Merge pull request #432 from FAIRDataTeam/release/1.17.0

Release 1.17.0

.github/workflows/build.yml

@@ -9,7 +9,10 @@ jobs:
     name: Test
     strategy:
       matrix:
-        os: [ubuntu-20.04, windows-2022, macos-12]
+        os:
+          - ubuntu-20.04
+          # - windows-2022 (MongoDB issues in CI)
+          - macos-12
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -28,7 +31,7 @@ jobs:
           mongo --eval "db.version()"
 
       - name: Set up JDK 17 (Temurin)
-        uses: actions/setup-java@v3.9.0
+        uses: actions/setup-java@v3
         with:
           java-version: '17'
           distribution: 'temurin'
@@ -87,7 +90,7 @@ jobs:
             type=sha
 
       - name: Docker build+push [test]
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v4
         with:
           context: .
           file: ./Dockerfile.build
@@ -117,7 +120,7 @@ jobs:
             type=semver,pattern={{version}}
 
       - name: Docker build+push [private]
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v4
         if: github.event_name == 'push' && env.PRIVATE_REGISTRY_URL != '' && steps.meta-private.outputs.tags != ''
         with:
           context: .
@@ -150,7 +153,7 @@ jobs:
             type=semver,pattern={{major}},enable=${{ !startsWith(github.ref, 'refs/tags/v0.') }}
 
       - name: Docker build+push [public]
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v4
         if: github.event_name == 'push' && env.DOCKER_HUB_USERNAME != '' && steps.meta-public.outputs.tags != ''
         with:
           context: .

.github/workflows/code-style.yml

@@ -19,7 +19,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Setup Java
-        uses: actions/setup-java@v3.9.0
+        uses: actions/setup-java@v3
         with:
           distribution: ${{ env.JAVA_DISTRIBUTION }}
           java-version: ${{ env.JAVA_VERSION }}
@@ -46,7 +46,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Setup Java
-        uses: actions/setup-java@v3.9.0
+        uses: actions/setup-java@v3
         with:
           distribution: ${{ env.JAVA_DISTRIBUTION }}
           java-version: ${{ env.JAVA_VERSION }}
@@ -73,7 +73,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Setup Java
-        uses: actions/setup-java@v3.9.0
+        uses: actions/setup-java@v3
         with:
           distribution: ${{ env.JAVA_DISTRIBUTION }}
           java-version: ${{ env.JAVA_VERSION }}

.github/workflows/security.yml

@@ -18,64 +18,33 @@ jobs:
       security-events: write
 
     env:
-      JDK_VERSION: 17
-      JDK_FILE: openjdk-17_linux-x64_bin.tar.gz
-      JDK_URL: https://download.java.net/java/GA/jdk17/0d483333a00540d886896bac774ff48b/35/GPL/openjdk-17_linux-x64_bin.tar.gz
+      JAVA_DISTRIBUTION: temurin
+      JAVA_VERSION: 17
 
     steps:
-      - uses: actions/checkout@v3
-
-      - name: Fetch all history for all tags and branches
-        run: git fetch --prune --unshallow
-
-      - name: Prepare JDK folder
-        run: mkdir -p ~/jdk
-
-      # (1) -> Prepare cache and Java
-      - name: Cache ~/.m2
-        uses: actions/[email protected]
-        with:
-          path: ~/.m2
-          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
-
-      - name: Cache JDK folder
-        uses: actions/[email protected]
-        with:
-          path: ~/jdk
-          key: ${{ env.JDK_FILE }}
-
-      # (2) -> Prepare Java
-      - name: Download JDK
-        run: |
-          if [ ! -f ~/jdk/$JDK_FILE ]; then
-            wget --quiet $JDK_URL -O ~/jdk/$JDK_FILE
-          fi
-          cp ~/jdk/$JDK_FILE .
+      - name: Checkout repository
+        uses: actions/checkout@v3
 
       - name: Setup Java
-        uses: actions/setup-java@v3.9.0
+        uses: actions/setup-java@v3
         with:
-          distribution: 'jdkfile'
-          java-version: ${{ env.JDK_VERSION }}
-          jdkFile: ${{ env.JDK_FILE }}
-          architecture: x64
+          distribution: ${{ env.JAVA_DISTRIBUTION }}
+          java-version: ${{ env.JAVA_VERSION }}
+          cache: 'maven'
 
       - name: Verify Maven and Java
         run: |
           mvn --version
 
-      # (3) -> Init CodeQL
       - name: Initialize CodeQL
         uses: github/codeql-action/init@v2
         with:
           languages: 'java'
 
-      # (3) -> Build
       - name: Build package
         run: |
           mvn --quiet -B -U --fail-fast -DskipTests package
 
-      # (4) -> CodeQL Analysis
       - name: Perform CodeQL Analysis
         uses: github/codeql-action/analyze@v2
 

CHANGELOG.md

@@ -8,6 +8,22 @@ to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 ## [Unreleased]
 
 
+## [1.17.0]
+
+### Added
+
+- Support for configuration using environment variables
+
+### Changed
+
+- Updated to Spring Boot 3
+- Updated several other dependencies
+
+### Fixed
+
+- Reset metadata schema to defaults
+- Validation on metadata record deletion
+
 ## [1.16.2]
 
 ### Fixed
@@ -351,3 +367,4 @@ The first release of reference FAIR Data Point implementation.
 [1.16.0]: /../../tree/v1.16.0
 [1.16.1]: /../../tree/v1.16.1
 [1.16.2]: /../../tree/v1.16.2
+[1.17.0]: /../../tree/v1.17.0

CITATION.cff

@@ -0,0 +1,36 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: FAIR Data Point
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Luiz Olavo
+    family-names: Bonino da Silva Santos
+    email: [email protected]
+    affiliation: University of Twente
+    orcid: 'https://orcid.org/0000-0002-1164-1351'
+  - given-names: Kees
+    family-names: Burger
+    affiliation: Leiden University Medical Center
+  - given-names: Rajaram
+    family-names: Kaliyaperumal
+    affiliation: 'Leiden University Medical Center '
+    email: [email protected]
+    orcid: 'https://orcid.org/0000-0002-1215-167X'
+  - given-names: Marek
+    family-names: Suchánek
+    affiliation: Czech Technical University in Prague
+    orcid: 'https://orcid.org/0000-0001-7525-9218'
+  - given-names: Jan
+    family-names: Slifka
+    orcid: 'https://orcid.org/0000-0002-4941-0575'
+    affiliation: Czech Technical University in Prague
+  - given-names: Mark
+    family-names: Wilkinson
+    affiliation: Universidad Politécnica de Madrid (UPM)
+    orcid: 'https://orcid.org/0000-0001-6960-357X'
+license: MIT

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2017 Dutch Techncentre for Life Sciences
+Copyright (c) 2017 FAIR Data Team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

SECURITY.md

@@ -6,12 +6,12 @@ We support the latest major and minor version with patch versions that fix vulne
 
 | Version | Supported          |
 |---------| ------------------ |
-| 1.16.2  | :white_check_mark: |
-| < 1.16  | :x:                |
+| 1.17.0  | :white_check_mark: |
+| < 1.17  | :x:                |
 
 ## Current Recommendations
 
-* Use 1.16.1 with the newest dependencies (and no known vulnerabilities)
+* Use 1.17.0 with the newest dependencies (and no known vulnerabilities)
 
 ## Reporting a Vulnerability
 

pom.xml

@@ -5,12 +5,12 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>2.7.5</version>
+        <version>3.1.1</version>
         <relativePath/> <!-- lookup parent from repository -->
     </parent>
     <groupId>nl.dtls</groupId>
     <artifactId>fairdatapoint</artifactId>
-    <version>1.16.2</version>
+    <version>1.17.0</version>
     <packaging>jar</packaging>
 
     <name>FairDataPoint</name>
@@ -55,28 +55,26 @@
         <spring.security.acl.mongo.version>5.2.4.RELEASE</spring.security.acl.mongo.version>
 
         <!-- Core -->
-        <springdoc.version>1.6.14</springdoc.version>
-        <mongock.version>5.2.2</mongock.version>
-        <mongodb.spring-data.v3.version>3.4.5</mongodb.spring-data.v3.version>
-        <rdf4j.version>4.2.2</rdf4j.version>
+        <springdoc.version>2.1.0</springdoc.version>
+        <mongock.version>5.3.1</mongock.version>
+        <mongodb.spring-data.version>4.1.1</mongodb.spring-data.version>
+        <rdf4j.version>4.3.2</rdf4j.version>
         <jwt.version>0.11.5</jwt.version>
-        <lombok.version>1.18.24</lombok.version>
+        <lombok.version>1.18.28</lombok.version>
         <rdf-resolver.version>0.1.2-SNAPSHOT</rdf-resolver.version>
-        <log4j2.version>2.17.1</log4j2.version>
+
+        <!-- Test -->
+        <httpclient5.version>5.2.1</httpclient5.version>
 
         <!-- Plugins -->
-        <plugin.license.version>4.1</plugin.license.version>
+        <plugin.license.version>4.2</plugin.license.version>
         <plugin.jacoco.version>0.7.6.201602180812</plugin.jacoco.version>
         <plugin.coveralls.version>4.3.0</plugin.coveralls.version>
         <plugin.javax_xml_bind.version>2.3.1</plugin.javax_xml_bind.version>
-        <plugin.git_commit_id.version>5.0.0</plugin.git_commit_id.version>
+        <plugin.git_commit_id.version>6.0.0</plugin.git_commit_id.version>
         <plugin.rdf4j_generator.version>0.2.0</plugin.rdf4j_generator.version>
-        <plugin.checkstyle.version>3.2.0</plugin.checkstyle.version>
-        <plugin.spotbugs.version>4.7.3.0</plugin.spotbugs.version>
-
-        <!-- override for security -->
-        <snakeyaml.version>1.31</snakeyaml.version>
-        <spring-security.version>5.7.5</spring-security.version>
+        <plugin.checkstyle.version>3.3.0</plugin.checkstyle.version>
+        <plugin.spotbugs.version>4.7.3.5</plugin.spotbugs.version>
     </properties>
 
     <repositories>
@@ -189,20 +187,20 @@
         </dependency>
         <dependency>
             <groupId>io.mongock</groupId>
-            <artifactId>mongodb-springdata-v3-driver</artifactId>
+            <artifactId>mongodb-springdata-v4-driver</artifactId>
         </dependency>
         <dependency>
             <groupId>org.springframework.data</groupId>
             <artifactId>spring-data-mongodb</artifactId>
-            <version>${mongodb.spring-data.v3.version}</version>
+            <version>${mongodb.spring-data.version}</version>
         </dependency>
 
         <!-- ////////////////// -->
         <!--   Core             -->
         <!-- ////////////////// -->
         <dependency>
             <groupId>org.springdoc</groupId>
-            <artifactId>springdoc-openapi-ui</artifactId>
+            <artifactId>springdoc-openapi-starter-webmvc-ui</artifactId>
             <version>${springdoc.version}</version>
         </dependency>
         <dependency>
@@ -279,6 +277,12 @@
             <artifactId>spring-security-test</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.apache.httpcomponents.client5</groupId>
+            <artifactId>httpclient5</artifactId>
+            <version>${httpclient5.version}</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <build>
@@ -370,12 +374,12 @@
                     <dependency>
                         <groupId>com.puppycrawl.tools</groupId>
                         <artifactId>checkstyle</artifactId>
-                        <version>10.6.0</version>
+                        <version>10.12.1</version>
                     </dependency>
                     <dependency>
                         <groupId>io.spring.javaformat</groupId>
                         <artifactId>spring-javaformat-checkstyle</artifactId>
-                        <version>0.0.35</version>
+                        <version>0.0.39</version>
                     </dependency>
                 </dependencies>
             </plugin>
@@ -456,5 +460,4 @@
             </plugin>
         </plugins>
     </build>
-
 </project>