Merge pull request #235 from kit-data-manager/development

PR for v1.0.2

.github/workflows/docker-publish.yml

@@ -60,7 +60,7 @@ jobs:
       # It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository.
       # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.
       - name: Build and push Docker image
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           push: true
@@ -109,7 +109,7 @@ jobs:
       # It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository.
       # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.
       - name: Build and push Docker image
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           push: true

.github/workflows/gradle.yml

@@ -5,13 +5,13 @@ name: build
 
 on:
   push:
-    branches: [ master, main ]
+    branches: [ main ]
   pull_request:
-    branches: [ master, main, development ]
+    branches: [ main, development ]
 
 env:
     # JDK version used for building jar file
-    currentBuildVersion: 17
+    currentBuildVersion: 21
 jobs:
   build:
     runs-on: ${{ matrix.operating-system }}
@@ -20,7 +20,7 @@ jobs:
 #        operating-system: [ubuntu-latest, macOS-latest, windows-latest]
         operating-system: [ubuntu-latest]
          # Use both LTS releases and latest one for tests
-        jdk: [ 17, 19 ]
+        jdk: [ 21, 23 ]
     steps:
     - name: Checkout repo
       uses: actions/checkout@v4
@@ -76,6 +76,6 @@ jobs:
     - name: Build with Gradle (JDK ${{ env.currentBuildVersion }})
       run: ./gradlew clean check jacocoTestReport
     - name: Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v5
       with:
         files: ./build/reports/jacoco/test/jacocoTestReport.xml #optional

CHANGELOG.md

@@ -11,6 +11,33 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+## [1.0.2] - date 2024-11-22
+### Changed
+- Update python Docker tag to v3.13 
+- Upgrade to Java 21.
+- Update dependency gradle to v8.11.1
+
+### Libs
+- Bump com.github.jknack:handlebars from 4.3.1 to 4.4.0
+- Bump com.gorylenko.gradle-git-properties from 2.4.1 to 2.4.2 
+- Bump commons-codec:commons-codec from 1.16.0 to 1.16.1 
+- Update dependency edu.kit.datamanager:service-base to v1.3.2
+- Update plugin io.freefair.lombok to v8.11 
+- Update plugin io.freefair.maven-publish-java to v8.11 
+- Update javersVersion to v7.7.0
+- Update dependency org.apache.tika:tika-core to v3
+- Bump org.asciidoctor.jvm.convert from 4.0.1 to 4.0.2
+- Bump org.json:json from 20231013 to 20240205 
+- Bump org.mockito:mockito-core from 5.8.0 to 5.10.0 
+- Bump org.owasp.dependencycheck from 9.0.8 to 9.0.9 
+- Bump org.postgresql:postgresql from 42.7.1 to 42.7.3 
+- Update plugin org.springframework.boot to v3.3.6
+- Bump org.springframework.data:spring-data-elasticsearch from 5.2.2 to 5.2.3.
+- Bump org.springframework:spring-messaging from 6.1.3 to 6.1.6
+
+### Github Actions
+- Bump codecov/codecov-action from 3 to 4 
+
 ## [1.0.1] - date 2024-01-12
 ### Changed
 - Use softlink to jar file in start script.
@@ -150,7 +177,8 @@ and mapping of metadata documents delivered by RabbitMQ
 - Mapping of metadata documents with Gemma
 - Ingest to elasticsearch
 
-[Unreleased]: https://github.com/kit-data-manager/indexing-service/compare/v1.0.1...HEAD
+[Unreleased]: https://github.com/kit-data-manager/indexing-service/compare/v1.0.2...HEAD
+[1.0.2]: https://github.com/kit-data-manager/indexing-service/compare/v1.0.1...v1.0.2
 [1.0.1]: https://github.com/kit-data-manager/indexing-service/compare/v1.0.0...v1.0.1
 [1.0.0]: https://github.com/kit-data-manager/indexing-service/compare/v0.9.0...v1.0.0
 [0.9.0]: https://github.com/kit-data-manager/indexing-service/compare/v0.1.3...v0.9.0

CITATION.cff

@@ -19,8 +19,8 @@ authors:
 title: "Indexing and Mapping Service"
 type: software
 abstract: Indexing and Mapping Service is a software for (optional) mapping and indexing metadata documents for (elastic)search.
-version: 0.9.0
-date-released: 2023-07-25
+version: 1.0.2
+date-released: 2024-11-22
 url: "https://github.com/kit-data-manager/indexing-service"
 repository-code:  "https://github.com/kit-data-manager/indexing-service"
 license: Apache-2.0

Dockerfile

@@ -11,15 +11,16 @@ ARG SERVICE_ROOT_DIRECTORY_DEFAULT=/spring/
 ####################################################
 # Building environment (java & git)
 ####################################################
-FROM python:3.10 AS build-env-java
+FROM python:3.13 AS build-env-java
 LABEL [email protected]
 LABEL stage=build-env
 
 # Install git as additional requirement
 RUN apt-get update && \
     apt-get upgrade --no-install-recommends --assume-yes && \
     apt-get install --no-install-recommends --assume-yes git && \
-    apt-get install --no-install-recommends --assume-yes openjdk-17-jdk && \
+    wget https://download.oracle.com/java/21/latest/jdk-21_linux-x64_bin.deb && \
+    dpkg -i jdk-21_linux-x64_bin.deb && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
@@ -50,7 +51,7 @@ RUN bash ./build4docker.sh $SERVICE_DIRECTORY
 ####################################################
 # Runtime environment 4 indexing-service
 ####################################################
-FROM python:3.10 AS run-service-indexing
+FROM python:3.13 AS run-service-indexing
 LABEL [email protected]
 LABEL stage=run
 
@@ -67,7 +68,8 @@ ENV REPO_PORT=${REPO_PORT_DEFAULT}
 # Install JDK17
 RUN apt-get update && \
     apt-get upgrade --no-install-recommends --assume-yes && \
-    apt-get install --no-install-recommends --assume-yes openjdk-17-jdk && \
+    wget https://download.oracle.com/java/21/latest/jdk-21_linux-x64_bin.deb && \
+    dpkg -i jdk-21_linux-x64_bin.deb && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 

build.gradle

@@ -1,20 +1,20 @@
 plugins { 
-    id "org.springframework.boot" version "3.2.1"
-    id "io.spring.dependency-management" version "1.1.4" 
-    id "io.freefair.lombok" version "8.4"
-    id "io.freefair.maven-publish-java" version "8.4"
-    id "org.owasp.dependencycheck" version "9.0.8"
-    id 'org.asciidoctor.jvm.convert' version '4.0.1'
+    id "org.springframework.boot" version "3.3.6"
+    id "io.spring.dependency-management" version "1.1.6" 
+    id "io.freefair.lombok" version "8.11"
+    id "io.freefair.maven-publish-java" version "8.11"
+    id "org.owasp.dependencycheck" version "11.1.0"
+    id 'org.asciidoctor.jvm.convert' version '4.0.3'
     id 'net.researchgate.release' version '3.0.2'
-    id "com.gorylenko.gradle-git-properties" version "2.4.1"
+    id "com.gorylenko.gradle-git-properties" version "2.4.2"
     id 'java'
     id 'jacoco'
 }
 
 ext {
   // versions of dependencies
-  javersVersion     = '7.3.7'
-  springDocVersion  = '2.3.0'
+  javersVersion     = '7.7.0'
+  springDocVersion  = '2.6.0'
 }
 
 description = 'Generic indexing service supporting different mapping implementations.'
@@ -30,8 +30,8 @@ repositories {
 }
 
 java {
-    sourceCompatibility = JavaVersion.VERSION_17
-    targetCompatibility = JavaVersion.VERSION_17
+    sourceCompatibility = JavaVersion.VERSION_21
+    targetCompatibility = JavaVersion.VERSION_21
 }
 
 configurations {
@@ -51,8 +51,8 @@ if (System.getProperty('profile') == 'minimal') {
 
 dependencies {
     // Spring
-    implementation 'org.springframework:spring-messaging:6.1.3'
-    implementation 'org.springframework.cloud:spring-cloud-gateway-mvc:4.1.1'
+    implementation 'org.springframework:spring-messaging:6.2.0'
+    implementation 'org.springframework.cloud:spring-cloud-gateway-mvc:4.1.5'
 
     // Spring Boot
     // boot starter
@@ -63,49 +63,49 @@ dependencies {
     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:5.2.2'
+    implementation 'org.springframework.data:spring-data-elasticsearch:5.4.0'
 
     // springdoc
     implementation "org.springdoc:springdoc-openapi-starter-webmvc-ui:${springDocVersion}"
     implementation "org.springdoc:springdoc-openapi-starter-common:${springDocVersion}"
     implementation "org.springdoc:springdoc-openapi-starter-webmvc-api:${springDocVersion}"
 
     // driver for postgres
-    implementation "org.postgresql:postgresql:42.7.1"
+    implementation "org.postgresql:postgresql:42.7.4"
     //driver for h2
-    implementation "com.h2database:h2:2.2.224"
+    implementation "com.h2database:h2:2.3.232"
 
     //apache
-    implementation "org.apache.tika:tika-core:2.9.1"
-    implementation "commons-codec:commons-codec:1.16.0"
+    implementation "org.apache.tika:tika-core:3.0.0"
+    implementation "commons-codec:commons-codec:1.17.1"
 
-    implementation "com.github.jknack:handlebars:4.3.1"
-    implementation "org.json:json:20231013"
+    implementation "com.github.jknack:handlebars:4.4.0"
+    implementation "org.json:json:20240303"
 
     // javers
     implementation "org.javers:javers-spring-boot-starter-sql:${javersVersion}"
     implementation "org.javers:javers-core:${javersVersion}"
 
     // datamanager
     implementation "edu.kit.datamanager:generic-message-consumer:1.1.1"
-    implementation "edu.kit.datamanager:repo-core:1.2.1"
-    implementation "edu.kit.datamanager:service-base:1.2.0"
+    implementation "edu.kit.datamanager:repo-core:1.2.3"
+    implementation "edu.kit.datamanager:service-base:1.3.2"
 
     // actuator
-    implementation 'de.codecentric:spring-boot-admin-starter-client:3.2.1'
+    implementation 'de.codecentric:spring-boot-admin-starter-client:3.3.6'
 
     runtimeOnly    'org.apache.httpcomponents:httpclient:4.5.14'
 
     // Additional libraries for tests
-    testImplementation "com.google.guava:guava:33.0.0-jre"
+    testImplementation "com.google.guava:guava:33.3.1-jre"
 
     //Java 11 Support 
-    testImplementation "org.mockito:mockito-core:5.8.0"
+    testImplementation "org.mockito:mockito-core:5.14.2"
     testImplementation "junit:junit:4.13.2"
 
      // boot starter
     testImplementation "org.springframework.boot:spring-boot-starter-test"
-    testImplementation 'org.springframework.restdocs:spring-restdocs-mockmvc:3.0.1'
+    testImplementation 'org.springframework.restdocs:spring-restdocs-mockmvc:3.0.3'
     testImplementation "org.springframework.security:spring-security-test"
     testImplementation "org.springframework:spring-test"
 }
@@ -132,7 +132,7 @@ bootJar {
 }
 
 jacoco {
-    toolVersion = "0.8.10"
+    toolVersion = "0.8.12"
 }
 
 // task for printing project name.

gradle.properties

@@ -15,4 +15,3 @@ action.custom-3=asciidoctor
 action.custom-3.args=--configure-on-demand -w -x check asciidoctor
 action.custom-4=buildBootableJar
 action.custom-4.args=--configure-on-demand -w -x check -x test -Prelease build
-netbeans.hint.jdkPlatform=JDK_17

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.2.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.11.1-bin.zip
 networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -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" \