Merge pull request #7 from JPL-Devin/devin/1776584030-upgrade-jena-6.0.0

Upgrade Apache Jena from 4.10.0 to 6.0.0

Author: dlamoris

Dockerfile

@@ -1,9 +1,9 @@
-FROM openjdk:17.0.2-jdk-slim as build
+FROM eclipse-temurin:21-jdk as build
 WORKDIR application
 COPY . .
 RUN ./gradlew installDist
 
-FROM openjdk:17.0.2-jdk-slim
+FROM eclipse-temurin:21-jre
 WORKDIR application
 RUN apt-get update && apt-get install -y procps
 COPY --from=build application/build/install/org.openmbee.flexo.mms.layer1/ .

build.gradle.kts

@@ -28,6 +28,10 @@ repositories {
     mavenCentral()
 }
 
+jacoco {
+    toolVersion = "0.8.12"
+}
+
 tasks.withType<Test>().configureEach {
     useJUnitPlatform()
 }
@@ -49,7 +53,7 @@ dependencies {
     val kotlinxJsonVersion = "1.8.1"
     implementation("org.jetbrains.kotlinx:kotlinx-serialization-json:$kotlinxJsonVersion")
 
-    val jenaVersion = "4.10.0"
+    val jenaVersion = "6.0.0"
     implementation("org.apache.jena:jena-arq:${jenaVersion}")
     testImplementation("org.apache.jena:jena-rdfconnection:${jenaVersion}");
     testFuseki("org.apache.jena:jena-fuseki-server:$jenaVersion")
@@ -140,5 +144,5 @@ compileKotlin.compilerOptions {
 }
 
 kotlin {
-    jvmToolchain(17)
-}
+    jvmToolchain(21)
+}

src/main/kotlin/org/openmbee/flexo/mms/Compressor.kt

@@ -1,6 +1,5 @@
 package org.openmbee.flexo.mms
 
-import org.apache.jena.atlas.lib.Trie
 import org.apache.jena.rdf.model.Model
 
 fun c1Subject() {
@@ -10,7 +9,7 @@ fun c1Subject() {
 private val COMPRESS_IRI = """(.*?)([^/#]*)""".toRegex()
 
 class Compressor {
-    var prefixes: Trie<Int> = Trie()
+    var prefixes: HashMap<String, Int> = HashMap()
     var prefixCount = 0
 
     fun load(model: Model) {
@@ -21,10 +20,10 @@ class Compressor {
                 val subjectIri = subject.uri
                 val (prefix, suffix) = COMPRESS_IRI.matchEntire(subjectIri)!!.destructured
 
-                var prefixId: Int? = prefixes.get(prefix)
+                var prefixId: Int? = prefixes[prefix]
                 if(prefixId == null) {
                     prefixId = prefixCount++
-                    prefixes.add(prefix, prefixId)
+                    prefixes[prefix] = prefixId
                 }
 
                 subjectC1 = ">"+prefixId.toChar().toString()+suffix
@@ -36,4 +35,4 @@ class Compressor {
          //   prefixes[]
         }
     }
-}
+}

src/main/kotlin/org/openmbee/flexo/mms/Content.kt

@@ -16,7 +16,7 @@ import org.apache.jena.riot.Lang
 import org.apache.jena.riot.RDFLanguages
 import org.apache.jena.riot.RDFParser
 import org.apache.jena.riot.system.ErrorHandlerFactory
-import org.apache.jena.riot.system.PrefixMapAdapter
+import org.apache.jena.riot.system.PrefixMapFactory
 import java.nio.charset.StandardCharsets
 
 val COMMA_SEPARATED = """\s*,\s*""".toRegex()
@@ -147,7 +147,7 @@ fun ApplicationCall.negotiateRdfResponseContentType(): ContentType {
     return destinationType
 }
 
-class KModel(val prefixes: PrefixMapBuilder=PrefixMapBuilder(), setup: (KModel.() -> Unit)?=null): ModelCom(GraphMemFactory.createGraphMem()) {
+class KModel(val prefixes: PrefixMapBuilder=PrefixMapBuilder(), setup: (KModel.() -> Unit)?=null): ModelCom(GraphMemFactory.createDefaultGraph()) {
     companion object {
         fun fromModel(model: Model): KModel {
             return KModel().apply {
@@ -212,7 +212,7 @@ class KModel(val prefixes: PrefixMapBuilder=PrefixMapBuilder(), setup: (KModel.(
 fun parseRdf(language: Lang, body: String, model: Model, baseIri: String?=null, prefixes: PrefixMapBuilder?=null) {
     // parse input document
     RDFParser.create().apply {
-        prefixes?.let {prefixes(PrefixMapAdapter(it.toPrefixMappings())) }
+        prefixes?.let {prefixes(PrefixMapFactory.create(it.toPrefixMappings())) }
         lang(language)
         errorHandler(ErrorHandlerFactory.errorHandlerWarn)
         if(baseIri != null) base(baseIri)

src/main/kotlin/org/openmbee/flexo/mms/UpdateRewriter.kt

@@ -8,7 +8,6 @@ import org.apache.jena.shared.PrefixMapping
 import org.apache.jena.shared.impl.PrefixMappingImpl
 import org.apache.jena.sparql.core.Quad
 import org.apache.jena.sparql.syntax.*
-import org.checkerframework.checker.units.qual.Prefix
 
 class RequirementsNotMetException(conditions: List<String>): Http400Exception("The following conditions failed after the transaction attempt:\n"
     +conditions.mapIndexed { i, v -> "${i}. $v" }.joinToString("\n"))
@@ -86,6 +85,18 @@ object NoQuadsElementVisitor: ElementVisitor {
     override fun visit(el: ElementLateral?) {
         throw SparqlFeatureNotSupportedException("LATERAL keyword not standardized")
     }
+
+    override fun visit(el: ElementUnfold?) {
+        throw SparqlFeatureNotSupportedException("UNFOLD keyword not supported")
+    }
+
+    override fun visit(el: ElementSemiJoin?) {
+        throw SparqlFeatureNotSupportedException("SEMI JOIN not supported")
+    }
+
+    override fun visit(el: ElementAntiJoin?) {
+        throw SparqlFeatureNotSupportedException("ANTI JOIN not supported")
+    }
 }
 
 fun assertNoQuads(element: Element1?) {
@@ -100,7 +111,7 @@ fun assertNoQuads(elements: List<Element>?) {
 
 
 fun asSparqlGroup(mapping: PrefixMapping?=null, vararg elements: Element): String {
-    return QueryFactory.make().apply {
+    return QueryFactory.create().apply {
         setQueryAskType()
         if(mapping != null) prefixMapping = mapping
         queryPattern = ElementGroup().apply {