Merge pull request #372 from FAIRDataTeam/release/1.16.0

Release 1.16.0

.github/workflows/build.yml

@@ -9,7 +9,7 @@ jobs:
     name: Test
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        os: [ubuntu-20.04, windows-2022, macos-12]
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -23,8 +23,12 @@ jobs:
         with:
           mongodb-version: '5.0'
 
+      - name: Check MongoDB
+        run: |
+          mongo --eval "db.version()"
+
       - name: Set up JDK 17 (Temurin)
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v3.9.0
         with:
           java-version: '17'
           distribution: 'temurin'
@@ -54,6 +58,8 @@ jobs:
     env:
       PUBLIC_IMAGE: fairdata/fairdatapoint
       PRIVATE_IMAGE: ${{ secrets.PRIVATE_REGISTRY_URL }}/fairdatapoint
+      PRIVATE_REGISTRY_URL: ${{ secrets.PRIVATE_REGISTRY_URL }}
+      DOCKER_HUB_USERNAME: ${{ secrets.DOCKER_HUB_USERNAME }}
 
     steps:
       - name: Checkout repo
@@ -92,7 +98,7 @@ jobs:
 
       # PRIVATE: DOCKER REGISTRY
       - name: Docker login [private]
-        if: github.event_name != 'pull_request'
+        if: github.event_name == 'push' && env.PRIVATE_REGISTRY_URL != ''
         uses: docker/login-action@v2
         with:
           registry: ${{ secrets.PRIVATE_REGISTRY_URL }}
@@ -101,7 +107,7 @@ jobs:
 
       - name: Docker meta [private]
         id: meta-private
-        if: github.event_name != 'pull_request'
+        if: github.event_name == 'push' && env.PRIVATE_REGISTRY_URL != ''
         uses: docker/metadata-action@v4
         with:
           images: |
@@ -112,7 +118,7 @@ jobs:
 
       - name: Docker build+push [private]
         uses: docker/build-push-action@v3
-        if: github.event_name != 'pull_request' && steps.meta-private.outputs.tags != ''
+        if: github.event_name == 'push' && env.PRIVATE_REGISTRY_URL != '' && steps.meta-private.outputs.tags != ''
         with:
           context: .
           file: ./Dockerfile.build
@@ -123,15 +129,15 @@ jobs:
 
       # PUBLIC: DOCKER HUB
       - name: Docker login [public]
-        if: github.event_name != 'pull_request'
+        if: github.event_name == 'push' && env.DOCKER_HUB_USERNAME != ''
         uses: docker/login-action@v2
         with:
           username: ${{ secrets.DOCKER_HUB_USERNAME }}
           password: ${{ secrets.DOCKER_HUB_PASSWORD }}
 
       - name: Docker meta [public]
         id: meta-public
-        if: github.event_name != 'pull_request'
+        if: github.event_name == 'push' && env.DOCKER_HUB_USERNAME != ''
         uses: docker/metadata-action@v4
         with:
           images: |
@@ -145,7 +151,7 @@ jobs:
 
       - name: Docker build+push [public]
         uses: docker/build-push-action@v3
-        if: github.event_name != 'pull_request' && steps.meta-public.outputs.tags != ''
+        if: github.event_name == 'push' && env.DOCKER_HUB_USERNAME != '' && steps.meta-public.outputs.tags != ''
         with:
           context: .
           file: ./Dockerfile.build

.github/workflows/code-style.yml

@@ -0,0 +1,88 @@
+name: "Code Style"
+
+on:
+  push:
+  pull_request:
+
+jobs:
+
+  checkstyle:
+    name: Checkstyle
+    runs-on: ubuntu-latest
+
+    env:
+      JAVA_DISTRIBUTION: temurin
+      JAVA_VERSION: 17
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Setup Java
+        uses: actions/[email protected]
+        with:
+          distribution: ${{ env.JAVA_DISTRIBUTION }}
+          java-version: ${{ env.JAVA_VERSION }}
+          cache: 'maven'
+
+      - name: Verify Maven and Java
+        run: |
+          mvn --version
+
+      - name: Run Checkstyle
+        run: |
+          mvn -B checkstyle:checkstyle
+
+  spotbugs:
+    name: SpotBugs
+    runs-on: ubuntu-latest
+
+    env:
+      JAVA_DISTRIBUTION: temurin
+      JAVA_VERSION: 17
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Setup Java
+        uses: actions/[email protected]
+        with:
+          distribution: ${{ env.JAVA_DISTRIBUTION }}
+          java-version: ${{ env.JAVA_VERSION }}
+          cache: 'maven'
+
+      - name: Verify Maven and Java
+        run: |
+          mvn --version
+
+      - name: Run SpotBugs
+        run: |
+          mvn -B spotbugs:check
+
+  license-head:
+    name: License Headers
+    runs-on: ubuntu-latest
+
+    env:
+      JAVA_DISTRIBUTION: temurin
+      JAVA_VERSION: 17
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Setup Java
+        uses: actions/[email protected]
+        with:
+          distribution: ${{ env.JAVA_DISTRIBUTION }}
+          java-version: ${{ env.JAVA_VERSION }}
+          cache: 'maven'
+
+      - name: Verify Maven and Java
+        run: |
+          mvn --version
+
+      - name: Check license
+        run: |
+          mvn -B license:check

.github/workflows/security.yml

@@ -23,7 +23,7 @@ jobs:
       JDK_URL: https://download.java.net/java/GA/jdk17/0d483333a00540d886896bac774ff48b/35/GPL/openjdk-17_linux-x64_bin.tar.gz
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
@@ -33,13 +33,13 @@ jobs:
 
       # (1) -> Prepare cache and Java
       - name: Cache ~/.m2
-        uses: actions/cache@v2.1.7
+        uses: actions/cache@v3.2.2
         with:
           path: ~/.m2
           key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
 
       - name: Cache JDK folder
-        uses: actions/cache@v2.1.7
+        uses: actions/cache@v3.2.2
         with:
           path: ~/jdk
           key: ${{ env.JDK_FILE }}
@@ -53,7 +53,7 @@ jobs:
           cp ~/jdk/$JDK_FILE .
 
       - name: Setup Java
-        uses: actions/setup-java@v2.4.0
+        uses: actions/setup-java@v3.9.0
         with:
           distribution: 'jdkfile'
           java-version: ${{ env.JDK_VERSION }}
@@ -90,14 +90,14 @@ jobs:
     steps:
 
       - name: Checkout repository
-        uses: actions/checkout@master
+        uses: actions/checkout@v3
 
       - name: Perform Snyk Check (Maven)
         uses: snyk/actions/maven@master
         env:
           SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
         with:
-          args: --severity-threshold=high
+          args: --severity-threshold=critical
 
   snyk-docker:
     name: Snyk (Docker)
@@ -114,7 +114,7 @@ jobs:
     steps:
 
       - name: Checkout repository
-        uses: actions/checkout@master
+        uses: actions/checkout@v3
 
       - name: Docker build
         run: |
@@ -128,4 +128,4 @@ jobs:
           SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}
         with:
           image: fdp:snyk-test
-          args: --severity-threshold=high
+          args: --severity-threshold=critical

CHANGELOG.md

@@ -8,6 +8,19 @@ to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 ## [Unreleased]
 
 
+## [1.16.0]
+
+### Added
+
+- Application title and subtitle in config and settings
+- Possibility to configure ping endpoints in config file
+- SHACL preview for metadata schemas
+- (Index) Cleanup of harvested records before next harvesting
+
+### Fixed
+
+- Child UUIDs for a metadata schema repetition due to versions
+
 ## [1.15.0]
 
 ### Added
@@ -323,3 +336,4 @@ The first release of reference FAIR Data Point implementation.
 [1.13.2]: /../../tree/v1.13.2
 [1.14.0]: /../../tree/v1.14.0
 [1.15.0]: /../../tree/v1.15.0
+[1.16.0]: /../../tree/v1.16.0

CITATION.CFF

@@ -0,0 +1,34 @@
+# 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: Marek
+    family-names: Suchánek
+    orcid: https://orcid.org/0000-0001-7525-9218
+  - given-names: Vojtěch
+    family-names: Knaisl
+    orcid: https://orcid.org/0000-0003-0103-8468
+  - given-names: Jan
+    family-names: Slifka
+    orcid: https://orcid.org/0000-0002-4941-0575
+identifiers:
+  - type: url
+    value: 'https://github.com/FAIRDataTeam/FAIRDataPoint'
+    description: >-
+      URL for the GitHub repository of the FAIR Data
+      Point code
+repository-code: 'https://github.com/FAIRDataTeam/FAIRDataPoint'
+url: 'https://fairdatapoint.org'
+repository-artifact: 'https://hub.docker.com/r/fairdata/fairdatapoint'
+license: MIT

README.md

@@ -1,13 +1,10 @@
 # FAIR Data Point
 
 [![GitHub release (latest SemVer)](https://img.shields.io/github/v/release/FAIRDataTeam/FAIRDataPoint?sort=semver)](https://github.com/FAIRDataTeam/FAIRDataPoint/releases)
-[![GitHub Workflow Status](https://img.shields.io/github/workflow/status/FAIRDataTeam/FAIRDataPoint/FAIRDataPoint%20CI)](https://github.com/FAIRDataTeam/FAIRDataPoint/actions)
 [![Documentation Status](https://readthedocs.org/projects/fairdatapoint/badge/?version=latest)](https://fairdatapoint.readthedocs.io/en/latest/?badge=latest)
 [![License](https://img.shields.io/github/license/FAIRDataTeam/FAIRDataPoint)](https://github.com/FAIRDataTeam/FAIRDataPoint/blob/develop/LICENSE)
 [![Docker Pulls](https://img.shields.io/docker/pulls/fairdata/fairdatapoint)](https://hub.docker.com/r/fairdata/fairdatapoint)
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/61f029299b814ca8be2b8edbaab6ce50)](https://www.codacy.com/app/rajaram5/FAIRDataPoint?utm_source=github.com&utm_medium=referral&utm_content=DTL-FAIRData/FAIRDataPoint&utm_campaign=Badge_Grade)
-[![Coverage Status](https://coveralls.io/repos/github/DTL-FAIRData/FAIRDataPoint/badge.svg?branch=master)](https://coveralls.io/github/DTL-FAIRData/FAIRDataPoint?branch=master)
-[![Libraries.io dependency status for GitHub repo](https://img.shields.io/librariesio/github/FAIRDataTeam/FAIRDataPoint)](https://libraries.io/github/FAIRDataTeam/FAIRDataPoint)
+[![Libraries.io](https://img.shields.io/librariesio/github/FAIRDataTeam/FAIRDataPoint)](https://libraries.io/github/FAIRDataTeam/FAIRDataPoint)
 
 [**FAIR Data Point** (FDP)](https://www.fairdatapoint.org) is a REST API for creating, storing, and serving **FAIR
 metadata**. This FDP implementation also presents a Web-based graphical user interface (GUI). The metadata contents are
@@ -116,6 +113,22 @@ documentation.
 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).
 
+## Citation
+
+The following paper can be cite as a reference paper for the FAIR Data Point:
+
+    @article{10.1162/dint_a_00160,
+    author = {Bonino da Silva Santos, Luiz Olavo and Burger, Kees and Kaliyaperumal, Rajaram and Wilkinson, Mark D.},
+    title = "{FAIR Data Point: A FAIR-oriented approach for metadata publication}",
+    journal = {Data Intelligence},
+    pages = {1-21},
+    year = {2022},
+    month = {08},
+    issn = {2641-435X},
+    doi = {10.1162/dint_a_00160},
+    url = {https://doi.org/10.1162/dint\_a\_00160},
+    eprint = {https://direct.mit.edu/dint/article-pdf/doi/10.1162/dint\_a\_00160/2038268/dint\_a\_00160.pdf}}
+
 ## License
 
 This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for more details.

SECURITY.md

@@ -6,12 +6,12 @@ We support the latest major and minor version with patch versions that fix vulne
 
 | Version | Supported          |
 |---------| ------------------ |
-| 1.15.0  | :white_check_mark: |
-| < 1.15  | :x:                |
+| 1.16.0  | :white_check_mark: |
+| < 1.16  | :x:                |
 
 ## Current Recommendations
 
-* Use 1.15.0 with the newest dependencies (and no known vulnerabilities)
+* Use 1.16.0 with the newest dependencies (and no known vulnerabilities)
 
 ## Reporting a Vulnerability