Merge pull request #253 from FAIRDataTeam/release/1.13.0

Release 1.13.0
FAIRDataTeam · Mar 4, 2022 · 6c276ce · 6c276ce
2 parents 293b11c + 030840c
commit 6c276ce
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -5,3 +5,13 @@ updates:
     schedule:
       interval: "daily"
     target-branch: "develop"
+    labels:
+      - "dependencies"
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    target-branch: "develop"
+    labels:
+      - "dependencies"
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -12,11 +12,13 @@ jobs:
     env:
       PUBLIC_IMAGE: fairdata/fairdatapoint
       PRIVATE_IMAGE: ${{ secrets.PRIVATE_REGISTRY_URL }}/fairdatapoint
+      DOCKER_HUB_USERNAME: ${{ secrets.DOCKER_HUB_USERNAME }}
+      PRIVATE_REGISTRY_URL: ${{ secrets.PRIVATE_REGISTRY_URL }}
       TAG_DEVELOP: develop
       TAG_LATEST: latest
-      JDK_VERSION: 16
-      JDK_FILE: openjdk-16.0.1_linux-x64_bin.tar.gz
-      JDK_URL: https://download.java.net/java/GA/jdk16.0.1/7147401fd7354114ac51ef3e1328291f/9/GPL/openjdk-16.0.1_linux-x64_bin.tar.gz
+      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
 
     services:
       mongo:
@@ -36,13 +38,13 @@ jobs:
 
 # (1) -> Prepare cache and Java
     - name: Cache ~/.m2
-      uses: actions/cache@v1
+      uses: actions/cache@v2.1.7
       with:
         path: ~/.m2
         key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
 
     - name: Cache JDK folder
-      uses: actions/cache@v1
+      uses: actions/cache@v2.1.7
       with:
         path: ~/jdk
         key: ${{ env.JDK_FILE }}
@@ -56,10 +58,12 @@ jobs:
         cp ~/jdk/$JDK_FILE .
 
     - name: Setup Java
-      uses: actions/setup-java@v1
+      uses: actions/setup-java@v2.5.0
       with:
+        distribution: 'jdkfile'
         java-version: ${{ env.JDK_VERSION }}
         jdkFile: ${{ env.JDK_FILE }}
+        architecture: x64
 
     - name: Verify Maven and Java
       run: |
@@ -88,28 +92,33 @@ jobs:
     - name: Docker build
       run: |
         docker pull $PUBLIC_IMAGE:$TAG_DEVELOP
-        docker build --cache-from $PUBLIC_IMAGE:$TAG_DEVELOP -t $PRIVATE_IMAGE:$GITHUB_SHA .
+        docker build --cache-from $PUBLIC_IMAGE:$TAG_DEVELOP -t ${PRIVATE_IMAGE#/}:$GITHUB_SHA .
 
 # (5) -> Docker image tagging
-    - name: Docker login
-      if: github.event_name == 'push'
+    - name: Docker login (private)
+      if: github.event_name == 'push' && env.PRIVATE_REGISTRY_URL != ''
       run: |
-        docker login -u "$DOCKER_HUB_USERNAME" -p "$DOCKER_HUB_PASSWORD"
         docker login -u "$PRIVATE_REGISTRY_USERNAME" -p "$PRIVATE_REGISTRY_PASSWORD" "$PRIVATE_REGISTRY_URL"
       env:
-        DOCKER_HUB_USERNAME: ${{ secrets.DOCKER_HUB_USERNAME }}
-        DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}
         PRIVATE_REGISTRY_URL: ${{ secrets.PRIVATE_REGISTRY_URL }}
         PRIVATE_REGISTRY_USERNAME: ${{ secrets.PRIVATE_REGISTRY_USERNAME }}
         PRIVATE_REGISTRY_PASSWORD: ${{ secrets.PRIVATE_REGISTRY_PASSWORD }}
 
+    - name: Docker login (public)
+      if: github.event_name == 'push' && env.DOCKER_HUB_USERNAME != ''
+      run: |
+        docker login -u "$DOCKER_HUB_USERNAME" -p "$DOCKER_HUB_PASSWORD"
+      env:
+        DOCKER_HUB_USERNAME: ${{ secrets.DOCKER_HUB_USERNAME }}
+        DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}
+
     - name: Docker push - commit SHA (private)
-      if: github.event_name == 'push' && !startsWith(github.ref, 'refs/tags/')
+      if: github.event_name == 'push' && !startsWith(github.ref, 'refs/tags/') && env.PRIVATE_REGISTRY_URL != ''
       run: |
         docker push $PRIVATE_IMAGE:$GITHUB_SHA
 
     - name: Docker tag and push - branch (private)
-      if: github.event_name == 'push' && startsWith(github.ref, 'refs/heads/') && !contains(github.ref, 'release')
+      if: github.event_name == 'push' && startsWith(github.ref, 'refs/heads/') && !contains(github.ref, 'release') && env.PRIVATE_REGISTRY_URL != ''
       run: |
         GITHUB_BRANCH=`echo $GITHUB_REF | cut -d/ -f3- | sed 's#/#-#g'`
         docker image tag $PRIVATE_IMAGE:$GITHUB_SHA $PRIVATE_IMAGE:$GITHUB_BRANCH

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,24 @@ to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 ## [Unreleased]
 
 
+## [1.13.0]
+
+### Added
+
+- Profile resources contain `rdfs:label` with Shape name
+
+### Changed
+
+- Replaced `**` wildcards with safer pattern
+- Added restriction to URL prefixes of Resource Definitions (`[a-zA-Z_-]*`)
+- Upgrade Java JDK from 16 to 17
+- Updated SpringDoc OpenAPI UI and several other dependencies
+- Compliance with FDP-O ontology (`fdp-o:FAIRDataPoint`)
+
+### Fixed
+
+- Missing `xsd` prefix in some default shapes
+
 ## [1.12.4]
 
 ### Changed
@@ -268,3 +286,4 @@ The first release of reference FAIR Data Point implementation.
 [1.12.2]: /../../tree/v1.12.2
 [1.12.3]: /../../tree/v1.12.3
 [1.12.4]: /../../tree/v1.12.4
+[1.13.0]: /../../tree/v1.13.0
diff --git a/Dockerfile b/Dockerfile
@@ -21,7 +21,7 @@
 # THE SOFTWARE.
 #
 
-FROM openjdk:16-jdk-slim
+FROM openjdk:17-jdk-slim
 
 WORKDIR /fdp
 

diff --git a/Dockerfile.build b/Dockerfile.build
@@ -22,7 +22,7 @@
 #
 ################################################################################
 # BUILD STAGE
-FROM maven:3-openjdk-16 as builder
+FROM maven:3-openjdk-17-slim as builder
 
 WORKDIR /builder
 
@@ -32,7 +32,7 @@ RUN mvn --quiet -B -U --fail-fast -DskipTests package
 
 ################################################################################
 # RUN STAGE
-FROM openjdk:16-jdk-slim
+FROM openjdk:17-jdk-slim
 
 WORKDIR /fdp
 

diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@ the [FAIR Data Point software specification](https://specs.fairdatapoint.org) do
 ## Usage
 
 More information about FDP, how to deploy it and use it can be found in
-the [FDP Deployment Documentation](https://fairdatapoint.readthedocs.io/).
+the [FDP Deployment and REST API usage Documentation](https://fairdatapoint.readthedocs.io/).
 
 ## Related GitHub Projects
 
@@ -33,16 +33,16 @@ details of API calls can be found there. It also allows trying out API calls dir
 document please visit the following url via web
 browser [localhost:8080/swagger-ui.html](http://localhost:8080/swagger-ui.html) (for local deployment)
 or `https://your.domain.tld/swagger-ui.html` for your deployment (
-e.g. [app.fairdatapoint.org/swagger-ui.html](https://app.fairdatapoint.org/swagger-ui.html)).
+e.g. [app.fairdatapoint.org/swagger-ui.html](https://app.fairdatapoint.org/swagger-ui.html)).  More detailed descriptions and examples of these API calls is available in the [Deployment and Usage instructions](https://fairdatapoint.readthedocs.io/)
 
 ## Development
 
 ### Technology Stack
 
-- **Java** (JDK 16)
+- **Java** (JDK 17)
 - **MongoDB** (4.2)
 - **Maven** (3.2.5 or higher)
-- **Docker** (17.09.0-ce or higher) - *for building Docker image only*
+- **Docker** (19.03.0-ce or higher) - *for building Docker image only*
 
 ### Build & Run
 
@@ -114,8 +114,7 @@ documentation.
 ## Contributing
 
 We maintain a [CHANGELOG](CHANGELOG.md), you should also take a look at our [Contributing guidelines](CONTRIBUTING.md)
-and
-[Code of Conduct](CODE_OF_CONDUCT.md).
+and [Code of Conduct](CODE_OF_CONDUCT.md).
 
 ## License
 

diff --git a/pom.xml b/pom.xml
@@ -5,12 +5,12 @@
     <parent>
         <groupId>org.springframework.boot</groupId>
         <artifactId>spring-boot-starter-parent</artifactId>
-        <version>2.5.3</version>
+        <version>2.6.3</version>
         <relativePath/> <!-- lookup parent from repository -->
     </parent>
     <groupId>nl.dtls</groupId>
     <artifactId>fairdatapoint</artifactId>
-    <version>1.12.4</version>
+    <version>1.13.0</version>
     <packaging>jar</packaging>
 
     <name>FairDataPoint</name>
@@ -47,22 +47,21 @@
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 
         <!-- Maven -->
-        <maven.compiler.source>16</maven.compiler.source>
-        <maven.compiler.target>16</maven.compiler.target>
+        <maven.compiler.source>17</maven.compiler.source>
+        <maven.compiler.target>17</maven.compiler.target>
 
         <!-- Project related -->
         <spring.rdf.migration.version>1.1.0.RELEASE</spring.rdf.migration.version>
         <spring.security.acl.mongo.version>5.2.4.RELEASE</spring.security.acl.mongo.version>
 
         <!-- Core -->
-        <springdoc.version>1.5.2</springdoc.version>
-        <mongock.version>4.3.8</mongock.version>
-        <mongodb.driver-sync.version>4.2.3</mongodb.driver-sync.version>
-        <mongodb.spring-data.v3.version>3.2.3</mongodb.spring-data.v3.version>
-        <rdf4j.version>3.7.2</rdf4j.version>
+        <springdoc.version>1.6.5</springdoc.version>
+        <mongock.version>5.0.35</mongock.version>
+        <mongodb.spring-data.v3.version>3.3.1</mongodb.spring-data.v3.version>
+        <rdf4j.version>3.7.4</rdf4j.version>
         <unirest.version>1.4.9</unirest.version>
         <jwt.version>0.11.2</jwt.version>
-        <lombok.version>1.18.20</lombok.version>
+        <lombok.version>1.18.22</lombok.version>
         <rdf-resolver.version>0.1.2-SNAPSHOT</rdf-resolver.version>
         <log4j2.version>2.17.1</log4j2.version>
 
@@ -105,7 +104,7 @@
     <dependencyManagement>
         <dependencies>
             <dependency>
-                <groupId>com.github.cloudyrock.mongock</groupId>
+                <groupId>io.mongock</groupId>
                 <artifactId>mongock-bom</artifactId>
                 <version>${mongock.version}</version>
                 <type>pom</type>
@@ -180,18 +179,13 @@
         <!--   Mongock          -->
         <!-- ////////////////// -->
         <dependency>
-            <groupId>com.github.cloudyrock.mongock</groupId>
-            <artifactId>mongock-spring-v5</artifactId>
+            <groupId>io.mongock</groupId>
+            <artifactId>mongock-springboot</artifactId>
         </dependency>
         <dependency>
-            <groupId>com.github.cloudyrock.mongock</groupId>
+            <groupId>io.mongock</groupId>
             <artifactId>mongodb-springdata-v3-driver</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.mongodb</groupId>
-            <artifactId>mongodb-driver-sync</artifactId>
-            <version>${mongodb.driver-sync.version}</version>
-        </dependency>
         <dependency>
             <groupId>org.springframework.data</groupId>
             <artifactId>spring-data-mongodb</artifactId>
@@ -417,8 +411,8 @@
                             <url>https://raw.githubusercontent.com/re3data/ontology/master/r3dOntology.ttl</url>
                         </vocabulary>
                         <vocabulary>
-                            <url>https://raw.githubusercontent.com/DTL-FAIRData/FDP-O/develop/fdp-ontology.owl</url>
-                            <namespace>http://rdf.biosemantics.org/ontologies/fdp-o#</namespace>
+                            <url>https://raw.githubusercontent.com/FAIRDataTeam/FDP-O/v1.1/fdp-ontology.owl</url>
+                            <namespace>https://w3id.org/fdp/fdp-o#</namespace>
                             <prefix>fdp</prefix>
                         </vocabulary>
                         <vocabulary>

diff --git a/src/main/java/nl/dtls/fairdatapoint/api/controller/dashboard/DashboardController.java b/src/main/java/nl/dtls/fairdatapoint/api/controller/dashboard/DashboardController.java
@@ -58,8 +58,8 @@ public class DashboardController {
     @GetMapping(produces = MediaType.APPLICATION_JSON_VALUE)
     public ResponseEntity<List<DashboardItemDTO>> getDashboard(HttpServletRequest request) throws MetadataServiceException {
         IRI uri = i(getRequestURL(request, persistentUrl));
-        IRI repositoryUri = removeLastPartOfIRI(uri);
-        List<DashboardItemDTO> dto = dashboardService.getDashboard(repositoryUri);
+        IRI fdpUri = removeLastPartOfIRI(uri);
+        List<DashboardItemDTO> dto = dashboardService.getDashboard(fdpUri);
         return new ResponseEntity<>(dto, HttpStatus.OK);
     }