Merge pull request #321 from kit-data-manager/development

Development 2.1.1

Author: Pfeil

.devcontainer/Dockerfile

@@ -0,0 +1,10 @@
+FROM mcr.microsoft.com/devcontainers/java:25
+
+# Install Node.js LTS
+RUN curl -fsSL https://deb.nodesource.com/setup_24.x | bash - && \
+    apt-get install -y nodejs && \
+    rm -rf /var/lib/apt/lists/*
+RUN npm install -g ro-crate-html-js
+
+# Verify installations
+RUN node --version && npm --version

.devcontainer/devcontainer.json

@@ -0,0 +1,12 @@
+{
+    "name": "Java (Gradle)",
+    "build": {
+        "dockerfile": "Dockerfile"
+    },
+    "customizations": {
+        "zed": {
+            "extensions": ["java"]
+        }
+    },
+    "forwardPorts": [8080]
+}

.github/workflows/codeql-analysis.yml

@@ -38,11 +38,11 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+      uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v4
+      uses: github/codeql-action/init@8aad20d150bbac5944a9f9d289da16a4b0d87c1e # v4.36.2
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -56,7 +56,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v4
+      uses: github/codeql-action/autobuild@8aad20d150bbac5944a9f9d289da16a4b0d87c1e # v4.36.2
 
     # Command-line programs to run using the OS shell.
     # See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -69,4 +69,4 @@ jobs:
     #   ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v4
+      uses: github/codeql-action/analyze@8aad20d150bbac5944a9f9d289da16a4b0d87c1e # v4.36.2

.github/workflows/gradle.yml

@@ -9,43 +9,59 @@ name: Build & Tests
 
 on:
   push:
-    branches: [ main, development ]
+    branches: [main, development]
   pull_request:
   workflow_dispatch:
 
-env:
-  COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-
 jobs:
   build:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        jdk: [ 17, 21 ]  # (open)JDK releases
+        jdk: [17, 21, 25, 26] # (open)JDK releases
     runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
-    - name: Set up openJDK version
-      uses: actions/setup-java@v5
-      with:
-        java-version: ${{ matrix.jdk }}
-        distribution: 'zulu'
-    - name: Install Dependencies
-      run: npm install -g ro-crate-html-js
-    - name: Setup Gradle
-      uses: gradle/actions/setup-gradle@v5
-    - name: Build and Test with Gradle
-      run: ./gradlew -Dprofile=release build
-    - name: Upload (test) reports as artifact on GitHub on manual runs
-      if: github.event_name == 'workflow_dispatch'
-      uses: actions/upload-artifact@v5
-      with:
-        name: test-report ${{ matrix.os }} JDK ${{ matrix.jdk }}
-        path: build/reports
-    - name: Do one Coveralls test report
-      if: matrix.os == 'ubuntu-latest' && matrix.jdk == 21
-      run: ./gradlew -Dprofile=release jacocoTestReport coveralls
-    - name: Compile Javadoc
-      if: matrix.os == 'ubuntu-latest' && matrix.jdk == 21
-      run: ./gradlew javadoc
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7
+      - name: Set up openJDK version
+        uses: actions/setup-java@ad2b38190b15e4d6bdf0c97fb4fca8412226d287 # v5.3.0
+        with:
+          java-version: ${{ matrix.jdk }}
+          distribution: "zulu"
+      - name: Install Dependencies
+        run: npm install -g ro-crate-html-js
+      - name: Setup Gradle
+        uses: gradle/actions/setup-gradle@3f131e8634966bd73d06cc69884922b02e6faf92 # v6.2.0
+      - name: Build and Test with Gradle
+        run: ./gradlew -Dprofile=release build
+      - name: Upload (test) reports as artifact on GitHub on manual runs
+        if: github.event_name == 'workflow_dispatch'
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: test-report ${{ matrix.os }} JDK ${{ matrix.jdk }}
+          path: build/reports
+  coverage:
+    needs: build
+    runs-on: ubuntu-latest
+    env:
+      jdkversion: 25
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7
+      - name: Set up OpenJDK version ...
+        uses: actions/setup-java@ad2b38190b15e4d6bdf0c97fb4fca8412226d287 # v5.3.0
+        with:
+          distribution: "zulu"
+          java-version: ${{ env.jdkversion }}
+      - name: Install Dependencies
+        run: npm install -g ro-crate-html-js
+      - name: Grant execute permission for gradlew
+        run: chmod +x gradlew
+      - name: Build with Gradle (JDK ${{ env.jdkversion }})
+        run: ./gradlew clean check jacocoTestReport
+      - name: Codecov
+        uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7
+        with:
+          files: ./build/reports/jacoco/test/jacocoTestReport.xml #optional
+      - name: Compile Javadoc
+        run: ./gradlew javadoc

.github/workflows/publishRelease.yml

@@ -8,9 +8,9 @@ jobs:
   publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7
       - name: Set up Java
-        uses: actions/setup-java@v5
+        uses: actions/setup-java@ad2b38190b15e4d6bdf0c97fb4fca8412226d287 # v5.3.0
         with:
           java-version: 21
           distribution: 'zulu' # openjdk

build.gradle

@@ -3,8 +3,6 @@ plugins {
     id 'jvm-test-suite'
     id 'application'
     id 'jacoco'
-    // Adds coveralls task for CI to send results to the coveralls service.
-    id "com.github.kt3k.coveralls" version "2.12.2"
 
     // Instructions: https://github.com/researchgate/gradle-release
     // Available versions: https://plugins.gradle.org/plugin/net.researchgate.release
@@ -13,7 +11,7 @@ plugins {
     // Publishing of JAR to Nexus instances (e.g., OSSRH)
     // https://github.com/gradle-nexus/publish-plugin
     id "io.github.gradle-nexus.publish-plugin" version "2.0.0"
-    id "io.freefair.maven-publish-java" version "9.1.0"
+    id "io.freefair.maven-publish-java" version "9.5.0"
 }
 
 group = 'edu.kit.datamanager'
@@ -45,7 +43,7 @@ ext {
 
 dependencies {
     // JUnit setup for testing
-    testImplementation(platform("org.junit:junit-bom:6.0.1"))
+    testImplementation(platform("org.junit:junit-bom:6.1.0"))
     testImplementation('org.junit.jupiter:junit-jupiter')
     testRuntimeOnly('org.junit.platform:junit-platform-launcher')
     // JSON object mapping / (de-)serialization
@@ -54,22 +52,22 @@ dependencies {
     // http client
     implementation group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.5.14'
     // common file system operations
-    implementation group: 'commons-io', name: 'commons-io', version: '2.21.0'
+    implementation group: 'commons-io', name: 'commons-io', version: '2.22.0'
     // read from and write to zip files
-    implementation group: 'net.lingala.zip4j', name: 'zip4j', version: '2.11.5'
+    implementation group: 'net.lingala.zip4j', name: 'zip4j', version: '2.11.6'
     // compare json documents in tests
-    implementation 'com.github.fslev:json-compare:7.2'
+    implementation 'com.github.fslev:json-compare:8.1'
     // url validator
     implementation group: 'commons-validator', name: 'commons-validator', version: '1.10.1'
     // logging
-    implementation group: 'org.slf4j', name: 'slf4j-jdk14', version: '2.0.17'
+    implementation group: 'org.slf4j', name: 'slf4j-jdk14', version: '2.0.18'
     // JSON-LD, Zenodo mapping
     implementation group: 'com.apicatalog', name: 'titanium-json-ld', version: '1.7.0'
     // metadata validation, profiles based on JSON schema
     implementation group: "com.networknt", name: "json-schema-validator", version: "1.5.9"
     implementation 'org.glassfish:jakarta.json:2.0.1'
     //JTE for template processing
-    implementation('gg.jte:jte:3.2.1')
+    implementation('gg.jte:jte:3.2.4')
     implementation("org.freemarker:freemarker:2.3.34")
 }
 
@@ -186,12 +184,12 @@ jacocoTestReport {
     dependsOn test
     reports {
         csv.required = true
-        xml.required = true // coveralls plugin depends on xml format report
+        xml.required = true // codecov plugin may depend on xml format report
     }
 }
 
 jacoco {
-    toolVersion = "0.8.14"
+    toolVersion = "0.8.15"
 }
 
 // maxParallelForks(2)

gradle/wrapper/gradle-wrapper.jar

@@ -1,7 +1,9 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.14.3-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.6.0-bin.zip
 networkTimeout=10000
+retries=0
+retryBackOffMs=500
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists