PR for v1.5.0

.github/workflows/codeql-analysis.yml

@@ -42,7 +42,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
+      uses: github/codeql-action/init@v2
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -53,7 +53,7 @@ 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@v1
+      uses: github/codeql-action/autobuild@v2
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -67,4 +67,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      uses: github/codeql-action/analyze@v2

.github/workflows/docker-publish.yml

@@ -29,7 +29,7 @@ jobs:
         uses: actions/setup-java@v2
         with:
           distribution: 'zulu' 
-          java-version: 11
+          java-version: 17
       - name: Grant execute permission for gradlew
         run: chmod +x gradlew
       - name: Build with Gradle

.github/workflows/gradle.yml

@@ -5,13 +5,12 @@ name: build with gradle
 
 on:
   push:
-    branches: [ master, main, dev ]
+    branches: [ master, main, development ]
   pull_request:
     branches: [ master, main ]
-
 env:
     # JDK version used for building jar file
-    currentBuildVersion: 8
+    currentBuildVersion: 17
 jobs:
   build:
     runs-on: ${{ matrix.operating-system }}

CHANGELOG.md

@@ -6,14 +6,36 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
-
-Security
-
-Added
-
 Changed
+* Java 17 is now mandatory
+* Indexing support now requires Elastic 8+
 
 Fixed
+* Correctly ignore user-provided primary keys (https://github.com/kit-data-manager/base-repo/pull/131)
+
+Security
+* Bump spring-boot to 3.1.0
+* Bump spring-cloud-starter-config to 4.0.3
+* Bump spring-cloud-starter-netflix-eureka-client to 4.0.2
+* Bump spring-cloud-gateway-mvc to 4.0.6
+* Bump spring-data-elasticsearch to 5.1.2
+* Bump spring-messaging to 6.0.2
+* Bump spring-security-web to 6.1.1
+* Bump spring-security-config to 6.1.1
+* Bump spring-boot-admin-starter-client to 3.1.0
+* Bump io.spring.dependency-management to 1.1.0
+* Bump io.freefair.lombok to 8.0.1
+* Bump io.freefair.maven-publish-java to 8.0.1
+* Bump org.owasp.dependencycheck to 8.3.1
+* Bump net.researchgate.release to 3.0.2
+* Bump com.gorylenko.gradle-git-properties to 2.4.1
+* Bump javers-core to 7.0.0
+* Bump httpclient to 4.5.14
+* Bump postgresql to 42.6.0
+* Bump spring-restdocs-mockmvc to 3.0.0
+* Bump mockito-inline to 5.2.0
+* Bump repo-core to 1.2.1
+* Bump service-base to 1.2.0
 
 ## [1.4.0] - 2023-03-17
 

INTERFACE.md

@@ -0,0 +1,117 @@
+# Interfaces Overview for base-repo
+
+This document aims to answer questions on how to configure external dependencies and which public interfaces are offered by base-repo in a comprehensive way. 
+It is meant to be used for getting an overview and guidance in addition to the official documentation, which is available at the official [base-repo web page](https://kit-data-manager.github.io/webpage/base-repo/).
+
+> ℹ️ **Note:** 
+> This document applies to the base-repo version it is shipped with. If you have a specific version running, please refer to `INTERFACE.md` of this particular release.
+
+## TOC
+
+- [Interfaces Overview for base-repo](#interfaces-overview-for-base-repo)
+   * [External Dependencies](#external-dependencies-) 📤
+      + [Relational Database (mandatory)](#relational-database-mandatory-) ⛁
+      + [Local Filesystem (mandatory)](#local-filesystem-mandatory-) 📂
+      + [Messaging (optional)](#messaging-optional-) 💬
+      + [Enhanced Search (optional)](#enhanced-search-optional-) 🔍
+      + [Access Control (optional)](#access-control-optional-) 🔐
+   * [Public Interfaces](#public-interfaces-) 📥
+      + [HTTP / REST](#http--rest)
+      + [Elasticsearch Proxy](#elasticsearch-proxy-) 🔍
+      + [OAI-PMH](#oai-pmh)
+      + [Digital Object Interface Protocol (DOIP)](#digital-object-interface-protocol-doip)
+
+
+## External Dependencies 📤
+
+External dependencies are third-party services that are required for base-repo to work properly or that can be added optionally to provide additional functionality. Typically, external dependencies require
+additional software to be installed and configured, before they can be included in the base-repo configuration, which is typically done via the main configuration file `application.properties`.
+
+### Relational Database (mandatory) ⛁
+A relational database is required by base-repo to store administrative metadata for resources and content information. If not configured properly, base-repo will fail to start.
+
+#### Configuration ⚙️
+ - H2 In-Memory (driver included, used for testing, not recommended for production) [Example](https://github.com/kit-data-manager/base-repo/blob/4e90c6aeaced4715d419482f3cb127cddc85bd37/src/test/resources/test-config/application-test.properties#L31-L34)
+ - H2 File-Based (driver included, used for basic Docker setup, not recommended for production) [Example](https://github.com/kit-data-manager/base-repo/blob/4e90c6aeaced4715d419482f3cb127cddc85bd37/config/application-docker.properties#L17C1-L24)
+ - PostgreSQL (driver included, requires a running PostgreSQL server, used for production) [PostgreSQL](https://www.postgresql.org/), [Example](https://github.com/kit-data-manager/base-repo/blob/4e90c6aeaced4715d419482f3cb127cddc85bd37/config/application-default.properties#L38-L45)
+
+> ℹ️ **Note:** 
+> Other relational databases, e.g., MariaDB, SQLite, or Oracle, may also work but require additional actions. To allow base-repo to connect, the source code repository must be cloned, an appropriate JDBC driver has to be added to `build.gradle`
+> and base-repo has be be compiled. Proper JDBC drivers are typically provided on the database's Web page. Afterwards, the database can be configured in `application.properties` similar to PostgreSQL but with database-specific property naming. Please refer
+> to the driver documentation for details.
+
+### Local Filesystem (mandatory) 📂
+Access to the local filesystem is required by base-repo to store and manage uploaded data. base-repo only needs access to a single folder, which can be located on the local hard drive or mounted, e.g., via NFS. 
+
+#### Configuration ⚙️
+ - see `application.properties` [Documentation1](https://github.com/kit-data-manager/base-repo/blob/4e90c6aeaced4715d419482f3cb127cddc85bd37/config/application-default.properties#L137-L139), [Documentation2](https://github.com/kit-data-manager/base-repo/blob/4e90c6aeaced4715d419482f3cb127cddc85bd37/config/application-default.properties#L154-L165)
+
+### Messaging (optional) 💬
+AMQP-based messaging is an optional feature of base-repo, which allows base-repo to emit messages about creation, modification, and deletion events related to resources and content information. These messages can be received by registered consumers and processed in an asynchronous way.
+
+#### Configuration ⚙️
+ - RabbitMQ (dependencies included, serves as messaging distributor, requires a running RabbitMQ server) [RabbitMQ](https://www.rabbitmq.com/), [Documentation](https://kit-data-manager.github.io/webpage/base-repo/documentation/messaging-configuration.html)
+
+### Enhanced Search (optional) 🔍
+By default, base-repo offers basic search via RESTful API by example document or certain query parameters. Optionally, enhanced search via a search index can be enabled and used for fine-grained and facetted search operations.
+
+#### Configuration ⚙️
+ - Elasticsearch (dependencies included, serves as seach index, requires a running Elasticsearch server) [Elasticsearch] (https://www.elastic.co/de/elasticsearch/), [Documentation](https://kit-data-manager.github.io/webpage/base-repo/documentation/search-configuration.html), [Example](https://github.com/kit-data-manager/base-repo/blob/4e90c6aeaced4715d419482f3cb127cddc85bd37/config/application-default.properties#L104-L107)
+
+
+### Access Control (optional) 🔐
+By default, base-repo itself is open for all kinds of operations, i.e., read and write, where write access should be restricted on the user interface level, e.g., by a password-protected area for critical operations. Optionally, authentication and authorization via JSON Web Tokens (JWT) issued by a Keycloak instance, can be configured.
+
+#### Configuration ⚙️
+ - Keycloak (dependencies included, serves as identity provider, requires a running Keycloak server) [Keycloak](https://www.keycloak.org/), [Documentation (TODO)](), [Example](https://github.com/kit-data-manager/base-repo/blob/4e90c6aeaced4715d419482f3cb127cddc85bd37/config/application-default.properties#L192-L201)
+
+## Public Interfaces 📥
+
+Public Interfaces are used to access base-repo in order to obtain its contents, typically this happens via HTTP/REST. Depending on the interface, special clients or protocols must be used to access a specific public interface.
+
+### HTTP / REST
+The default way to access base-repo is via RESTful interfaces. They allow to create, update, and delete resources and content information, as well as upload and download data.
+
+#### Documentation 📖
+ - [OpenAPI](https://kit-data-manager.github.io/webpage/base-repo/documentation/api-docs.html)
+ - [Usage with Examples](https://kit-data-manager.github.io/webpage/base-repo/documentation/index.html)
+
+#### Application Examples 📋   
+ - Scripts
+ - Graphical frontends ([frontend-collection/repo-management.html](https://github.com/kit-data-manager/frontend-collection))
+
+### Elasticsearch Proxy 🔍
+If [Enhanced Search](#enhanced-search-optional-) is enabled, an additional REST endpoint becomes available, which allows to tunnel search queries to the underlying Elasticsearch instance. The advantage for proxying Elasticsearch access is, that access restrictions enabled via [Access Control](#access-control-optional-) are included in the query such that only results accessible by the caller are returned.
+
+#### Documentation 📖
+ - [Search Configuration](https://kit-data-manager.github.io/webpage/base-repo/documentation/search-configuration.html)
+
+#### Application Examples 📋
+ - Scripts
+ - Graphical frontends ([frontend-collection/elastic-search-base-repo.html](https://github.com/kit-data-manager/frontend-collection))
+
+### OAI-PMH
+[OAI-PMH](https://www.openarchives.org/pmh/) is a standardized harvesting protocol that allows to build up external search indices that can be kept up to data by regular harvesting changes from an OAI-PMH source. For base-repo, OAI-PMH functionality can be optionally added via plugin.
+
+#### Source Code 📋
+ - [OAI-PMH-Controller-Plugin](https://git.scc.kit.edu/kitdatamanager/2.0/oai-pmh-controller-plugin)
+
+#### Documentation 📖
+ - [Plugin Configuration](https://git.scc.kit.edu/kitdatamanager/2.0/oai-pmh-controller-plugin)
+ - [base-repo Integration](https://github.com/kit-data-manager/base-repo#enhanced-startup)
+
+> ℹ️ **Note:** 
+> Currently, the plugin is only available from an internal repository, which will change in near future. Furthermore, the plugin might not work with the current version of base-repo, but will be revised as soon as it becomes publicly available.
+
+### Digital Object Interface Protocol (DOIP)
+[DOIP](https://www.dona.net/sites/default/files/2018-11/DOIPv2Spec_1.pdf) is a novel protocol to provide generic access to digital resources. Instead of using HTTP-based communication, the protocol acts directly on top of TCP/IP and is therefore mainly relevant for special ecosystems.
+
+#### Source Code 📋
+ - [DOIP-Plugin](https://git.scc.kit.edu/kitdatamanager/2.0/doip-plugin)
+
+#### Documentation 📖
+ - [Plugin Configuration](https://git.scc.kit.edu/kitdatamanager/2.0/doip-plugin)
+ - [base-repo Integration](https://github.com/kit-data-manager/base-repo#enhanced-startup)
+
+> ℹ️ **Note:** 
+> Currently, the plugin is only available from an internal repository, which will change in near future. Furthermore, the plugin might not work with the current version of base-repo, but will be revised as soon as it becomes publicly available.

README.md

@@ -15,7 +15,7 @@ data resource management, e.g. register DataCite-oriented metadata and upload/do
 
 In order to build this microservice you'll need:
 
-* Java SE Development Kit 11 or higher
+* Java SE Development Kit 17 or higher
 
 After obtaining the sources change to the folder where the sources are located perform the following steps:
 
@@ -39,7 +39,7 @@ libraries and finally build the base-repo microservice itself. As a result, a fa
 
 * PostgreSQL 9.1 or higher
 * RabbitMQ 3.7.3 or higher (in case you want to use the messaging feature, which is recommended)
-* Elastic 7.X or higher (in case you want to use the search feature)
+* Elastic 8.X or higher (in case you want to use the search feature)
 
 ### Setup
 

build.gradle

@@ -1,13 +1,12 @@
 plugins { 
-    id "org.springframework.boot" version "2.7.5"
-    id "io.spring.dependency-management" version "1.1.0" 
-    id "io.freefair.lombok" version "6.5.1"
-    id "io.freefair.maven-publish-java" version "6.5.1"
-    id "com.github.kt3k.coveralls" version "2.12.0" 
-    id "org.owasp.dependencycheck" version "7.3.0"
+      id 'org.springframework.boot' version '3.1.5'
+    id 'io.spring.dependency-management' version '1.1.0'
+    id 'io.freefair.lombok' version '8.4'
+    id 'io.freefair.maven-publish-java' version '8.4'
+    id 'org.owasp.dependencycheck' version '9.0.2'
     id 'org.asciidoctor.jvm.convert' version '3.3.2'
-    id "net.researchgate.release" version "3.0.2"
-    id "com.gorylenko.gradle-git-properties" version "2.4.1"
+    id 'net.researchgate.release' version '3.0.2'
+    id 'com.gorylenko.gradle-git-properties' version '2.4.1'
     id 'java'
     id 'jacoco'
 }
@@ -29,9 +28,9 @@ repositories {
 //}
 
 ext {
-    set('javersVersion', "6.8.0")
-    set('springBootVersion', "2.7.5")
-    set('springDocVersion', "1.6.9")
+    set('javersVersion', "7.0.0")
+    set('springBootVersion', "3.1.0")
+    set('springDocVersion', "2.1.0")
     set('keycloakVersion', "19.0.0")
 
     // directory for generated code snippets during tests
@@ -42,8 +41,8 @@ println "Running gradle version: $gradle.gradleVersion"
 println "Building ${name} version: ${version}"
 println "JDK version: ${JavaVersion.current()}"
 
-sourceCompatibility = 1.8
-targetCompatibility = 1.8
+sourceCompatibility = 1.17
+targetCompatibility = 1.17
 
 if (System.getProperty('profile') == 'minimal') {
     println 'Using minimal profile for building ' + project.getName()
@@ -60,57 +59,57 @@ dependencies {
     implementation "org.springframework.boot:spring-boot-starter-data-rest"
     implementation "org.springframework.boot:spring-boot-starter-mail"
     implementation "org.springframework.boot:spring-boot-starter-actuator"
-    implementation 'org.springframework.data:spring-data-elasticsearch:4.4.6'
+    implementation 'org.springframework.data:spring-data-elasticsearch:5.2.0'
 
-    implementation "org.springframework:spring-messaging:5.3.23"
-    implementation "org.springframework.security:spring-security-web:5.7.5"
-    implementation "org.springframework.security:spring-security-config:5.7.5"
+    implementation "org.springframework:spring-messaging:6.1.0"
+    implementation "org.springframework.security:spring-security-web:6.2.0"
+    implementation "org.springframework.security:spring-security-config:6.2.0"
 
     // cloud support
-    implementation "org.springframework.cloud:spring-cloud-starter-config:3.1.5"
-    implementation "org.springframework.cloud:spring-cloud-starter-netflix-eureka-client:3.1.4"
-    implementation "org.springframework.cloud:spring-cloud-gateway-mvc:3.1.4"
-    implementation 'de.codecentric:spring-boot-admin-starter-client:2.7.10'
+    implementation "org.springframework.cloud:spring-cloud-starter-config:4.0.4"
+    implementation "org.springframework.cloud:spring-cloud-starter-netflix-eureka-client:4.0.3"
+    implementation "org.springframework.cloud:spring-cloud-gateway-mvc:4.0.6"
+    implementation 'de.codecentric:spring-boot-admin-starter-client:3.1.8'
 
 
     // springdoc
-    implementation "org.springdoc:springdoc-openapi-ui:${springDocVersion}"
-    implementation "org.springdoc:springdoc-openapi-data-rest:${springDocVersion}"
-    implementation "org.springdoc:springdoc-openapi-webmvc-core:${springDocVersion}"
+    implementation "org.springdoc:springdoc-openapi-starter-webmvc-ui:${springDocVersion}"
+    implementation "org.springdoc:springdoc-openapi-starter-common:${springDocVersion}"
+    implementation "org.springdoc:springdoc-openapi-starter-webmvc-api:${springDocVersion}"
 
-    implementation "edu.kit.datamanager:repo-core:1.1.2"
-    implementation "edu.kit.datamanager:service-base:1.1.1"
+    implementation "edu.kit.datamanager:repo-core:1.2.1"
+    implementation "edu.kit.datamanager:service-base:1.2.0"
 
     //implementation "com.github.victools:jsonschema-generator:4.23.0"
 
     //Keycloak
     // implementation "org.keycloak:keycloak-spring-boot-starter:${keycloakVersion}"
-    implementation "com.nimbusds:nimbus-jose-jwt:9.24.3"
-    implementation "io.jsonwebtoken:jjwt-api:0.11.5"
-    implementation "io.jsonwebtoken:jjwt-impl:0.11.5"
-    implementation "io.jsonwebtoken:jjwt-jackson:0.11.5"
+    implementation "com.nimbusds:nimbus-jose-jwt:9.37"
+   // implementation "io.jsonwebtoken:jjwt-api:0.11.5"
+    //implementation "io.jsonwebtoken:jjwt-impl:0.11.5"
+    //implementation "io.jsonwebtoken:jjwt-jackson:0.11.5"
 
     implementation "org.javers:javers-core:${javersVersion}"
     implementation "com.github.fge:json-patch:1.9"
     implementation "com.bazaarvoice.jolt:jolt-core:0.1.7"    
-    implementation "com.bazaarvoice.jolt:json-utils:0.1.7"    
+    implementation "com.bazaarvoice.jolt:json-utils:0.1.8"    
 
-    implementation "javax.xml.bind:jaxb-api:2.3.1"
+   // implementation "javax.xml.bind:jaxb-api:2.3.1"
 
-    runtimeOnly    "org.apache.httpcomponents:httpclient:4.5.13"
+    runtimeOnly    "org.apache.httpcomponents:httpclient:4.5.14"
 
      // driver for postgres
-    implementation "org.postgresql:postgresql:42.5.0"
+    implementation "org.postgresql:postgresql:42.7.0"
     //driver for h2
-    implementation "com.h2database:h2:2.1.214"
+    implementation "com.h2database:h2:2.2.224"
 
-    testImplementation "org.springframework.restdocs:spring-restdocs-mockmvc:2.0.6.RELEASE"
+    testImplementation "org.springframework.restdocs:spring-restdocs-mockmvc:3.0.0"
     testImplementation "org.springframework.boot:spring-boot-starter-test"
     testImplementation "org.springframework:spring-test"
     testImplementation "org.springframework.security:spring-security-test"
 
     //Java 11 Support 
-    testImplementation "org.mockito:mockito-inline:4.9.0"
+    testImplementation "org.mockito:mockito-inline:5.2.0"
     testImplementation "junit:junit:4.13.2"
 }
 

gradle.properties

@@ -7,3 +7,4 @@ action.custom-2=release
 action.custom-2.args=--configure-on-demand -w -x check -Dprofile=minimal clean build asciidoctor
 action.custom-3=jacoco
 action.custom-3.args=--configure-on-demand -w -x check clean build jacocoTestReport
+netbeans.org-netbeans-modules-web-clientproject-api.js_2e_libs_2e_folder=js/libs

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.6-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.6.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists