chore: Patch dependency updates

.git-blame-ignore-revs

@@ -6,3 +6,6 @@
 
 # Scala Steward: Reformat with scalafmt 3.8.3
 a5523a0b097ee63e511bff6abf018d5ac6740288
+
+# Scala Steward: Reformat with scalafmt 3.8.4
+fb8d6ba614e93997749443355c7e59cdb12edf58

.scalafmt.conf

@@ -1,4 +1,4 @@
-version = "3.8.3"
+version = "3.8.4"
 runner.dialect = scala3
 maxColumn = 120
 align.preset = most

integration/src/test/scala/org/knora/webapi/models/filemodels/FileModelUtil.scala

@@ -207,7 +207,7 @@ object FileModelUtil {
     }
     val lines = ontologies.toList
       .map(x => s"""    "${x._1}": "${x._2}\"""")
-      .reduce({ (a, b) => a + ",\n" + b })
+      .reduce((a, b) => a + ",\n" + b)
     s"""|"@context" : {
         |$lines
         |  }

project/Dependencies.scala

@@ -16,25 +16,22 @@ object Dependencies {
 
   val ScalaVersion = "3.3.4"
 
-  val PekkoActorVersion = "1.1.2"
+  val PekkoActorVersion = "1.1.3"
   val PekkoHttpVersion  = "1.1.0"
 
   val MonocleVersion = "3.3.0"
 
-  // rdf and graph libraries
-  // topbraid/shacl is not yet compatible with jena 5 so we need to use jena 4 for now
-  // see: https://github.com/TopQuadrant/shacl/pull/177
-  val JenaVersion          = "4.10.0"
   val Rdf4jVersion         = "5.1.0"
-  val TopbraidShaclVersion = "1.4.3"
+  val TopbraidShaclVersion = "1.4.4"
+  val JenaVersion          = "5.2.0" // should be aligned with the version topbraid-shacl uses
 
-  val ZioConfigVersion            = "4.0.2"
+  val ZioConfigVersion            = "4.0.3"
   val ZioLoggingVersion           = "2.4.0"
   val ZioNioVersion               = "2.0.2"
   val ZioMetricsConnectorsVersion = "2.3.1"
   val ZioPreludeVersion           = "1.0.0-RC36"
   val ZioSchemaVersion            = "0.2.0"
-  val ZioVersion                  = "2.1.13"
+  val ZioVersion                  = "2.1.14"
 
   // ZIO
   val zio                   = "dev.zio"                       %% "zio"                       % ZioVersion
@@ -47,7 +44,7 @@ object Dependencies {
   val zioNio                = "dev.zio"                       %% "zio-nio"                   % ZioNioVersion
   val zioMacros             = "dev.zio"                       %% "zio-macros"                % ZioVersion
   val zioPrelude            = "dev.zio"                       %% "zio-prelude"               % ZioPreludeVersion
-  val zioSttp               = "com.softwaremill.sttp.client3" %% "zio"                       % "3.10.1"
+  val zioSttp               = "com.softwaremill.sttp.client3" %% "zio"                       % "3.10.2"
 
   // refined
   val refined = Seq(
@@ -75,6 +72,7 @@ object Dependencies {
   val pekkoStream        = "org.apache.pekko" %% "pekko-stream"          % PekkoActorVersion
 
   // rdf and graph libraries
+  val jenaCore      = "org.apache.jena"   % "jena-core"           % JenaVersion
   val jenaText      = "org.apache.jena"   % "jena-text"           % JenaVersion
   val rdf4jClient   = "org.eclipse.rdf4j" % "rdf4j-client"        % Rdf4jVersion
   val rdf4jShacl    = "org.eclipse.rdf4j" % "rdf4j-shacl"         % Rdf4jVersion
@@ -96,7 +94,7 @@ object Dependencies {
   val jwtSprayJson = "com.github.jwt-scala" %% "jwt-zio-json" % "10.0.1"
   // jwtSprayJson -> 9.0.2 is the latest version that's compatible with spray-json; if it wasn't for spray, this would be Scala 3 compatible
   val springSecurityCore =
-    "org.springframework.security" % "spring-security-core" % "6.3.5" exclude (
+    "org.springframework.security" % "spring-security-core" % "6.3.6" exclude (
       "commons-logging",
       "commons-logging",
     ) exclude ("org.springframework", "spring-aop")
@@ -129,7 +127,7 @@ object Dependencies {
   // found/added by the plugin but deleted anyway
   val commonsLang3 = "org.apache.commons" % "commons-lang3" % "3.17.0"
 
-  val tapirVersion = "1.11.10"
+  val tapirVersion = "1.11.12"
 
   val tapir = Seq(
     "com.softwaremill.sttp.tapir" %% "tapir-pekko-http-server" % tapirVersion,

project/build.properties

@@ -1 +1 @@
-sbt.version=1.10.6
+sbt.version=1.10.7

project/plugins.sbt

@@ -9,6 +9,6 @@ addSbtPlugin("com.eed3si9n"            % "sbt-assembly"        % "2.3.0")
 addSbtPlugin("com.github.sbt"          % "sbt-javaagent"       % "0.1.8")
 addSbtPlugin("org.scoverage"           % "sbt-scoverage"       % "2.2.2")
 addSbtPlugin("com.eed3si9n"            % "sbt-buildinfo"       % "0.12.0")
-addSbtPlugin("org.scalameta"           % "sbt-scalafmt"        % "2.5.2")
+addSbtPlugin("org.scalameta"           % "sbt-scalafmt"        % "2.5.3")
 addSbtPlugin("ch.epfl.scala"           % "sbt-scalafix"        % "0.12.1")
 addSbtPlugin("de.heikoseeberger"       % "sbt-header"          % "5.10.0")

webapi/src/main/scala/org/knora/webapi/messages/StringFormatter.scala

@@ -260,7 +260,7 @@ object StringFormatter {
   private def getOrCacheSmartIri(iriStr: IRI, creationFun: () => SmartIri): SmartIri =
     smartIriCache.computeIfAbsent(
       iriStr,
-      JavaUtil.function({ (_: Object) => creationFun() }),
+      JavaUtil.function((_: Object) => creationFun()),
     )
 
   val live: ZLayer[AppConfig, Nothing, StringFormatter] = ZLayer.fromFunction { (appConfig: AppConfig) =>

webapi/src/main/scala/org/knora/webapi/messages/util/rdf/JenaModel.scala

@@ -21,7 +21,7 @@ sealed trait JenaNode extends RdfNode {
 }
 
 case class JenaBlankNode(node: jena.graph.Node) extends JenaNode with BlankNode {
-  override def id: String = node.getBlankNodeId.getLabelString
+  override def id: String = node.getBlankNodeLabel
 
   override def stringValue: String = id
 }
@@ -126,7 +126,7 @@ object JenaContextFactory {
   /**
    * Converts a named graph IRI to a [[jena.graph.Node]].
    */
-  def contextIriToNode(context: IRI): jena.graph.Node =
+  private def contextIriToNode(context: IRI): jena.graph.Node =
     jena.graph.NodeFactory.createURI(context)
 
   /**
@@ -359,7 +359,7 @@ object JenaNodeFactory {
    * @return a [[DatatypeLiteral]].
    */
   def makeDatatypeLiteral(value: String, datatype: IRI): DatatypeLiteral =
-    JenaDatatypeLiteral(jena.graph.NodeFactory.createLiteral(value, typeMapper.getTypeByName(datatype)))
+    JenaDatatypeLiteral(jena.graph.NodeFactory.createLiteralDT(value, typeMapper.getTypeByName(datatype)))
 
   /**
    * Constructs a string with a language tag.
@@ -368,7 +368,7 @@ object JenaNodeFactory {
    * @param language the language tag.
    */
   def makeStringWithLanguage(value: String, language: String): StringWithLanguage =
-    JenaStringWithLanguage(jena.graph.NodeFactory.createLiteral(value, language))
+    JenaStringWithLanguage(jena.graph.NodeFactory.createLiteralLang(value, language))
 
   /**
    * Constructs a statement.

webapi/src/main/scala/org/knora/webapi/messages/v2/responder/ontologymessages/OntologyMessagesV2.scala

@@ -96,41 +96,40 @@ object CreateOntologyRequestV2 {
     apiRequestID: UUID,
     requestingUser: User,
   ): ZIO[StringFormatter, Throwable, CreateOntologyRequestV2] = ZIO.serviceWithZIO[StringFormatter] {
-    implicit sf: StringFormatter =>
-      for {
-        isShared <- ZIO
-                      .fromEither(jsonLDDocument.body.getBoolean(KnoraApiV2Complex.IsShared))
-                      .mapBoth(BadRequestException(_), _.exists(identity))
-        ontologyName <-
-          ZIO.attempt {
-            jsonLDDocument.body.requireStringWithValidation(
-              KnoraApiV2Complex.OntologyName,
-              ValuesValidator.validateProjectSpecificOntologyName(_).getOrElse(_),
-            )
-          }
-        label <-
-          ZIO.attempt(
-            jsonLDDocument.body.requireStringWithValidation(Rdfs.Label, Iri.toSparqlEncodedString(_).getOrElse(_)),
-          )
-        comment <-
-          ZIO.attempt(
-            jsonLDDocument.body.maybeStringWithValidation(Rdfs.Comment, Iri.toSparqlEncodedString(_).getOrElse(_)),
+    implicit sf: StringFormatter => for {
+      isShared <- ZIO
+                    .fromEither(jsonLDDocument.body.getBoolean(KnoraApiV2Complex.IsShared))
+                    .mapBoth(BadRequestException(_), _.exists(identity))
+      ontologyName <-
+        ZIO.attempt {
+          jsonLDDocument.body.requireStringWithValidation(
+            KnoraApiV2Complex.OntologyName,
+            ValuesValidator.validateProjectSpecificOntologyName(_).getOrElse(_),
           )
-        projectIri <- ZIO.attempt {
-                        jsonLDDocument.body.requireIriInObject(
-                          KnoraApiV2Complex.AttachedToProject,
-                          sf.toSmartIriWithErr,
-                        )
-                      }
-      } yield CreateOntologyRequestV2(
-        ontologyName = ontologyName,
-        projectIri = projectIri,
-        isShared = isShared,
-        label = label,
-        comment = comment,
-        apiRequestID = apiRequestID,
-        requestingUser = requestingUser,
-      )
+        }
+      label <-
+        ZIO.attempt(
+          jsonLDDocument.body.requireStringWithValidation(Rdfs.Label, Iri.toSparqlEncodedString(_).getOrElse(_)),
+        )
+      comment <-
+        ZIO.attempt(
+          jsonLDDocument.body.maybeStringWithValidation(Rdfs.Comment, Iri.toSparqlEncodedString(_).getOrElse(_)),
+        )
+      projectIri <- ZIO.attempt {
+                      jsonLDDocument.body.requireIriInObject(
+                        KnoraApiV2Complex.AttachedToProject,
+                        sf.toSmartIriWithErr,
+                      )
+                    }
+    } yield CreateOntologyRequestV2(
+      ontologyName = ontologyName,
+      projectIri = projectIri,
+      isShared = isShared,
+      label = label,
+      comment = comment,
+      apiRequestID = apiRequestID,
+      requestingUser = requestingUser,
+    )
   }
 }
 

webapi/src/main/scala/org/knora/webapi/messages/v2/responder/valuemessages/ValueMessagesV2.scala

@@ -2186,14 +2186,11 @@ case class StillImageExternalFileValueContentV2(
       case ApiV2Complex =>
         JsonLDObject(
           toJsonLDObjectMapInComplexSchema(makeFileUrl) ++ Map(
-            StillImageFileValueHasIIIFBaseUrl -> JsonLDUtil
-              .makeUriObject(
-                {
-                  val uri = externalUrl.value.toURI
-                  if (uri.getPort == -1) URI.create(s"${uri.getScheme}://${uri.getHost}").toURL
-                  else URI.create(s"${uri.getScheme}://${uri.getHost}:${uri.getPort}").toURL
-                },
-              ),
+            StillImageFileValueHasIIIFBaseUrl -> JsonLDUtil.makeUriObject {
+              val uri = externalUrl.value.toURI
+              if (uri.getPort == -1) URI.create(s"${uri.getScheme}://${uri.getHost}").toURL
+              else URI.create(s"${uri.getScheme}://${uri.getHost}:${uri.getPort}").toURL
+            },
             StillImageFileValueHasExternalUrl -> JsonLDUtil.makeUriObject(externalUrl.value),
           ),
         )

webapi/src/main/scala/org/knora/webapi/responders/IriLocker.scala

@@ -134,16 +134,16 @@ object IriLocker {
     val newLock = lockMap.merge(
       iri,
       IriLock(apiRequestID, 1),
-      JavaUtil.biFunction({ (currentLock, _) =>
+      JavaUtil.biFunction((currentLock, _) =>
         // The lock is already in use. Who has it?
         if (currentLock.apiRequestID == apiRequestID) {
           // We already have it, so increment the entry count.
           currentLock.copy(entryCount = currentLock.entryCount + 1)
         } else {
           // Another API request has it, so leave it as is.
           currentLock
-        }
-      }),
+        },
+      ),
     )
     // Do we have the lock?
     if (newLock.apiRequestID == apiRequestID) {
@@ -174,7 +174,7 @@ object IriLocker {
   private def decrementOrReleaseLock(iri: IRI, apiRequestID: UUID): Unit = {
     val _ = lockMap.compute(
       iri,
-      JavaUtil.biFunction({ (_, maybeCurrentLock) =>
+      JavaUtil.biFunction((_, maybeCurrentLock) =>
         Option(maybeCurrentLock) match {
           case Some(currentLock) =>
             if (currentLock.apiRequestID == apiRequestID) {
@@ -198,8 +198,8 @@ object IriLocker {
             throw ApplicationLockException(
               s"API request $apiRequestID was supposed to have an update lock on $iri, but the lock is unused",
             )
-        }
-      }),
+        },
+      ),
     )
   }
 }

webapi/src/main/scala/org/knora/webapi/responders/v2/ResourcesResponderV2.scala

@@ -1628,14 +1628,13 @@ final case class ResourcesResponderV2(
                                                                  )
 
       // If there is a version history for deletion of the event, create a delete resource event for it.
-      (deletionRep, resourceAtValueChanges) = fullReps.tail.partition { case (resHist, resource) =>
-                                                resource
-                                                  .asInstanceOf[ReadResourceV2]
-                                                  .deletionInfo
-                                                  .exists(deletionInfo =>
-                                                    deletionInfo.deleteDate == resHist.versionDate,
-                                                  )
-                                              }
+      (deletionRep, resourceAtValueChanges) =
+        fullReps.tail.partition { case (resHist, resource) =>
+          resource
+            .asInstanceOf[ReadResourceV2]
+            .deletionInfo
+            .exists(deletionInfo => deletionInfo.deleteDate == resHist.versionDate)
+        }
       resourceDeleteEvent = getResourceDeletionEvents(deletionRep)
 
       // For each value version, form an event

webapi/src/main/scala/org/knora/webapi/responders/v2/SearchResponderV2.scala

@@ -997,10 +997,9 @@ final case class SearchResponderV2Live(
     mainResourceVar: QueryVariable,
   ): SparqlSelectResult = {
     // Make a Map of merged results per main resource IRI.
-    val prequeryRowsMergedMap: Map[IRI, VariableResultsRow] = prequeryResponseNotMerged.results.bindings.groupBy {
-      row =>
-        // Get the rows for each main resource IRI.
-        row.rowMap(mainResourceVar.variableName)
+    val prequeryRowsMergedMap: Map[IRI, VariableResultsRow] = prequeryResponseNotMerged.results.bindings.groupBy { row =>
+      // Get the rows for each main resource IRI.
+      row.rowMap(mainResourceVar.variableName)
     }.map { case (resourceIri: IRI, rows: Seq[VariableResultsRow]) =>
       // Make a Set of all the column names in the rows to be merged.
       val columnNamesToMerge: Set[String] = rows.flatMap(_.rowMap.keySet).toSet

webapi/src/main/scala/org/knora/webapi/responders/v2/ontology/OntologyHelpers.scala

@@ -778,8 +778,7 @@ object OntologyHelpers {
         OntologyConstants.KnoraBase.IsAudioSegmentOfValue.toSmartIri
       case subProps if subProps.contains(OntologyConstants.KnoraBase.IsVideoSegmentOf.toSmartIri) =>
         OntologyConstants.KnoraBase.IsVideoSegmentOfValue.toSmartIri
-      case subProps
-          if subProps.size == 1 => // if subPropertyOf is neither isPartOf nor HasLinkTo it inherits from a custom link property
+      case subProps if subProps.size == 1 => // if subPropertyOf is neither isPartOf nor HasLinkTo it inherits from a custom link property
         internalPropertyDef.subPropertyOf.head.fromLinkPropToLinkValueProp
       case _ =>
         throw BadRequestException(