From 627b4707ea90c79c909edc055938804f3fd6db58 Mon Sep 17 00:00:00 2001
From: Jim Balhoff <jim@balhoff.org>
Date: Mon, 7 Aug 2023 12:45:49 -0400
Subject: [PATCH] Update to Jena 4.9.0. (#114)

---
 build.sbt                                       |  2 +-
 src/main/scala/org/phenoscape/owlet/Owlet.scala | 12 +++++-------
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/build.sbt b/build.sbt
index 29d5438..63d4464 100644
--- a/build.sbt
+++ b/build.sbt
@@ -33,7 +33,7 @@ libraryDependencies ++= {
     Seq(
       "org.scalaz"                 %% "scalaz-core"              % "7.3.7",
       "net.sourceforge.owlapi"     %  "owlapi-distribution"      % "4.5.26",
-      "org.apache.jena"            %  "apache-jena-libs"         % "4.1.0",
+      "org.apache.jena"            %  "apache-jena-libs"         % "4.9.0",
       "com.typesafe.scala-logging" %% "scala-logging"            % "3.9.5",
       "org.scala-lang.modules"     %% "scala-xml"                % "2.0.1",
       "org.slf4j"                  %  "slf4j-log4j12"            % "1.7.32" % Test,
diff --git a/src/main/scala/org/phenoscape/owlet/Owlet.scala b/src/main/scala/org/phenoscape/owlet/Owlet.scala
index ba9acdc..e76c07e 100644
--- a/src/main/scala/org/phenoscape/owlet/Owlet.scala
+++ b/src/main/scala/org/phenoscape/owlet/Owlet.scala
@@ -1,7 +1,5 @@
 package org.phenoscape.owlet
 
-import java.util.UUID
-
 import org.apache.jena.graph._
 import org.apache.jena.graph.impl.GraphBase
 import org.apache.jena.query._
@@ -17,9 +15,9 @@ import org.semanticweb.owlapi.apibinding.OWLManager
 import org.semanticweb.owlapi.model._
 import org.semanticweb.owlapi.reasoner.OWLReasoner
 
+import java.util.UUID
 import scala.collection.JavaConverters._
 import scala.collection.Map
-import scala.collection.immutable.Set
 
 /**
  * Processes SPARQL queries containing triple patterns with embedded OWL class expressions.
@@ -42,16 +40,16 @@ class Owlet(reasoner: OWLReasoner) {
     newQuery
   }
 
-  private class SPARQLVisitor(prefixes: Map[String, String], asValues: Boolean) extends RecursiveElementVisitor(new ElementVisitorBase()) {
+  private class SPARQLVisitor(prefixes: Map[String, String], asValues: Boolean) extends ElementVisitorBase {
 
-    override def endElement(filter: ElementFilter): Unit = filter.getExpr match {
+    override def visit(filter: ElementFilter): Unit = filter.getExpr match {
       case existsLike: ExprFunctionOp => existsLike.getElement.visit(this)
       case _                          => ()
     }
 
-    override def endElement(subquery: ElementSubQuery): Unit = subquery.getQuery.getQueryPattern.visit(this)
+    override def visit(subquery: ElementSubQuery): Unit = subquery.getQuery.getQueryPattern.visit(this)
 
-    override def endElement(group: ElementGroup): Unit = {
+    override def visit(group: ElementGroup): Unit = {
       for (pathBlock <- group.getElements.asScala.collect({ case pb: ElementPathBlock => pb })) {
         val patterns = pathBlock.getPattern.iterator
         while (patterns.hasNext) {