Dead code ast query

.github/dependabot.yml

@@ -0,0 +1,8 @@
+version: 2
+updates:
+  - package-ecosystem: "gradle"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 1
+    target-branch: "develop"

.github/workflows/ci.yml

@@ -11,6 +11,7 @@ on:
       - "main"
       - "develop"
       - "feature/corese-next"
+  workflow_dispatch:
 
 permissions:
   contents: read
@@ -24,11 +25,14 @@ jobs:
 
     env:
       PACKAGE_TOKEN: ${{ secrets.JLS_TOKEN }}
+      SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
 
     steps:
-      - name: Checkout of head
+      - name: Checkout sources
         id: ci-sources-checkout
         uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
       - name: Set up JDK 21
         id: ci-java-setup
@@ -37,16 +41,32 @@ jobs:
           java-version: 21
           distribution: 'temurin'
 
+      - name: Cache Gradle
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.gradle/caches
+            ~/.gradle/wrapper
+          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties', '**/gradle.properties') }}
+          restore-keys: |
+            ${{ runner.os }}-gradle-
+
       - name: Gradle build
         id: ci-gradle-build
         run: ./gradlew clean assemble
 
       - name: Gradle tests
         run: ./gradlew test
 
-      - name: Run Coverage
+      - name: Generate JaCoCo Coverage Report
         run: ./gradlew jacocoTestReport
 
+      - name: SonarQube analysis
+        run: |
+          ./gradlew sonar -Dsonar.projectKey=crs-core-new \
+                          -Dsonar.host.url=https://sonarqube.inria.fr/sonarqube \
+                          -Dsonar.login=${{ secrets.SONAR_TOKEN }}
+
       - name: Add coverage to PR
         id: jacoco
         uses: madrapps/jacoco-report@v1.7.0
@@ -58,7 +78,7 @@ jobs:
           min-coverage-changed-files: 60
           update-comment: true
 
-      - name: Get the Coverage info
+      - name: Display Coverage info
         run: |
           echo "Total coverage ${{ steps.jacoco.outputs.coverage-overall }}"
           echo "Changed Files coverage ${{ steps.jacoco.outputs.coverage-changed-files }}"
@@ -70,8 +90,8 @@ jobs:
           files: |
             build/test-results/**/*.xml
 
-      - name: Get test artifacts
-        if: ${{ failure() }}
+      - name: Archive test artifacts
+        if: failure()
         uses: actions/upload-artifact@v4
         with:
           name: Package

.github/workflows/publish-prerelease.yml

@@ -22,11 +22,11 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
 
-      - name: Set up JDK 11
+      - name: Set up JDK 21
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: '11'
+          java-version: '21'
           cache: 'gradle'
 
       - name: Cache Gradle

.github/workflows/release-github.yml

@@ -23,11 +23,11 @@ jobs:
         with:
           ref: ${{ github.event.inputs.ref || github.ref_name }}
 
-      - name: Set up JDK 11
+      - name: Set up JDK 21
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: '11'
+          java-version: '21'
           cache: 'gradle'
 
       - name: Cache Gradle

.github/workflows/release-maven-central.yml

@@ -21,11 +21,11 @@ jobs:
         with:
           ref: ${{ github.event.inputs.ref || github.ref }}
 
-      - name: Set up JDK 11
+      - name: Set up JDK 21
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
-          java-version: '11'
+          java-version: '21'
           cache: 'gradle'
 
       - name: Cache Gradle

.gitignore

@@ -66,16 +66,26 @@ target/
 /dist/
 /nbdist/
 /.nb-gradle/
+.continue/
 
 # Logs and coverage reports
 *.log
 *.out
 *.coverage
 *.reports
 
+# Generated files
+gradle/gradle-daemon-jvm.properties
+
 ## #################################################################
 ## Miscellaneous ignores
 ## #################################################################
 
 # Other build directories and generated files
 /bin/
+/out/
+
+# Fichiers de logs
+logs/
+*.log
+.sonarlint/

build.gradle.kts

@@ -1,3 +1,6 @@
+import java.time.LocalDate
+import java.time.format.DateTimeFormatter
+
 plugins {
     // Core Gradle plugins
     `java-library`                                              // For creating reusable Java libraries
@@ -9,9 +12,59 @@ plugins {
 
     // Tooling plugins
     `jacoco`                                                    // For code coverage reports
-    id("com.gradleup.shadow") version "8.3.7"                   // Bundles dependencies into a single JAR
+    id("com.gradleup.shadow") version "8.3.7"
+    id("org.sonarqube") version "6.1.0.5360"                    // SonarQube integration
+    id("com.intershop.gradle.javacc") version "5.0.1"           // JavaCC plugin for parsing JavaCC files
+    id("antlr")                                                 // Antlr plugin for generating parsers from grammar files
+}
+
+// SonarQube configuration
+
+val currentDate: String = LocalDate.now().format(DateTimeFormatter.ISO_DATE)
+
+sonar {
+    properties {
+        property("sonar.projectKey", "crs-core-new")
+        property("sonar.host.url", "https://sonarqube.inria.fr/sonarqube")
+        property("sonar.login", System.getenv("SONAR_TOKEN"))
+        property("sonar.coverage.jacoco.xmlReportPaths", "build/reports/jacoco/test/jacocoTestReport.xml")
+        property("sonar.sourceEncoding", "UTF-8")
+        property("sonar.projectDate", currentDate)
+    }
+}
+
+// === Generated sources directories ===
+val javaccGeneratedDir = layout.buildDirectory.dir("generated-src/javacc").get().asFile
+val antlrGeneratedDir = layout.buildDirectory.dir("generated-src/antlr").get().asFile
+val antlrPackageDir = layout.buildDirectory.dir("generated-src/antlr/fr/inria/corese/core/next/impl/parser/antlr").get().asFile
+
+// JavaCC configuration
+javacc {
+    configs {
+        register("sparqlCorese") {
+            inputFile = file("src/main/java/fr/inria/corese/core/sparql/triple/javacc1/sparql_corese.jj")
+            packageName = "fr.inria.corese.core.sparql.triple.javacc1"
+            outputDir = javaccGeneratedDir
+        }
+    }
 }
 
+// Configure source sets to include generated sources
+sourceSets {
+    main {
+        java {
+            srcDir(javaccGeneratedDir)
+            srcDir(antlrGeneratedDir)
+        }
+    }
+}
+
+// Ensure JavaCC generation happens before compilation
+tasks.named("compileJava") {
+    dependsOn("javaccSparqlCorese")
+}
+
+
 /////////////////////////
 // Project metadata    //
 /////////////////////////
@@ -25,7 +78,7 @@ object Meta {
     // Project description
     const val desc = "Corese is a Semantic Web Factory (triple store and SPARQL endpoint) implementing RDF, RDFS, SPARQL 1.1 Query and Update, Shacl. STTL. LDScript."
     const val githubRepo = "corese-stack/corese-core"
-  
+
     // License information
     const val license = "CeCILL-C License"
     const val licenseUrl = "https://opensource.org/licenses/CeCILL-C"
@@ -37,8 +90,11 @@ object Meta {
 
 // Java compilation settings
 java {
-    // Note: withJavadocJar() and withSourcesJar() are handled by com.vanniktech.maven.publish plugin
-    sourceCompatibility = JavaVersion.VERSION_11 // Configure minimum Java version
+    withJavadocJar()                             // Include Javadoc JAR in publications
+    withSourcesJar()                             // Include sources JAR in publications
+    toolchain {
+        languageVersion.set(JavaLanguageVersion.of(21))
+    }
 }
 
 /////////////////////////
@@ -51,7 +107,6 @@ repositories {
     mavenCentral()  // Then, check Maven Central
 }
 
-// Define dependencies
 dependencies {
     // === Logging ===
     // As a library, corese-core should only depend on the SLF4J API.
@@ -60,23 +115,41 @@ dependencies {
     api("org.slf4j:slf4j-api:2.0.17")                                                  // Logging API only (SLF4J)
 
     // === Core dependencies ===
-    api("fr.com.hp.hpl.jena.rdf.arp:arp:2.2.b")                             // RDF/XML parser (Jena ARP)
+    api("fr.com.hp.hpl.jena.rdf.arp:arp:2.2.b")                                        // RDF/XML parser (Jena ARP)
     implementation("fr.inria.corese.org.semarglproject:semargl-rdfa:0.7.2")            // RDFa parser (Semargl)
     implementation("com.github.jsonld-java:jsonld-java:0.13.4")                        // JSON-LD processing
 
+    // === Antlr dependencies ===
+    antlr("org.antlr:antlr4:4.13.2")                                                   // Antlr for parsing (ANTLR 4)
+    implementation("org.antlr:antlr4-runtime:4.13.2")                                  // Antlr runtime for parsing
+
     // === HTTP and XML ===
     implementation("org.glassfish.jersey.core:jersey-client:3.1.10")                   // HTTP client (Jersey)
     implementation("org.glassfish.jersey.inject:jersey-hk2:3.1.10")                    // Dependency injection for Jersey
     implementation("com.sun.activation:jakarta.activation:2.0.1")                      // MIME type handling (Jakarta Activation)
 
+    // === JSONLD Parsing ===
+    implementation("com.apicatalog:titanium-json-ld:1.6.0")                            // JSON-LD processing library
+    implementation("com.apicatalog:titanium-rdf-api:1.0.0")                            // Titanium RDF API for JSON-LD processing
+    implementation("org.eclipse.parsson:parsson:1.1.7")                                // JSON parser for JSON-LD
+    implementation("jakarta.json:jakarta.json-api:2.1.3")                              // Jakarta JSON API for JSON processing
+
+
+    // === XML parsing ===
+    implementation("com.typesafe.akka:akka-stream_2.13:2.6.20")                        // Akka Streams for reactive streams processing
+    implementation("com.lightbend.akka:akka-stream-alpakka-xml_2.13:3.0.4")            // Alpakka XML for XML processing with Akka Streams
+
     // === Utilities ===
     implementation("org.apache.commons:commons-text:1.13.1")                           // Text manipulation utilities (Commons Text)
     implementation("org.json:json:20250517")                                           // JSON processing
     implementation("com.typesafe:config:1.4.3")                                        // Configuration library (Typesafe Config)
 
     // === Test dependencies ===
-    testImplementation("junit:junit:4.13.2")                                           // Unit testing framework
-    testRuntimeOnly("ch.qos.logback:logback-classic:1.5.20")                           // Logging implementation for tests and development
+    testImplementation(platform("org.junit:junit-bom:5.13.2"))                         // JUnit BOM for consistent test versions
+    testImplementation("org.junit.jupiter:junit-jupiter:5.13.2")                       // JUnit Jupiter API and engine
+    testRuntimeOnly("org.junit.platform:junit-platform-launcher:1.13.2")               // JUnit platform launcher (runtime)
+    testImplementation("org.mockito:mockito-core:5.18.0")                              // Mockito core for mocking in tests
+    testImplementation("org.mockito:mockito-junit-jupiter:5.18.0")                     // Mockito integration with JUnit Jupiter
 }
 
 /////////////////////////
@@ -146,7 +219,7 @@ mavenPublishing {
 /////////////////////////
 
 // Set UTF-8 encoding for Java compilation tasks
-tasks.withType<JavaCompile>() {
+tasks.withType<JavaCompile> {
     options.encoding = "UTF-8"
     options.compilerArgs.add("-Xlint:none")
 }
@@ -167,7 +240,7 @@ tasks.withType<Javadoc>().configureEach {
 tasks {
     shadowJar {
         this.archiveClassifier = "jar-with-dependencies"
-            }
+    }
 }
 
 // Configure the build task to depend on the shadow JAR task.
@@ -190,10 +263,11 @@ tasks.jacocoTestReport {
 // Set the test task to be followed by Jacoco report generation.
 // This ensures that test coverage reports are always generated after tests.
 tasks.test {
+    useJUnitPlatform()
     testLogging {
-        events("passed", "skipped", "failed") // Affiche les résultats des tests
-        showStandardStreams = true           // Affiche les sorties console des tests (y compris les logs)
+        events("passed", "skipped", "failed")
     }
+    systemProperty("java.util.logging.config.file", "src/test/resources/logging.properties")
     finalizedBy(tasks.jacocoTestReport)
 }
 
@@ -208,3 +282,53 @@ tasks.withType<PublishToMavenLocal>().configureEach {
 tasks.withType<PublishToMavenRepository>().configureEach {
     dependsOn(tasks.withType<Sign>())
 }
+
+// === Antlr generated sources configuration ===
+
+// Configure the Antlr task to generate parser code with specific arguments
+tasks.named<AntlrTask>("generateGrammarSource") {
+    arguments.addAll(listOf("-visitor", "-long-messages", "-package", "fr.inria.corese.core.next.impl.parser.antlr"))
+    outputDirectory = antlrPackageDir
+    inputs.files(fileTree("src/main/antlr"))
+    outputs.dir(antlrPackageDir)
+}
+
+// Ensure Java compilation depends on both JavaCC and Antlr code generation
+tasks.named("compileJava") {
+    dependsOn("generateGrammarSource", "javaccSparqlCorese")
+}
+
+// Ensure sources JAR includes generated sources and depends on code generation
+tasks.named<Jar>("sourcesJar") {
+    dependsOn("generateGrammarSource", "javaccSparqlCorese")
+    from(javaccGeneratedDir)
+    from(antlrGeneratedDir)
+    includeEmptyDirs = false
+    duplicatesStrategy = DuplicatesStrategy.EXCLUDE
+}
+
+// Clean up generated sources on clean
+tasks.clean {
+    doLast {
+        delete(javaccGeneratedDir)
+        delete(antlrGeneratedDir)
+    }
+}
+
+// Ensure generated directories exist before generation
+tasks.register("createGeneratedDirs") {
+    doLast {
+        javaccGeneratedDir.mkdirs()
+        antlrGeneratedDir.mkdirs()
+        antlrPackageDir.mkdirs()
+    }
+}
+
+// Make generation tasks depend on directory creation
+tasks.named("generateGrammarSource") {
+    dependsOn("createGeneratedDirs")
+}
+
+tasks.named("javaccSparqlCorese") {
+    dependsOn("createGeneratedDirs")
+}