Use Jena and Topbraid versions

build.sbt

@@ -41,7 +41,7 @@ val fs2AwsVersion              = "6.1.1"
 val googleAuthClientVersion    = "1.35.0"
 val handleBarsVersion          = "4.4.0"
 val hikariVersion              = "5.1.0"
-val jenaVersion                = "4.2.0"
+val jenaVersion                = "4.10.0"
 val jsonldjavaVersion          = "0.13.6"
 val kamonVersion               = "2.7.1"
 val kanelaAgentVersion         = "1.0.18"
@@ -57,7 +57,7 @@ val postgresJdbcVersion        = "42.7.3"
 val pureconfigVersion          = "0.17.6"
 val scalaTestVersion           = "3.2.18"
 val scalaXmlVersion            = "2.2.0"
-val topBraidVersion            = "1.3.2" // 1.4.1 fails to validate some test schemas
+val topBraidVersion            = "1.4.3" // 1.4.1 fails to validate some test schemas
 val testContainersVersion      = "1.19.7"
 val testContainersScalaVersion = "0.41.3"
 
@@ -109,7 +109,7 @@ lazy val fs2Aws                        = "io.laserdisc"                 %% "fs2-
 lazy val fs2AwsS3                      = "io.laserdisc"                 %% "fs2-aws-s3"                         % fs2AwsVersion
 lazy val googleAuthClient              = "com.google.oauth-client"       % "google-oauth-client"                % googleAuthClientVersion
 lazy val handleBars                    = "com.github.jknack"             % "handlebars"                         % handleBarsVersion
-lazy val jenaArq                       = "org.apache.jena"               % "jena-arq"                           % jenaVersion
+lazy val jenaArq                       = "org.apache.jena"               % "jena-arq"                           % jenaVersion exclude ("com.apicatalog", "titanium-json-ld")
 lazy val jsonldjava                    = "com.github.jsonld-java"        % "jsonld-java"                        % jsonldjavaVersion
 lazy val kamonAkkaHttp                 = "io.kamon"                     %% "kamon-akka-http"                    % kamonVersion
 lazy val kamonCore                     = "io.kamon"                     %% "kamon-core"                         % kamonVersion
@@ -127,7 +127,7 @@ lazy val pureconfigCats                = "com.github.pureconfig"        %% "pure
 lazy val scalaReflect                  = "org.scala-lang"                % "scala-reflect"                      % scalaCompilerVersion
 lazy val scalaTest                     = "org.scalatest"                %% "scalatest"                          % scalaTestVersion
 lazy val scalaXml                      = "org.scala-lang.modules"       %% "scala-xml"                          % scalaXmlVersion
-lazy val topBraidShacl                 = "org.topbraid"                  % "shacl"                              % topBraidVersion
+lazy val topBraidShacl                 = "org.topbraid"                  % "shacl"                              % topBraidVersion exclude ("com.apicatalog", "titanium-json-ld")
 lazy val testContainers                = "org.testcontainers"            % "testcontainers"                     % testContainersVersion
 lazy val testContainersScala           = "com.dimafeng"                 %% "testcontainers-scala-munit"         % testContainersScalaVersion
 lazy val testContainersScalaLocalStack = "com.dimafeng"                 %% "testcontainers-scala-localstack-v2" % testContainersScalaVersion

delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/wiring/ResourcesModule.scala

@@ -6,6 +6,7 @@ import ch.epfl.bluebrain.nexus.delta.config.AppConfig
 import ch.epfl.bluebrain.nexus.delta.kernel.utils.UUIDF
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.api.JsonLdApi
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.RemoteContextResolution
+import ch.epfl.bluebrain.nexus.delta.rdf.shacl.ValidateShacl
 import ch.epfl.bluebrain.nexus.delta.rdf.utils.JsonKeyOrdering
 import ch.epfl.bluebrain.nexus.delta.routes.ResourcesRoutes
 import ch.epfl.bluebrain.nexus.delta.sdk.IndexingAction.AggregateIndexingAction
@@ -36,9 +37,8 @@ object ResourcesModule extends ModuleDef {
     ResourceResolution.schemaResource(aclCheck, resolvers, fetchSchema, excludeDeprecated = false)
   }
 
-  make[ValidateResource].from {
-    (resourceResolution: ResourceResolution[Schema], rcr: RemoteContextResolution @Id("aggregate")) =>
-      ValidateResource(resourceResolution)(rcr)
+  make[ValidateResource].from { (resourceResolution: ResourceResolution[Schema], validateShacl: ValidateShacl) =>
+    ValidateResource(resourceResolution, validateShacl)
   }
 
   make[ResourcesConfig].from { (config: AppConfig) => config.resources }

delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/wiring/SchemasModule.scala

@@ -7,7 +7,7 @@ import ch.epfl.bluebrain.nexus.delta.kernel.utils.{ClasspathResourceLoader, UUID
 import ch.epfl.bluebrain.nexus.delta.rdf.Vocabulary.contexts
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.api.JsonLdApi
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.{ContextValue, RemoteContextResolution}
-import ch.epfl.bluebrain.nexus.delta.rdf.shacl.ShaclShapesGraph
+import ch.epfl.bluebrain.nexus.delta.rdf.shacl.ValidateShacl
 import ch.epfl.bluebrain.nexus.delta.rdf.utils.JsonKeyOrdering
 import ch.epfl.bluebrain.nexus.delta.routes.SchemasRoutes
 import ch.epfl.bluebrain.nexus.delta.sdk.IndexingAction.AggregateIndexingAction
@@ -36,10 +36,9 @@ object SchemasModule extends ModuleDef {
 
   implicit private val loader: ClasspathResourceLoader = ClasspathResourceLoader.withContext(getClass)
 
-  make[ValidateSchema].fromEffect { (api: JsonLdApi, rcr: RemoteContextResolution @Id("aggregate")) =>
-    ShaclShapesGraph.shaclShaclShapes.map(ValidateSchema(api, _, rcr))
+  make[ValidateShacl].fromEffect { (rcr: RemoteContextResolution @Id("aggregate")) => ValidateShacl(rcr) }
 
-  }
+  make[ValidateSchema].from { (validateShacl: ValidateShacl, api: JsonLdApi) => ValidateSchema(validateShacl)(api) }
 
   make[SchemaDefinition].from { (validateSchema: ValidateSchema, clock: Clock[IO]) =>
     Schemas.definition(validateSchema, clock)

delta/app/src/test/resources/schemas/errors/invalid-schema.json

@@ -21,6 +21,6 @@
       },
       "value": "nxv:42"
     },
-    "targetedNodes": 417
+    "targetedNodes": 412
   }
 }

delta/app/src/test/scala/ch/epfl/bluebrain/nexus/delta/routes/ResourcesRoutesSpec.scala

@@ -10,6 +10,7 @@ import ch.epfl.bluebrain.nexus.delta.kernel.utils.{UUIDF, UrlUtils}
 import ch.epfl.bluebrain.nexus.delta.rdf.IriOrBNode.Iri
 import ch.epfl.bluebrain.nexus.delta.rdf.Vocabulary.{contexts, nxv, schema, schemas}
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.JsonLdContext.keywords
+import ch.epfl.bluebrain.nexus.delta.rdf.shacl.ValidateShacl
 import ch.epfl.bluebrain.nexus.delta.sdk.IndexingAction
 import ch.epfl.bluebrain.nexus.delta.sdk.acls.AclSimpleCheck
 import ch.epfl.bluebrain.nexus.delta.sdk.acls.model.AclAddress
@@ -96,7 +97,8 @@ class ResourcesRoutesSpec extends BaseRouteSpec with CatsIOValues {
   }
 
   private val validator: ValidateResource                          = ValidateResource(
-    ResourceResolutionGen.singleInProject(projectRef, fetchSchema)
+    ResourceResolutionGen.singleInProject(projectRef, fetchSchema),
+    ValidateShacl(rcr).accepted
   )
   private val fetchContext                                         = FetchContextDummy(List(project.value))
   private val resolverContextResolution: ResolverContextResolution = ResolverContextResolution(rcr)

delta/app/src/test/scala/ch/epfl/bluebrain/nexus/delta/routes/SchemasRoutesSpec.scala

@@ -9,7 +9,7 @@ import ch.epfl.bluebrain.nexus.delta.rdf.IriOrBNode.Iri
 import ch.epfl.bluebrain.nexus.delta.rdf.Vocabulary
 import ch.epfl.bluebrain.nexus.delta.rdf.Vocabulary.{contexts, nxv}
 import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.JsonLdContext.keywords
-import ch.epfl.bluebrain.nexus.delta.rdf.shacl.ShaclShapesGraph
+import ch.epfl.bluebrain.nexus.delta.rdf.shacl.ValidateShacl
 import ch.epfl.bluebrain.nexus.delta.sdk.IndexingAction
 import ch.epfl.bluebrain.nexus.delta.sdk.acls.AclSimpleCheck
 import ch.epfl.bluebrain.nexus.delta.sdk.acls.model.AclAddress
@@ -23,7 +23,7 @@ import ch.epfl.bluebrain.nexus.delta.sdk.permissions.Permissions.schemas
 import ch.epfl.bluebrain.nexus.delta.sdk.projects.FetchContextDummy
 import ch.epfl.bluebrain.nexus.delta.sdk.projects.model.ApiMappings
 import ch.epfl.bluebrain.nexus.delta.sdk.resolvers.ResolverContextResolution
-import ch.epfl.bluebrain.nexus.delta.sdk.schemas.{SchemaImports, Schemas, SchemasConfig, SchemasImpl, ValidateSchema}
+import ch.epfl.bluebrain.nexus.delta.sdk.schemas._
 import ch.epfl.bluebrain.nexus.delta.sdk.utils.BaseRouteSpec
 import ch.epfl.bluebrain.nexus.delta.sourcing.ScopedEventLog
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.Identity.{Anonymous, Authenticated, Group, Subject, User}
@@ -37,9 +37,8 @@ import java.util.UUID
 
 class SchemasRoutesSpec extends BaseRouteSpec with IOFromMap with CatsIOValues {
 
-  private val uuid                                        = UUID.randomUUID()
-  implicit private val uuidF: UUIDF                       = UUIDF.fixed(uuid)
-  implicit private val shaclShaclShapes: ShaclShapesGraph = ShaclShapesGraph.shaclShaclShapes.accepted
+  private val uuid                  = UUID.randomUUID()
+  implicit private val uuidF: UUIDF = UUIDF.fixed(uuid)
 
   private val reader = User("reader", realm)
   private val writer = User("writer", realm)
@@ -79,7 +78,7 @@ class SchemasRoutesSpec extends BaseRouteSpec with IOFromMap with CatsIOValues {
 
   private val config = SchemasConfig(eventLogConfig)
 
-  private val schemaDef      = Schemas.definition(ValidateSchema.apply, clock)
+  private val schemaDef      = Schemas.definition(ValidateSchema(ValidateShacl(rcr).accepted), clock)
   private lazy val schemaLog = ScopedEventLog(schemaDef, config.eventLog, xas)
 
   private lazy val routes =

delta/rdf/src/main/scala/ch/epfl/bluebrain/nexus/delta/rdf/graph/Graph.scala

@@ -27,7 +27,7 @@ import org.apache.jena.sparql.graph.GraphFactory
 import org.apache.jena.sparql.util.IsoMatcher
 
 import java.util.UUID
-import scala.annotation.tailrec
+import scala.annotation.{nowarn, tailrec}
 import scala.jdk.CollectionConverters._
 import scala.util.Try
 
@@ -39,6 +39,7 @@ import scala.util.Try
   * @param value
   *   the Jena dataset graph
   */
+@nowarn("cat=deprecation")
 final case class Graph private (rootNode: IriOrBNode, value: DatasetGraph) { self =>
 
   val rootResource: Node = subject(rootNode)

delta/rdf/src/main/scala/ch/epfl/bluebrain/nexus/delta/rdf/jsonld/api/JsonLdJavaApi.scala

@@ -20,12 +20,14 @@ import org.apache.jena.riot.system.ErrorHandlerFactory
 import org.apache.jena.riot._
 import org.apache.jena.sparql.core.DatasetGraph
 
+import scala.annotation.nowarn
 import scala.jdk.CollectionConverters._
 import scala.util.Try
 
 /**
   * Json-LD high level API implementation by Json-LD Java library
   */
+@nowarn("cat=deprecation")
 final class JsonLdJavaApi(config: JsonLdApiConfig) extends JsonLdApi {
 
   System.setProperty(DocumentLoader.DISALLOW_REMOTE_CONTEXT_LOADING, "true")
@@ -76,7 +78,7 @@ final class JsonLdJavaApi(config: JsonLdApiConfig) extends JsonLdApi {
     val ds          = DatasetFactory.create
     val initBuilder = RDFParser.create
       .fromString(input.noSpaces)
-      .lang(Lang.JSONLD)
+      .lang(Lang.JSONLD10)
       .context(c)
       .strict(config.strict)
       .checking(config.extraChecks)

delta/rdf/src/main/scala/ch/epfl/bluebrain/nexus/delta/rdf/shacl/ShaclEngine.scala

@@ -1,15 +1,12 @@
 package ch.epfl.bluebrain.nexus.delta.rdf.shacl
 
-import cats.effect.IO
 import ch.epfl.bluebrain.nexus.delta.rdf.IriOrBNode.Iri
 import ch.epfl.bluebrain.nexus.delta.rdf.Vocabulary.nxsh
-import ch.epfl.bluebrain.nexus.delta.rdf.graph.Graph
-import ch.epfl.bluebrain.nexus.delta.rdf.jsonld.context.RemoteContextResolution
-import org.apache.jena.query.{Dataset, DatasetFactory}
+import org.apache.jena.query.Dataset
 import org.apache.jena.rdf.model._
 import org.topbraid.jenax.util.JenaDatatypes
 import org.topbraid.shacl.engine.{Constraint, ShapesGraph}
-import org.topbraid.shacl.validation.{ValidationEngine, ValidationEngineConfiguration}
+import org.topbraid.shacl.validation.ValidationEngine
 
 import java.net.URI
 import java.util
@@ -26,7 +23,7 @@ import java.util
   *   the ShapesGraph with the shapes to validate against
   */
 @SuppressWarnings(Array("NullParameter"))
-final class ShaclEngine private (dataset: Dataset, shapesGraphURI: URI, shapesGraph: ShapesGraph)
+final class ShaclEngine(dataset: Dataset, shapesGraphURI: URI, shapesGraph: ShapesGraph)
     extends ValidationEngine(dataset, shapesGraphURI, shapesGraph, null) {
   private var targetedNodes = 0
 
@@ -43,82 +40,3 @@ final class ShaclEngine private (dataset: Dataset, shapesGraphURI: URI, shapesGr
   private def toProperty(iri: Iri): Property =
     ResourceFactory.createProperty(iri.toString)
 }
-
-object ShaclEngine {
-
-  /**
-    * Validates a given graph against the SHACL shapes spec.
-    *
-    * @param shapesGraph
-    *   the shapes Graph to test against the SHACL shapes spec
-    * @param reportDetails
-    *   true to also include the sh:detail (more verbose) and false to omit them
-    * @return
-    *   an option of [[ValidationReport]] with the validation results
-    */
-  def apply(
-      shapesGraph: Graph,
-      reportDetails: Boolean
-  )(implicit shaclShapesGraph: ShaclShapesGraph, rcr: RemoteContextResolution): IO[ValidationReport] =
-    apply(shapesGraph, shaclShapesGraph, validateShapes = true, reportDetails = reportDetails)
-
-  /**
-    * Validates a given data Graph against all shapes from a given shapes Model.
-    *
-    * @param dataGraph
-    *   the data Graph
-    * @param shapesGraph
-    *   the shapes Graph
-    * @param reportDetails
-    *   true to also include the sh:detail (more verbose) and false to omit them
-    * @return
-    *   an option of [[ValidationReport]] with the validation results
-    */
-  def apply(
-      dataGraph: Graph,
-      shapesGraph: Graph,
-      reportDetails: Boolean
-  )(implicit rcr: RemoteContextResolution): IO[ValidationReport] =
-    apply(dataGraph, ShaclShapesGraph(shapesGraph), validateShapes = false, reportDetails)
-
-  /**
-    * Validates a given data Graph against all shapes from a given shapes graph.
-    *
-    * @param graph
-    *   the data Graph
-    * @param shapesGraph
-    *   the shapes graph
-    * @param validateShapes
-    *   true to also validate the shapes graph
-    * @param reportDetails
-    *   true to also include the sh:detail (more verbose) and false to omit them
-    * @return
-    *   an option of [[ValidationReport]] with the validation results
-    */
-  def apply(
-      graph: Graph,
-      shapesGraph: ShaclShapesGraph,
-      validateShapes: Boolean,
-      reportDetails: Boolean
-  )(implicit rcr: RemoteContextResolution): IO[ValidationReport] =
-    apply(DatasetFactory.wrap(graph.value), shapesGraph, validateShapes, reportDetails)
-
-  private def apply(
-      dataset: Dataset,
-      shapesGraph: ShaclShapesGraph,
-      validateShapes: Boolean,
-      reportDetails: Boolean
-  )(implicit rcr: RemoteContextResolution): IO[ValidationReport] = {
-    // Create Dataset that contains both the data model and the shapes model
-    // (here, using a temporary URI for the shapes graph)
-    dataset.addNamedModel(shapesGraph.uri.toString, shapesGraph.model)
-    val engine = new ShaclEngine(dataset, shapesGraph.uri, shapesGraph.value)
-    engine.setConfiguration(
-      new ValidationEngineConfiguration().setReportDetails(reportDetails).setValidateShapes(validateShapes)
-    )
-    IO.delay {
-      engine.applyEntailments()
-      engine.validateAll()
-    }.flatMap(ValidationReport(_))
-  }
-}

delta/rdf/src/main/scala/ch/epfl/bluebrain/nexus/delta/rdf/shacl/ShaclFileLoader.scala

@@ -0,0 +1,28 @@
+package ch.epfl.bluebrain.nexus.delta.rdf.shacl
+
+import cats.effect.IO
+import ch.epfl.bluebrain.nexus.delta.kernel.utils.ClasspathResourceLoader
+import org.apache.jena.graph.GraphMemFactory.createDefaultGraph
+import org.apache.jena.rdf.model.{Model, ModelFactory}
+import org.apache.jena.util.FileUtils
+import org.topbraid.shacl.vocabulary.SH
+
+object ShaclFileLoader {
+
+  private val loader = ClasspathResourceLoader()
+
+  private def readFromTurtleFile(base: String, resourcePath: String) =
+    loader
+      .streamOf(resourcePath)
+      .use { is =>
+        IO.blocking {
+          ModelFactory
+            .createModelForGraph(createDefaultGraph())
+            .read(is, base, FileUtils.langTurtle)
+        }
+      }
+
+  def readShaclShapes: IO[Model] = readFromTurtleFile("http://www.w3.org/ns/shacl-shacl#", "shacl-shacl.ttl")
+
+  def readShaclVocabulary: IO[Model] = readFromTurtleFile(SH.BASE_URI, "rdf/shacl.ttl")
+}