Merge branch 'fix/sonarqube-code-quality-improvements' into develop

Author: remiceres

CHANGELOG.md

@@ -1,6 +1,21 @@
 <!-- markdownlint-disable MD024 -->
 # Corese Changelog
 
+## Version 4.6.3
+
+### Changed
+
+- Major code refactoring to improve code quality and maintainability.
+- Introduced custom exception hierarchy for better error handling.
+- Reorganized format handling classes and package structure.
+- Added wrapper classes to encapsulate Corese-Core functionality.
+- Standardized error messages and improved code documentation.
+
+### Fixed
+
+- Fixed inconsistent error handling across commands.
+- Improved test reliability and code quality.
+
 ## Version 4.6.2 - 2025-08-01
 
 ### Changed

build.gradle.kts

@@ -60,22 +60,48 @@ repositories {
 
 dependencies {
     val coreseVersion = "4.6.4"
-    val picocliVersion = "4.7.6"
-
-    implementation("fr.inria.corese:corese-core:$coreseVersion") // Core module of Corese
+    val picocliVersion = "4.7.7"
+    val jacksonVersion = "2.17.1" // Version compatible with WireMock 3.13.1
+
+    implementation("fr.inria.corese:corese-core:$coreseVersion") {
+        // Exclude Log4j2 dependencies to avoid SLF4J multiple bindings warning
+        // corese-core includes Log4j2, but corese-command uses Logback
+        exclude(group = "org.apache.logging.log4j", module = "log4j-slf4j2-impl")
+        exclude(group = "org.apache.logging.log4j", module = "log4j-core")
+    }
     implementation("info.picocli:picocli:$picocliVersion") // Library for building a Command-Line Interface (CLI)
 
-    implementation("org.apache.commons:commons-lang3:3.17.0") // Library for utility functions (e.g., StringUtils)
+    implementation("org.apache.commons:commons-lang3:3.19.0") // Library for utility functions (e.g., StringUtils)
     implementation("com.github.jsonld-java:jsonld-java:0.13.6") // Library for JSON-LD support
-    implementation("jakarta.ws.rs:jakarta.ws.rs-api:3.0.0") // Jakarta REST API specifications
-    implementation("jakarta.activation:jakarta.activation-api:2.1.3") // Jakarta Activation API
+    implementation("jakarta.ws.rs:jakarta.ws.rs-api:4.0.0") // Jakarta REST API specifications
+    implementation("jakarta.activation:jakarta.activation-api:2.2.0-M1") // Jakarta Activation API
     implementation("fr.com.hp.hpl.jena.rdf.arp:arp:2.2.b") // Jena implementation for RDF parsing
-    implementation("org.slf4j:slf4j-api:2.0.16") // Simple Logging Facade for Java (SLF4J)
-    runtimeOnly("ch.qos.logback:logback-classic:1.5.12") // Logging framework for SLF4J
+    implementation("org.slf4j:slf4j-api:2.0.17") // Simple Logging Facade for Java (SLF4J)
+    runtimeOnly("ch.qos.logback:logback-classic:1.5.20") // Logging framework for SLF4J
 
-    testImplementation("org.wiremock:wiremock:3.9.2") // HTTP server mocking for API testing
-    testImplementation("org.junit.jupiter:junit-jupiter:5.11.3") // JUnit 5 for testing
+    testImplementation("org.wiremock:wiremock:3.13.1") // HTTP server mocking for API testing
+    testImplementation("org.junit.jupiter:junit-jupiter:6.0.0") // JUnit 5 for testing
+    testImplementation("org.mockito:mockito-core:5.15.2") // Mockito for mocking in tests
+    testImplementation("org.mockito:mockito-junit-jupiter:5.15.2") // Mockito JUnit 5 integration
     testRuntimeOnly("org.junit.platform:junit-platform-launcher") // JUnit Platform launcher for running tests
+
+    // Force Jackson version to fix compatibility issues with WireMock
+    // WireMock 3.13.1 requires Jackson 2.17.x for the configure(DatatypeFeature, boolean) method
+    // Without this, running tests from IDE may fail with NoSuchMethodError
+    testImplementation("com.fasterxml.jackson.core:jackson-core:$jacksonVersion")
+    testImplementation("com.fasterxml.jackson.core:jackson-annotations:$jacksonVersion")
+    testImplementation("com.fasterxml.jackson.core:jackson-databind:$jacksonVersion")
+}
+
+// Force Jackson version across all configurations to prevent version conflicts
+// This ensures that transitive dependencies from corese-core or other libraries
+// do not introduce older Jackson versions that are incompatible with WireMock
+configurations.all {
+    resolutionStrategy {
+        force("com.fasterxml.jackson.core:jackson-core:2.17.1")
+        force("com.fasterxml.jackson.core:jackson-annotations:2.17.1")
+        force("com.fasterxml.jackson.core:jackson-databind:2.17.1")
+    }
 }
 
 /////////////////////////

packaging/flatpak/appdata/fr.inria.corese.CoreseCommand.appdata.xml

@@ -136,6 +136,20 @@
     </screenshots>
 
     <releases>
+        <release version="4.6.3" date="2025-10-30">
+            <url type="details">https://github.com/corese-stack/corese-command/releases/tag/v4.6.3</url>
+            <description>
+                <ul>
+                    <li>Major code refactoring for improved quality and maintainability.</li>
+                    <li>Introduced custom exception hierarchy and wrapper classes.</li>
+                    <li>Reorganized package structure and standardized error messages.</li>
+                    
+                    <li xml:lang="fr">Refonte majeure du code pour améliorer la qualité et la maintenabilité.</li>
+                    <li xml:lang="fr">Introduction d'une hiérarchie d'exceptions personnalisée et de classes wrapper.</li>
+                    <li xml:lang="fr">Réorganisation de la structure des packages et standardisation des messages d'erreur.</li>
+                </ul>
+            </description>
+        </release>
         <release version="4.6.2" date="2025-08-01">
             <url type="details">https://github.com/corese-stack/corese-command/releases/tag/v4.6.2</url>
             <description>

src/main/java/fr/inria/corese/command/App.java

@@ -5,27 +5,40 @@
 import fr.inria.corese.command.programs.Query;
 import fr.inria.corese.command.programs.QueryEndpoint;
 import fr.inria.corese.command.programs.Validate;
+import fr.inria.corese.command.utils.wrapper.CoreseVersionProvider;
+
 import picocli.AutoComplete.GenerateCompletion;
 import picocli.CommandLine;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Help.Ansi.Style;
 import picocli.CommandLine.Help.ColorScheme;
 
-@Command(name = "Corese", versionProvider = VersionProvider.class, mixinStandardHelpOptions = true, subcommands = {
-        Convert.class, Query.class, QueryEndpoint.class, Validate.class, Canonicalize.class, GenerateCompletion.class })
+@Command(
+        name = "Corese",
+        versionProvider = CoreseVersionProvider.class,
+        mixinStandardHelpOptions = true,
+        subcommands = {
+            Convert.class,
+            Query.class,
+            QueryEndpoint.class,
+            Validate.class,
+            Canonicalize.class,
+            GenerateCompletion.class
+        })
 public final class App implements Runnable {
 
     public static void main(String[] args) {
         // Define the color scheme
-        ColorScheme colorScheme = new ColorScheme.Builder()
-                .commands(Style.bold) // Commands in blue
-                .options(Style.fg_yellow) // Options in yellow
-                .parameters(Style.fg_cyan, Style.bold) // Parameters in cyan and bold
-                .optionParams(Style.italic, Style.fg_cyan) // Option parameters in italic
-                .errors(Style.fg_red, Style.bold) // Errors in red and bold
-                .stackTraces(Style.italic) // Stack traces in italic
-                .applySystemProperties() // Apply system properties for colors
-                .build();
+        ColorScheme colorScheme =
+                new ColorScheme.Builder()
+                        .commands(Style.bold) // Commands in blue
+                        .options(Style.fg_yellow) // Options in yellow
+                        .parameters(Style.fg_cyan, Style.bold) // Parameters in cyan and bold
+                        .optionParams(Style.italic, Style.fg_cyan) // Option parameters in italic
+                        .errors(Style.fg_red, Style.bold) // Errors in red and bold
+                        .stackTraces(Style.italic) // Stack traces in italic
+                        .applySystemProperties() // Apply system properties for colors
+                        .build();
 
         CommandLine commandLine = new CommandLine(new App()).setColorScheme(colorScheme);
 
@@ -39,8 +52,9 @@ public static void main(String[] args) {
     }
 
     @Override
+    @SuppressWarnings("java:S106") // Standard output is appropriate for CLI usage display
     public void run() {
         // Print usage
         CommandLine.usage(new App(), System.out);
     }
-}
+}

src/main/java/fr/inria/corese/command/VersionProvider.java

@@ -0,0 +1,33 @@
+package fr.inria.corese.command.exceptions;
+
+/**
+ * Exception thrown when an error occurs while loading or processing configuration.
+ * 
+ * <p>This includes errors such as:
+ * <ul>
+ *   <li>Configuration file not found</li>
+ *   <li>Invalid configuration format</li>
+ *   <li>Configuration parsing errors</li>
+ * </ul>
+ */
+public class ConfigurationException extends CoreseCommandException {
+
+    /**
+     * Constructs a new ConfigurationException with the specified detail message.
+     *
+     * @param message the detail message
+     */
+    public ConfigurationException(String message) {
+        super(message);
+    }
+
+    /**
+     * Constructs a new ConfigurationException with the specified detail message and cause.
+     *
+     * @param message the detail message
+     * @param cause the cause of this exception
+     */
+    public ConfigurationException(String message, Throwable cause) {
+        super(message, cause);
+    }
+}

src/main/java/fr/inria/corese/command/exceptions/ConfigurationException.java

@@ -0,0 +1,39 @@
+package fr.inria.corese.command.exceptions;
+
+/**
+ * Base exception for all Corese Command errors.
+ * 
+ * <p>This is an unchecked exception (extends RuntimeException) to simplify
+ * error handling in the CLI application while still providing structured
+ * error information.
+ */
+public class CoreseCommandException extends RuntimeException {
+
+    /**
+     * Constructs a new CoreseCommandException with the specified detail message.
+     *
+     * @param message the detail message
+     */
+    public CoreseCommandException(String message) {
+        super(message);
+    }
+
+    /**
+     * Constructs a new CoreseCommandException with the specified detail message and cause.
+     *
+     * @param message the detail message
+     * @param cause the cause of this exception
+     */
+    public CoreseCommandException(String message, Throwable cause) {
+        super(message, cause);
+    }
+
+    /**
+     * Constructs a new CoreseCommandException with the specified cause.
+     *
+     * @param cause the cause of this exception
+     */
+    public CoreseCommandException(Throwable cause) {
+        super(cause);
+    }
+}

src/main/java/fr/inria/corese/command/exceptions/CoreseCommandException.java

@@ -0,0 +1,44 @@
+package fr.inria.corese.command.exceptions;
+
+/**
+ * Exception thrown when an HTTP error occurs while communicating with a SPARQL endpoint.
+ * 
+ * <p>This exception includes the HTTP status code to allow for specific error handling
+ * based on the type of HTTP error encountered.
+ */
+public class HttpClientException extends CoreseCommandException {
+
+    private final int statusCode;
+
+    /**
+     * Constructs a new HttpClientException with the specified detail message and HTTP status code.
+     *
+     * @param message the detail message
+     * @param statusCode the HTTP status code
+     */
+    public HttpClientException(String message, int statusCode) {
+        super(message);
+        this.statusCode = statusCode;
+    }
+
+    /**
+     * Constructs a new HttpClientException with the specified detail message, HTTP status code, and cause.
+     *
+     * @param message the detail message
+     * @param statusCode the HTTP status code
+     * @param cause the cause of this exception
+     */
+    public HttpClientException(String message, int statusCode, Throwable cause) {
+        super(message, cause);
+        this.statusCode = statusCode;
+    }
+
+    /**
+     * Returns the HTTP status code associated with this exception.
+     *
+     * @return the HTTP status code
+     */
+    public int getStatusCode() {
+        return statusCode;
+    }
+}

src/main/java/fr/inria/corese/command/exceptions/HttpClientException.java

@@ -0,0 +1,33 @@
+package fr.inria.corese.command.exceptions;
+
+/**
+ * Exception thrown when an invalid input format is encountered.
+ * 
+ * <p>This includes errors such as:
+ * <ul>
+ *   <li>Unknown or unsupported serialization format</li>
+ *   <li>Format detection failures</li>
+ *   <li>Format mismatch with actual data</li>
+ * </ul>
+ */
+public class InputFormatException extends CoreseCommandException {
+
+    /**
+     * Constructs a new InputFormatException with the specified detail message.
+     *
+     * @param message the detail message
+     */
+    public InputFormatException(String message) {
+        super(message);
+    }
+
+    /**
+     * Constructs a new InputFormatException with the specified detail message and cause.
+     *
+     * @param message the detail message
+     * @param cause the cause of this exception
+     */
+    public InputFormatException(String message, Throwable cause) {
+        super(message, cause);
+    }
+}

src/main/java/fr/inria/corese/command/exceptions/InputFormatException.java

@@ -0,0 +1,33 @@
+package fr.inria.corese.command.exceptions;
+
+/**
+ * Exception thrown when an error occurs during RDF export operations.
+ * 
+ * <p>This includes errors such as:
+ * <ul>
+ *   <li>File write errors</li>
+ *   <li>Unsupported export format</li>
+ *   <li>Serialization errors</li>
+ * </ul>
+ */
+public class RdfExportException extends CoreseCommandException {
+
+    /**
+     * Constructs a new RdfExportException with the specified detail message.
+     *
+     * @param message the detail message
+     */
+    public RdfExportException(String message) {
+        super(message);
+    }
+
+    /**
+     * Constructs a new RdfExportException with the specified detail message and cause.
+     *
+     * @param message the detail message
+     * @param cause the cause of this exception
+     */
+    public RdfExportException(String message, Throwable cause) {
+        super(message, cause);
+    }
+}