INSTALLER_CERTIFICATE_PW }}" -P "de.unijena.bioinf.build.WIN_INSTALLER_CERTIFICATE_TIMESTAMP_URL=${{ secrets.GENERIC_INSTALLER_CERTIFICATE_TIMESTAMP_URL }}"
 
 #      - name: Sirius Run
 #        run: |
@@ -389,9 +391,11 @@ jobs:
 #    needs: [ distCLI, distGUI]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - 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

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -3,7 +3,7 @@
 # https://github.com/gradle/gradle
 #image: gradle:alpine
 default:
-  image: azul/zulu-openjdk:17-latest
+  image: azul/zulu-openjdk:21-latest
   tags: [$RUNNER_TAGS]
 
 #  image: git.bio.informatik.uni-jena.de:5050/bioinf-mit/docker-images/ubuntu-zulu-fx-gradle:22.04-15.42.15-6.9.2-12

diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 [![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blueviolet.svg)](https://www.gnu.org/licenses/agpl-3.0)
-[![Generic badge](https://img.shields.io/badge/Version-6.0.0-informational.svg)](https://shields.io/)
+[![Generic badge](https://img.shields.io/badge/Version-6.0.1--SNAPSHOT-informational.svg)](https://shields.io/)
 [![Build and Publish](https://github.com/sirius-ms/sirius/actions/workflows/distribute.yaml/badge.svg?branch=release-4-pre)](https://github.com/sirius-ms/sirius/actions/workflows/distribute.yaml)
 
 *<span style="color: #808080;">Our methods are offered to the scientific community as freely available resources. (Re-)distribution of the
@@ -22,18 +22,22 @@ Main developers of SIRIUS are the [Böcker group](https://bio.informatik.uni-jen
 - [Online Documentation](https://v6.docs.sirius-ms.io/)
 - [Video tutorials](https://www.youtube.com/channel/UCIbW_ZFSADRUQ-T5nmgU4VA/featured)
 - [Bookchapter on using SIRIUS 4](https://doi.org/10.1007/978-1-0716-0239-3_11) ([Preprint](https://bio.informatik.uni-jena.de/wp/wp-content/uploads/2020/12/SIRIUS4_book_chapter_preprint-2.pdf)) -- does not cover the new LC-MS/MS processing option
-- [Demo data](https://bio.informatik.uni-jena.de/wp/wp-content/uploads/2015/05/demo.zip)
+- [Demo data](data/demo.zip)
 - [Logos for publications and presentations](https://bio.informatik.uni-jena.de/software/sirius/sirius-logos/)
 
 <!--begin download-->
 
-### SIRIUS+CSI:FingerID GUI and CLI - Version 6.0.0 (2024-06-03)
+### SIRIUS+CSI:FingerID GUI and CLI - Version 6.0.1-SNAPSHOT (2024-06-20)
 ##### These versions include the Java Runtime Environment, so there is no need to install Java separately! Just download, install/unpack and execute.
-- for Windows (64bit): [msi](https://github.com/sirius-ms/sirius/releases/download/v6.0.0/sirius-6.0.0-win64.msi) / [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.0/sirius-6.0.0-win64.zip) / - for Mac (64bit): [pkg](https://github.com/sirius-ms/sirius/releases/download/v6.0.0/sirius-6.0.0-osx64.pkg) / [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.0/sirius-6.0.0-osx64.zip) / - for Linux (64bit): [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.0/sirius-6.0.0-linux64.zip)
+- for Windows (64bit): [msi](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-win64.msi) / [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-win64.zip)
+- for Mac (64bit): [pkg](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-osx64.pkg) / [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-osx64.zip)
+- for Linux (64bit): [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-linux64.zip)
 
-### SIRIUS+CSI:FingerID Command-Line Interface only - Version 6.0.0 (2024-06-03)
+### SIRIUS+CSI:FingerID Command-Line Interface only - Version 6.0.1-SNAPSHOT (2024-06-20)
 ##### These versions include the Java Runtime Environment, so there is no need to install Java separately! Just download, install/unpack and execute.
-- for Windows (64bit): [msi](https://github.com/sirius-ms/sirius/releases/download/v6.0.0/sirius-6.0.0-win64-headless.msi) / [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.0/sirius-6.0.0-win64-headless.zip) / - for Mac (64bit): [pkg](https://github.com/sirius-ms/sirius/releases/download/v6.0.0/sirius-6.0.0-osx64-headless.pkg) / [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.0/sirius-6.0.0-osx64-headless.zip) / - for Linux (64bit): [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.0/sirius-6.0.0-linux64-headless.zip)
+- for Windows (64bit): [msi](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-win64-headless.msi) / [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-win64-headless.zip)
+- for Mac (64bit): [pkg](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-osx64-headless.pkg) / [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-osx64-headless.zip)
+- for Linux (64bit): [zip](https://github.com/sirius-ms/sirius/releases/download/v6.0.1-SNAPSHOT/sirius-6.0.1-SNAPSHOT-linux64-headless.zip)
 
 
 <!--end download-->
@@ -62,6 +66,8 @@ may be required.
 ### [Sources on GitHub](https://github.com/sirius-ms)
 - [SIRIUS frontend](https://github.com/sirius-ms/sirius)
 - [SIRIUS library](https://github.com/sirius-ms/sirius-libs)
+- [SIRIUS-API Java SDK](sirius_nightsky_sdk/sirius_nightsky_sdk.openapi/README.md)
+- [SIRIUS-API SDKs](https://github.com/sirius-ms/sirius-client-openAPI)
 
 ### [Changelog](https://v6.docs.sirius-ms.io/changelog/)
 

diff --git a/build.gradle b/build.gradle
@@ -1,7 +1,7 @@
-import java.nio.file.Files
-import java.nio.file.StandardOpenOption
 import org.gradle.nativeplatform.platform.internal.DefaultNativePlatform
 
+import java.nio.file.Files
+import java.nio.file.StandardOpenOption
 
 buildscript {
     repositories {
@@ -13,29 +13,29 @@ buildscript {
         classpath 'commons-configuration:commons-configuration:1.10'
         classpath 'com.github.viswaramamoorthy:gradle-util-plugins:0.1.0-RELEASE'
         classpath 'org.yaml:snakeyaml:1.29'
+        classpath 'org.jfrog.buildinfo:build-info-extractor-gradle:5.2.2'
     }
 }
 
 plugins {
-    id "com.jfrog.artifactory" version "4.25.1"
     id "de.undercouch.download" version "4.1.1"
 }
 
 //this task is used to update the gradle wrapper properties to a new version
 // it also ensures that wrapper scripts and gradle-wrapper.jar are updates if necessary
 wrapper {
-    gradleVersion = '7.6'
+    gradleVersion = '8.8'
 }
 
 //Global Properties
 ext {
     junit_version = '5.10.0'
     jackson_version = "2.16.1"
-    spring_boot_version = "3.2.3"
+    spring_boot_version = "3.3.1"
     springdoc_version = "2.3.0"
     //version for external libraries
     slf4j_version = '1.7.36'
-    jjobs_version = '0.9.36-SNAPSHOT'
+    jjobs_version = '0.9.36'
     jaxb_version = "2.3.9"
     cdk_version = "2.8"
 
@@ -66,7 +66,7 @@ ext {
     excludeJFX = Boolean.parseBoolean((project.findProperty("build.sirius.native.openjfx.exclude") ?: "false") as String)
     System.out.println("----> excludeJFX: ${excludeJFX} | ${project.findProperty("build.sirius.native.openjfx.exclude")}")
 
-    jetbrains_version = "22.0.0"
+    jetbrains_version = "24.1.0"
 
     // mainly for IDE execution, ilp libs are not shipped with distributions anyways
     cplex_version = '12.7.1'
@@ -99,11 +99,11 @@ project.ext.set("distPath", file('dist').absolutePath)
 
 
 allprojects {
-    apply plugin: "com.jfrog.artifactory"
+    apply plugin: 'com.jfrog.artifactory'
     apply plugin: 'java'
     apply plugin: 'maven-publish'
 
-    targetCompatibility = 17
+    targetCompatibility = 21
 
     compileJava.options.encoding = "UTF-8"
     compileTestJava.options.encoding = "UTF-8"
@@ -118,10 +118,6 @@ allprojects {
         mavenCentral()
         maven {//public libs only so anybody can build the frontend without login
             url "https://bio.informatik.uni-jena.de/repository/libs-oss"
-            metadataSources {
-                mavenPom()
-                artifact()
-            }
         }
         maven {
             url "https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/"
@@ -130,27 +126,21 @@ allprojects {
             url "https://repo1.maven.org/maven2/" //glazed lists
         }
         maven {
+            // only used for spectral hashs (Splash)
             url "http://gose.fiehnlab.ucdavis.edu:55000/content/groups/public"
             allowInsecureProtocol = true
-            // only used for spectral hashs (Splash)
         }
     }
 
     dependencies {
-
-        annotationProcessor "de.unijena.bioinf.ms:processor:$siriusVersion"
-        implementation 'net.sf.trove4j:core:3.1.0'
-
         implementation "org.jetbrains:annotations:$jetbrains_version"
-
-        implementation "org.slf4j:log4j-over-slf4j:$slf4j_version"
-        implementation "org.slf4j:jcl-over-slf4j:$slf4j_version"
         implementation "org.slf4j:slf4j-api:$slf4j_version"
-
         //NOTE: cannot be provided as transitive dependency
         implementation "jakarta.persistence:jakarta.persistence-api:$jakarta_version"
         implementation "org.glassfish.jaxb:jaxb-runtime:$jaxb_version"
-
+        // TEST DEPENDENCIES
+        testImplementation "org.slf4j:log4j-over-slf4j:$slf4j_version"
+        testImplementation "org.slf4j:jcl-over-slf4j:$slf4j_version"
         // Aggregator dependency that also brings JUnit 5 parameterized tests etc.
         testImplementation("org.junit.jupiter:junit-jupiter:$junit_version")
         testImplementation("org.junit.jupiter:junit-jupiter-params:$junit_version")
@@ -166,7 +156,7 @@ allprojects {
 
     //there are some outdated incompatible trove dependencies in some libs.
     // this is to exclude them and enforce the one we need.
-    configurations.all {
+    configurations.configureEach {
         //replaced by log4j-over-slf4j
         it.exclude group: "log4j", module: "log4j"
         //replaced by jcl-over-slf4j
@@ -181,62 +171,38 @@ allprojects {
     }
 }
 
-
 subprojects {
-    apply plugin: 'application'
-}
-
-
-task sourceJar(type: Jar) {
-    group = 'build'
-    archiveClassifier.set('sources')
-    from sourceSets.main.allSource
-}
-
-task javadocJar(type: Jar, dependsOn: javadoc) {
-    group = 'documentation'
-    archiveClassifier.set('javadoc')
-    from javadoc.destinationDir
-}
-
-def javaProjects() {
-    subprojects.findAll { new File(it.projectDir, 'src').directory }
-}
-
-allprojects {
-    configure(javaProjects()) {
+    java {
+        withJavadocJar()
+        withSourcesJar()
+    }
+    //do not build javadoc for snapshot version to reduce build time
+    components.java.withVariantsFromConfiguration(configurations.javadocElements) {
+        if (version.toString().endsWith('-SNAPSHOT'))
+            skip()
+    }
+    //build only artifacts from modules that contain code
+    if (new File(projectDir, "src/main").isDirectory() && !"sirius_rest_service".equalsIgnoreCase(project.name) && !"buildSrc".equalsIgnoreCase(project.name)) {
         publishing {
             publications {
                 mavenJava(MavenPublication) {
-                    if (version.toString().endsWith('-SNAPSHOT'))
-                        setArtifacts([jar, sourceJar])
-                    else
-                        setArtifacts([jar, sourceJar, javadocJar])
-                }
-            }
-        }
-    }
-
-    publishing {
-        publications {
-            mavenJava(MavenPublication) {
-                from project.components.java
-                //adding submodules to pom
-                pom.withXml {
-                    if (!project.subprojects.isEmpty()) {
-                        def modlules = asNode().appendNode('modules', '')
-                        project.subprojects.each {
-                            new Node(modlules, 'module', it.name)
+                    from project.components.java
+
+                    pom {
+                        licenses {
+                            license {
+                                name = 'GNU Affero General Public License, Version 3.0'
+                                url = 'https://www.gnu.org/licenses/agpl-3.0.txt'
+                            }
                         }
                     }
                 }
-                setArtifacts([])
             }
         }
     }
 }
 
-task refreshDownloadLinks {
+tasks.register('refreshDownloadLinks') {
     File webPath = getBuildDir().toPath().resolve('tmp/webSite/').toFile()
     group = 'publishing'
     File outfile = new File(webPath, "sirius-download.md")
@@ -250,18 +216,18 @@ task refreshDownloadLinks {
                 "### SIRIUS+CSI:FingerID GUI and CLI - Version $version (${new Date().format('yyyy-MM-dd')})",
                 "##### These versions include the Java Runtime Environment, so there is no need to install Java separately! Just download, install/unpack and execute.",
                 "- for Windows (64bit): [msi](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-win64.msi) / " +
-                        "[zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-win64.zip) / " +
+                        "[zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-win64.zip)",
                 "- for Mac (64bit): [pkg](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-osx64.pkg) / " +
-                        "[zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-osx64.zip) / " +
+                        "[zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-osx64.zip)",
                 "- for Linux (64bit): [zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-linux64.zip)",
 
                 "",
                 "### SIRIUS+CSI:FingerID Command-Line Interface only - Version $version (${new Date().format('yyyy-MM-dd')})",
                 "##### These versions include the Java Runtime Environment, so there is no need to install Java separately! Just download, install/unpack and execute.",
                 "- for Windows (64bit): [msi](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-win64-headless.msi) / " +
-                        "[zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-win64-headless.zip) / " +
+                        "[zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-win64-headless.zip)",
                 "- for Mac (64bit): [pkg](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-osx64-headless.pkg) / " +
-                        "[zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-osx64-headless.zip) / " +
+                        "[zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-osx64-headless.zip)",
                 "- for Linux (64bit): [zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-linux64-headless.zip)",
                 ""
         ] as List
@@ -274,7 +240,7 @@ task refreshDownloadLinks {
 String cleanVersion = fingeridVersion.toString().replace('-SNAPSHOT', '')
 String minorVersion = "${cleanVersion.split('[.]')[0]}.${cleanVersion.split('[.]')[1]}"
 
-task refreshTrainingLinks {
+tasks.register('refreshTrainingLinks') {
     File webPath = getBuildDir().toPath().resolve('tmp/webSite/').toFile()
     group = 'publishing'
     File outfile = new File(webPath, "sirius-training.md")
@@ -292,7 +258,7 @@ task refreshTrainingLinks {
     }
 }
 
-task refreshReadMe {
+tasks.register('refreshReadMe') {
     inputs.files(refreshDownloadLinks.outputs.files.singleFile, refreshTrainingLinks.outputs.files.singleFile)
     outputs.file("${getRootDir()}/README.md")
     group = 'publishing'
@@ -342,6 +308,7 @@ task refreshReadMe {
 }
 refreshReadMe.dependsOn refreshTrainingLinks
 refreshReadMe.dependsOn refreshDownloadLinks
+
 // publication artifactory
 artifactory {
     contextUrl = 'https://bio.informatik.uni-jena.de/repository/'