Merge branch 'development' into dependabot/bundler/corese-unit-test/s…

…rc/test/resources/data/rdf-star-main/rexml-3.3.3

.github/workflows/nightly-build.yml

@@ -0,0 +1,88 @@
+name: Nightly Build
+
+on:
+  push:
+    branches:
+      - development
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+        with:
+          ref: development
+
+      - name: Set up JDK 11
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: '11'
+
+      - name: Build with Maven
+        run: mvn clean install
+
+      - name: Rename and Copy Artifacts
+        run: |
+          short_commit=$(git rev-parse --short HEAD)
+          cp $(find ./corese-core/target/ -name 'corese-core-*-jar-with-dependencies.jar') ./corese-core-${short_commit}-nightly.jar
+          cp $(find ./corese-command/target/ -name 'corese-command-*.jar') ./corese-command-${short_commit}-nightly.jar
+          cp $(find ./corese-gui/target/ -name 'corese-gui-*.jar') ./corese-gui-${short_commit}-nightly.jar
+          cp $(find ./corese-jena/target/ -name 'corese-jena-*.jar') ./corese-jena-${short_commit}-nightly.jar
+          cp $(find ./corese-rdf4j/target/ -name 'corese-rdf4j-*.jar') ./corese-rdf4j-${short_commit}-nightly.jar
+          cp $(find ./corese-server/target/ -name 'corese-server-*.jar') ./corese-server-${short_commit}-nightly.jar
+
+      - name: Upload Build Artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: nightly-build
+          path: ./corese-*-nightly.jar
+
+  delete_previous_prerelease:
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+        with:
+          ref: development
+
+      - name: Delete previous nightly tag
+        run: |
+          latest_nightly_tag=$(gh release list --limit 1 --exclude-drafts --json tagName,isPrerelease -q '.[] | select(.isPrerelease) | .tagName')
+          if [ -n "$latest_nightly_tag" ]; then
+            gh release delete "$latest_nightly_tag" -y
+            gh api --method DELETE "/repos/${{ github.repository }}/git/refs/tags/$latest_nightly_tag"
+          else
+            echo "No previous nightly tag found."
+          fi
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  create_prerelease:
+    runs-on: ubuntu-latest
+    needs: delete_previous_prerelease
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+        with:
+          ref: development
+
+      - name: Download Build Artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: nightly-build
+          path: ./artifacts
+
+      - name: Create new prerelease
+        run: |
+          short_commit=$(git rev-parse --short HEAD)
+          date=$(date +'%Y%m%d')
+          tag_name="nightly-${date}-${short_commit}"
+          gh release create "$tag_name" -p -t "Nightly Build ${short_commit}" -n "This is an automated nightly build. It is a development version and not stable." --target development
+          gh release upload "$tag_name" ./artifacts/corese-*-nightly.jar
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/sphinx.yml

@@ -0,0 +1,36 @@
+name: "Sphinx: Render docs"
+
+on: push
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+
+    - name: Checkout development branch
+      uses: actions/checkout@v4
+      with:
+        ref: development
+
+    - name: Build Sphinx Docs
+      uses: ammaraskar/sphinx-action@master
+      with:
+        pre-build-command: "apt-get install doxygen -y"
+        build-command: "make html"
+        docs-folder: "docs/"
+
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: html-docs
+        path: docs/build/html/
+
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      if: github.ref == 'refs/heads/development'
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/build/html
+

.gitignore

@@ -99,4 +99,10 @@ earl-report-test.ttl
 ##############################
 ## flatpak
 ##############################
-.flatpak-builder/
+.flatpak-builder/
+
+##############################
+## test report
+##############################
+earlReport.ttl
+testReport.csv

CHANGELOG.md

@@ -2,6 +2,8 @@
 
 # Corese Changelog
 
+## 4.5.1 – 
+
 ## 4.5.0 – 2023/12/14
 
 ### Added

README.md

@@ -41,21 +41,21 @@ There are several interfaces for Corese:
 <dependency>
     <groupId>fr.inria.corese</groupId>
     <artifactId>corese-core</artifactId>
-    <version>4.5.0</version>
+    <version>4.5.1</version>
 </dependency>
 
 <!-- jena storage -->
 <dependency>
     <groupId>fr.inria.corese</groupId>
     <artifactId>corese-jena</artifactId>
-    <version>4.5.0</version>
+    <version>4.5.1</version>
 </dependency>
 
 <!-- rdf4j storage -->
 <dependency>
     <groupId>fr.inria.corese</groupId>
     <artifactId>corese-rdf4j</artifactId>
-    <version>4.5.0</version>
+    <version>4.5.1</version>
 </dependency>
 ```
 
@@ -74,8 +74,8 @@ docker run --name my-corese \
 - Alternatively, download [Corese-server jar file](https://project.inria.fr/corese/jar/).
 
 ```sh
-wget "https://github.com/Wimmics/corese/releases/download/release-4.5.0/corese-server-4.5.0.jar"
-java -jar "-Dfile.encoding=UTF8" "corese-server-4.5.0.jar"
+wget "https://github.com/Wimmics/corese/releases/download/release-4.5.1/corese-server-4.5.1.jar"
+java -jar "-Dfile.encoding=UTF8" "corese-server-4.5.1.jar"
 ```
 
 - Documentation:
@@ -94,8 +94,8 @@ java -jar "-Dfile.encoding=UTF8" "corese-server-4.5.0.jar"
 - Or download [Corese-gui jar file](https://project.inria.fr/corese/jar/).
 
 ```sh
-wget "https://github.com/Wimmics/corese/releases/download/release-4.5.0/corese-gui-4.5.0.jar"
-java -jar "-Dfile.encoding=UTF8" "corese-gui-4.5.0.jar"
+wget "https://github.com/Wimmics/corese/releases/download/release-4.5.1/corese-gui-4.5.1.jar"
+java -jar "-Dfile.encoding=UTF8" "corese-gui-4.5.1.jar"
 ```
 
 ### Corese-Command
@@ -110,8 +110,8 @@ java -jar "-Dfile.encoding=UTF8" "corese-gui-4.5.0.jar"
 - Or download [Corese-command jar file](https://project.inria.fr/corese/jar/).
 
 ```sh
-wget "https://github.com/Wimmics/corese/releases/download/release-4.5.0/corese-command-4.5.0.jar"
-java -jar "-Dfile.encoding=UTF8" "corese-command-4.5.0.jar"
+wget "https://github.com/Wimmics/corese/releases/download/release-4.5.1/corese-command-4.5.1.jar"
+java -jar "-Dfile.encoding=UTF8" "corese-command-4.5.1.jar"
 ```
 
 - Alternatively, use the installation script for Linux and MacOS systems.
@@ -135,8 +135,8 @@ curl -sSL https://files.inria.fr/corese/distrib/script/uninstall-corese-command.
 - Download [Corese-python jar file](https://project.inria.fr/corese/jar/).
 
 ```sh
-wget "https://github.com/Wimmics/corese/releases/download/release-4.5.0/corese-library-python-4.5.0.jar"
-java -jar "-Dfile.encoding=UTF8" "corese-library-python-4.5.0.jar"
+wget "https://github.com/Wimmics/corese/releases/download/release-4.5.1/corese-library-python-4.5.1.jar"
+java -jar "-Dfile.encoding=UTF8" "corese-library-python-4.5.1.jar"
 ```
 
 - Documentation: [Getting Started With Corese-python](/docs/corese-python/Corese-library%20with%20Python.md)
@@ -153,7 +153,7 @@ mvn clean install -DskipTests
 
 ## How to cite Corese
 
-Use the "Cite this repository" option on the right side of this page.
+Use the "Cite this repository" option on the right side of this page or Hal [hal-04170333](https://hal.science/hal-04170333).
 
 ## Contributions and discussions
 

corese-command/metadata/flatpak/fr.inria.corese.CoreseCommand.yml

@@ -31,7 +31,7 @@ modules:
 
     sources:
       - type: file
-        url: https://github.com/Wimmics/corese/releases/download/release-4.5.0/corese-command-4.5.0.jar
+        url: https://github.com/Wimmics/corese/releases/download/release-4.5.1/corese-command-4.5.1.jar
         sha256: 2b15c46a9643eafb1119db9579e4f259e576647d9f322f437089960120960393
         x-checker-data:
           type: json
@@ -42,6 +42,6 @@ modules:
       - type: git
         dest: git_repo
         url: https://github.com/Wimmics/corese
-        tag: metadata-4.5.0
+        tag: metadata-4.5.1
       - type: file
         path: run.sh

corese-command/metadata/fr.inria.corese.CoreseCommand.appdata.xml

@@ -109,6 +109,10 @@
     </screenshots>
 
     <releases>
+        <release version="4.5.1" date="">
+            <description>
+            </description>
+        </release>
         <release version="4.5.0" date="2023-12-14">
             <description>
                 <ul>
@@ -142,27 +146,36 @@
             <description>
                 <p>
                     - Enhanced 'convert' and 'sparql' to accept URL and standard input.&#10;
-                    - 'sparql' and 'convert' now support standard output and multiple file inputs.&#10;
-                    - Expanded 'sparql' to handle directories, recursive directories, and various query types (SELECT, CONSTRUCT, ASK, etc.).&#10;
+                    - 'sparql' and 'convert' now support standard output and multiple file
+                    inputs.&#10;
+                    - Expanded 'sparql' to handle directories, recursive directories, and various
+                    query types (SELECT, CONSTRUCT, ASK, etc.).&#10;
                     - User can choose result format in 'sparql', including markdown.&#10;
                     - Added mime type as a format name.&#10;
                     – Disabled owl:imports auto-import.&#10;
-                    - Docker users can pass custom options and adjust log level for Corese-server.&#10;
+                    - Docker users can pass custom options and adjust log level for
+                    Corese-server.&#10;
                     - Standardized format names in Corese-command.&#10;
                     - Removed 'owlProfile' and 'ldscript'; to return after refactoring.&#10;
                     - Fixed warning related to sun.reflect.Reflection.getCallerClass.
                 </p>
                 <!-- French translation -->
                 <p xml:lang="fr">
-                    - Amélioration des commandes 'convert' et 'sparql' pour accepter les URL et l'entrée standard.&#10;
-                    - 'sparql' et 'convert' supportent désormais la sortie standard et de multiples fichiers en entrée.&#10;
-                    - Extension de 'sparql' pour gérer les répertoires, les sous-répertoires et divers types de requêtes (SELECT, CONSTRUCT, ASK, etc.).&#10;
-                    - L'utilisateur peut choisir le format du résultat dans 'sparql', y compris en markdown.&#10;
+                    - Amélioration des commandes 'convert' et 'sparql' pour accepter les URL et
+                    l'entrée standard.&#10;
+                    - 'sparql' et 'convert' supportent désormais la sortie standard et de multiples
+                    fichiers en entrée.&#10;
+                    - Extension de 'sparql' pour gérer les répertoires, les sous-répertoires et
+                    divers types de requêtes (SELECT, CONSTRUCT, ASK, etc.).&#10;
+                    - L'utilisateur peut choisir le format du résultat dans 'sparql', y compris en
+                    markdown.&#10;
                     - Ajout du type MIME comme nom de format.&#10;
                     – Désactivation de l'auto-importation owl:imports.&#10;
-                    - Les utilisateurs de Docker peuvent passer des options personnalisées et ajuster le niveau de journalisation pour Corese-server.&#10;
+                    - Les utilisateurs de Docker peuvent passer des options personnalisées et
+                    ajuster le niveau de journalisation pour Corese-server.&#10;
                     - Standardisation des noms de format dans Corese-command.&#10;
-                    - Retrait des commandes 'owlProfile' et 'ldscript'; reviendront après refonte.&#10;
+                    - Retrait des commandes 'owlProfile' et 'ldscript'; reviendront après
+                    refonte.&#10;
                     - Correction d'un avertissement lié à sun.reflect.Reflection.getCallerClass.
                 </p>
             </description>

corese-command/pom.xml

@@ -16,29 +16,46 @@
 
   <dependencies>
 
-    <dependency>
-      <groupId>junit</groupId>
-      <artifactId>junit</artifactId>
-      <version>4.13.2</version>
-      <scope>test</scope>
-    </dependency>
-
+    <!-- CLI Interface -->
     <dependency>
       <groupId>info.picocli</groupId>
       <artifactId>picocli</artifactId>
-      <version>4.7.4</version>
+      <version>4.7.6</version>
     </dependency>
 
+    <!-- Corese -->
     <dependency>
       <groupId>${project.parent.groupId}</groupId>
       <artifactId>corese-core</artifactId>
     </dependency>
 
+    <!-- Unit Test -->
+    <dependency>
+      <groupId>org.junit.jupiter</groupId>
+      <artifactId>junit-jupiter-api</artifactId>
+      <version>5.11.0-M1</version>
+      <scope>test</scope>
+    </dependency>
     <dependency>
-      <groupId>jakarta.activation</groupId>
-      <artifactId>jakarta.activation-api</artifactId>
+      <groupId>org.junit.jupiter</groupId>
+      <artifactId>junit-jupiter-engine</artifactId>
+      <version>5.11.0-M1</version>
+      <scope>test</scope>
     </dependency>
 
+    <!-- Mock HTTPS Server for Test -->
+    <dependency>
+      <groupId>org.wiremock</groupId>
+      <artifactId>wiremock</artifactId>
+      <version>3.8.0</version>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.assertj</groupId>
+      <artifactId>assertj-core</artifactId>
+      <version>3.26.3</version>
+      <scope>test</scope>
+    </dependency>
 
   </dependencies>