Merge pull request #287 from kit-data-manager/development

PR for v1.2.3

Author: ThomasJejkal

.github/dependabot.yml

@@ -7,7 +7,6 @@ updates:
       interval: "weekly"
     open-pull-requests-limit: 0
 
-
   - package-ecosystem: "github-actions"
     directory: "/"
     target-branch: "development"

.github/workflows/codeql-analysis.yml

@@ -42,7 +42,7 @@ jobs:
 
     # Initialize minimum JDK version
     - name: Setup Java JDK
-      uses: actions/setup-java@v4.2.1
+      uses: actions/setup-java@v4.5.0
       with:
         distribution: zulu
         java-version: 17

.github/workflows/gradle.yml

@@ -24,7 +24,7 @@ jobs:
     - name: Checkout repo
       uses: actions/checkout@v4
     - name: Set up OpenJDK version ...
-      uses: actions/setup-java@v4.2.1
+      uses: actions/setup-java@v4.5.0
       with:
         distribution: 'zulu' 
         java-version: ${{ matrix.jdk }}
@@ -50,7 +50,7 @@ jobs:
     - name: Checkout repo
       uses: actions/checkout@v4
     - name: Set up OpenJDK version ...
-      uses: actions/setup-java@v4.2.1
+      uses: actions/setup-java@v4.5.0
       with:
         distribution: 'zulu' 
         java-version: ${{ env.currentBuildVersion }}

.github/workflows/publishRelease.yml

@@ -8,7 +8,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Java
-        uses: actions/setup-java@v4.2.1
+        uses: actions/setup-java@v4.5.0
         with:
           java-version: 17
           distribution: zulu

CHANGELOG.md

@@ -16,6 +16,47 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Removed
 
+## [1.2.3] - 2024-11-08
+
+### Added
+* Enhanced searching capabilities for related identifiers with new methods in the RelatedIdentifierSpec class.
+* Comprehensive unit tests added for the RelatedIdentifierSpec class to ensure robust functionality.
+
+### Fixed
+* Fixed potential issue with unprivileged find
+* Improved error messaging for missing publisher during updates in the DataResourceService.
+
+### Security
+* Update actions/setup-java action to v4.5.0
+* Update dependency com.fasterxml.jackson.datatype:jackson-datatype-joda to v2.18.1.
+* Update dependency com.fasterxml.jackson.datatype:jackson-datatype-jsr310 to v2.18.1
+* Update dependency com.fasterxml.jackson.module:jackson-module-afterburner to v2.18.1
+* Update dependency com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider to v2.18.1
+* Update dependency com.google.code.gson:gson to v2.11.0
+* Bump commons-io:commons-io from 2.16.1 to 2.17.0.
+* Update dependency de.codecentric:spring-boot-admin-starter-client to v3.3.5
+* Update dependency edu.kit.datamanager:service-base to v1.3.2
+* Update plugin io.freefair.lombok to v8.10.2
+* Update plugin io.freefair.maven-publish-java to v8.10.2
+* Update dependency gradle to v8.10.2
+* Update dependency jacoco to v0.8.12
+* Bump org.apache.tika:tika-core from 2.9.2 to 3.0.0
+* Update dependency org.javers:javers-spring-boot-starter-sql to v7.6.3
+* Bump org.javers:javers-spring-boot-starter-sql from 7.6.2 to 7.6.3
+* Update plugin org.owasp.dependencycheck to v11
+* Bump org.postgresql:postgresql from 42.7.3 to 42.7.4.
+* Update dependency org.springframework.boot:spring-boot-dependencies to v3.3.5
+* Update dependency org.springframework.data:spring-data-elasticsearch to v5.3.5
+* Update dependency org.springframework.restdocs:spring-restdocs-mockmvc to v3.0.2
+* Update dependency org.springframework:spring-messaging to v6.1.14
+
+### Deprecated
+
+### Removed
+* Removed outdated configuration for GitHub Actions in the project setup.
+
+### Security
+
 ## [1.2.2] - 2024-04-02
 
 ### Fixed
@@ -276,7 +317,8 @@ Extracted from the 'base-repo' project.
 ### Removed
 - none
 
-[Unreleased]: https://github.com/kit-data-manager/repo-core/compare/v1.2.2...HEAD
+[Unreleased]: https://github.com/kit-data-manager/repo-core/compare/v1.2.3...HEAD
+[1.2.3]: https://github.com/kit-data-manager/repo-core/compare/v1.2.2...v1.2.3
 [1.2.2]: https://github.com/kit-data-manager/repo-core/compare/v1.2.1...v1.2.2
 [1.2.1]: https://github.com/kit-data-manager/repo-core/compare/v1.2.0...v1.2.1
 [1.2.0]: https://github.com/kit-data-manager/repo-core/compare/v1.1.2...v1.2.0

build.gradle

@@ -14,12 +14,12 @@
  * limitations under the License.
  */
 plugins { 
-    id "io.freefair.lombok" version "8.6"
-    id "io.freefair.maven-publish-java" version "8.6"
-    id "io.spring.dependency-management" version "1.1.4" 
+    id "io.freefair.lombok" version "8.10.2"
+    id "io.freefair.maven-publish-java" version "8.10.2"
+    id "io.spring.dependency-management" version "1.1.6" 
     //id "com.github.kt3k.coveralls" version "2.8.1" 
-    id "org.owasp.dependencycheck" version "9.1.0"
-    id "org.asciidoctor.jvm.convert" version "4.0.2"
+    id "org.owasp.dependencycheck" version "11.1.0"
+    id "org.asciidoctor.jvm.convert" version "4.0.3"
     //id "org.ajoberstar.grgit" version "2.0.1"
     id "java"
     id "jacoco"
@@ -32,9 +32,9 @@ plugins {
 
 ext {
     // versions of dependencies
-    springBootVersion = '3.1.0'
-    springDocVersion  = '2.5.0'
-    javersVersion     = '7.4.2'
+    springBootVersion = '3.3.5'
+    springDocVersion  = '2.6.0'
+    javersVersion     = '7.6.3'
 }
 
 description = "Core module for data repositories based on metadata model of datacite."
@@ -69,15 +69,15 @@ if (project.hasProperty('release')) {
 
 dependencies {
     // Spring
-    implementation 'org.springframework:spring-messaging:6.0.2'
+    implementation 'org.springframework:spring-messaging:6.1.14'
     // Spring Boot
     implementation "org.springframework.boot:spring-boot-starter-data-rest"
     implementation "org.springframework.boot:spring-boot-starter-amqp"
     implementation "org.springframework.boot:spring-boot-starter-web"
     implementation "org.springframework.boot:spring-boot-starter-security"
     implementation "org.springframework.boot:spring-boot-starter-actuator"
     implementation "org.springframework.boot:spring-boot-starter-data-jpa"
-    implementation 'org.springframework.data:spring-data-elasticsearch:5.1.0'
+    implementation 'org.springframework.data:spring-data-elasticsearch:5.3.5'
 
 
     // springdoc
@@ -86,33 +86,34 @@ dependencies {
     implementation "org.springdoc:springdoc-openapi-starter-webmvc-api:${springDocVersion}"
     // apache
     implementation "commons-configuration:commons-configuration:1.10"
-    implementation "commons-io:commons-io:2.16.1"
+    implementation "commons-io:commons-io:2.17.0"
     implementation "org.apache.commons:commons-collections4:4.4"
     // includes commons-lang3
     implementation "org.apache.commons:commons-text:1.12.0"
     implementation 'org.apache.httpcomponents:httpclient:4.5.14'
-    implementation "org.apache.tika:tika-core:2.9.2"
+    implementation "org.apache.tika:tika-core:3.0.0"
     // javers
     implementation "org.javers:javers-spring-boot-starter-sql:${javersVersion}"
+    implementation "com.google.code.gson:gson:2.11.0"
 
     // Database
-    implementation "com.h2database:h2:2.2.224"
-    implementation "org.postgresql:postgresql:42.7.3"
+    implementation "com.h2database:h2:2.3.232"
+    implementation "org.postgresql:postgresql:42.7.4"
     // XML
-    implementation "com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider:2.17.0"
-    implementation "com.fasterxml.jackson.module:jackson-module-afterburner:2.17.0"
+    implementation "com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider:2.18.1"
+    implementation "com.fasterxml.jackson.module:jackson-module-afterburner:2.18.1"
 
-    implementation "com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.17.0"
-    implementation "com.fasterxml.jackson.datatype:jackson-datatype-joda:2.17.0"
+    implementation "com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.18.1"
+    implementation "com.fasterxml.jackson.datatype:jackson-datatype-joda:2.18.1"
 
     //implementation "com.monitorjbl:spring-json-view:1.0.1"
 
-    implementation "de.codecentric:spring-boot-admin-starter-client:3.0.4"
+    implementation "de.codecentric:spring-boot-admin-starter-client:3.3.5"
     // log4j core
     implementation "org.apache.logging.log4j:log4j-core"
     implementation "ch.qos.logback:logback-classic"
 
-    implementation "edu.kit.datamanager:service-base:1.3.1"
+    implementation "edu.kit.datamanager:service-base:1.3.2"
 
     implementation "com.github.java-json-tools:json-patch:1.13"
     implementation "com.github.dozermapper:dozer-core:7.0.0"
@@ -122,7 +123,7 @@ dependencies {
      // boot starter
     testImplementation 'org.springframework.boot:spring-boot-starter-validation'    
     testImplementation "org.springframework.boot:spring-boot-starter-test"
-    testImplementation 'org.springframework.restdocs:spring-restdocs-mockmvc:3.0.0'
+    testImplementation 'org.springframework.restdocs:spring-restdocs-mockmvc:3.0.2'
     testImplementation "org.springframework.security:spring-security-test"
 
     //Java 11 Support 
@@ -154,7 +155,7 @@ test {
 }
 
 jacoco {
-    toolVersion = "0.8.11"
+    toolVersion = "0.8.12"
 }
 
 tasks.withType(Test) {

gradle/wrapper/gradle-wrapper.jar

@@ -1,6 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.10.2-bin.zip
 networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradle/wrapper/gradle-wrapper.properties

@@ -15,6 +15,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+# SPDX-License-Identifier: Apache-2.0
+#
 
 ##############################################################################
 #
@@ -55,7 +57,7 @@
 #       Darwin, MinGW, and NonStop.
 #
 #   (3) This script is generated from the Groovy template
-#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       https://github.com/gradle/gradle/blob/HEAD/platforms/jvm/plugins-application/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
 #       within the Gradle project.
 #
 #       You can find Gradle at https://github.com/gradle/gradle/.
@@ -83,10 +85,9 @@ done
 # This is normally unused
 # shellcheck disable=SC2034
 APP_BASE_NAME=${0##*/}
-APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
+APP_HOME=$( cd -P "${APP_HOME:-./}" > /dev/null && printf '%s
+' "$PWD" ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
@@ -133,26 +134,29 @@ location of your Java installation."
     fi
 else
     JAVACMD=java
-    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+    if ! command -v java >/dev/null 2>&1
+    then
+        die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
+    fi
 fi
 
 # Increase the maximum file descriptors if we can.
 if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
         # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045 
+        # shellcheck disable=SC2039,SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
         # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045 
+        # shellcheck disable=SC2039,SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -197,11 +201,15 @@ if "$cygwin" || "$msys" ; then
     done
 fi
 
-# Collect all arguments for the java command;
-#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
-#     shell script including quotes and variable substitutions, so put them in
-#     double quotes to make sure that they get re-expanded; and
-#   * put everything else in single quotes, so that it's not re-expanded.
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Collect all arguments for the java command:
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#     and any embedded shellness will be escaped.
+#   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+#     treated as '${Hostname}' itself on the command line.
 
 set -- \
         "-Dorg.gradle.appname=$APP_BASE_NAME" \

gradlew

@@ -13,6 +13,8 @@
 @rem See the License for the specific language governing permissions and
 @rem limitations under the License.
 @rem
+@rem SPDX-License-Identifier: Apache-2.0
+@rem
 
 @if "%DEBUG%"=="" @echo off
 @rem ##########################################################################
@@ -43,11 +45,11 @@ set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
 if %ERRORLEVEL% equ 0 goto execute
 
-echo.
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
+echo. 1>&2
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
 
 goto fail
 
@@ -57,11 +59,11 @@ set JAVA_EXE=%JAVA_HOME%/bin/java.exe
 
 if exist "%JAVA_EXE%" goto execute
 
-echo.
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
-echo.
-echo Please set the JAVA_HOME variable in your environment to match the
-echo location of your Java installation.
+echo. 1>&2
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
 
 goto fail