Use Jena and Topbraid versions (#4837)

* Use Jena and Topbraid versions --------- Co-authored-by: Simon Dumas <simon.dumas@epfl.ch>
BlueBrain · Apr 5, 2024 · 58c751f · 58c751f
1 parent cd89fca
commit 58c751f
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Showing 62 changed files with 8,429 additions and 1,005 deletions.
diff --git a/build.sbt b/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"
 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

diff --git a/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/wiring/ResourcesModule.scala b/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 }

diff --git a/delta/app/src/main/scala/ch/epfl/bluebrain/nexus/delta/wiring/SchemasModule.scala b/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)

diff --git a/delta/app/src/test/resources/schemas/errors/invalid-schema.json b/delta/app/src/test/resources/schemas/errors/invalid-schema.json
@@ -21,6 +21,6 @@
       },
       "value": "nxv:42"
     },
-    "targetedNodes": 417
+    "targetedNodes": 412
   }
 }
diff --git a/delta/app/src/test/scala/ch/epfl/bluebrain/nexus/delta/routes/ResourcesRoutesSpec.scala b/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)

diff --git a/delta/app/src/test/scala/ch/epfl/bluebrain/nexus/delta/routes/SchemasRoutesSpec.scala b/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 =

diff --git a/delta/plugins/search/src/test/resources/contexts/search-document.json b/delta/plugins/search/src/test/resources/contexts/search-document.json
diff --git a/delta/plugins/search/src/test/resources/organization.json b/delta/plugins/search/src/test/resources/organization.json
diff --git a/delta/plugins/search/src/test/resources/person.json b/delta/plugins/search/src/test/resources/person.json