From 7d0c64015c777e0130e89d5d7f47a0138b447db8 Mon Sep 17 00:00:00 2001
From: Claus Stadler <RavenArkadon@googlemail.com>
Date: Tue, 29 Oct 2024 08:29:08 +0100
Subject: [PATCH] Update to jena 5.3.0-SNAPSHOT

---
 pom.xml                                       | 271 ++----------------
 rdf-processing-toolkit-cli/pom.xml            | 115 ++++----
 .../src/main/resources/log4j2.properties      |   2 +-
 3 files changed, 91 insertions(+), 297 deletions(-)

diff --git a/pom.xml b/pom.xml
index 32e8688..b1ff7bb 100644
--- a/pom.xml
+++ b/pom.xml
@@ -57,8 +57,8 @@
 
 		<spring-boot.version>2.3.3.RELEASE</spring-boot.version>
 
-		<jena.version>5.2.0-SNAPSHOT</jena.version>
-		<jenax.version>5.2.0-1-SNAPSHOT</jenax.version>
+		<jena.version>5.3.0-SNAPSHOT</jena.version>
+		<jenax.version>5.3.0-1-SNAPSHOT</jenax.version>
 		<rmltk.version>5.2.0-1-SNAPSHOT</rmltk.version>
 		<conjure.version>5.2.0-1-SNAPSHOT</conjure.version>
 		<sansa.version>0.9.6-SNAPSHOT</sansa.version>
@@ -85,6 +85,22 @@
 	</properties>
 	<dependencyManagement>
 		<dependencies>
+			<dependency>
+				<groupId>org.aksw.jenax</groupId>
+				<artifactId>jenax-bom</artifactId>
+				<version>${jenax.version}</version>
+				<type>pom</type>
+				<scope>import</scope>
+			</dependency>
+
+			<dependency>
+				<groupId>org.apache.jena</groupId>
+				<artifactId>apache-jena-libs</artifactId>
+				<version>${jena.version}</version>
+				<type>pom</type>
+				<scope>import</scope>
+			</dependency>
+
 			<dependency>
 				<groupId>org.eclipse.jetty</groupId>
 				<artifactId>jetty-bom</artifactId>
@@ -93,6 +109,16 @@
 				<scope>import</scope>
 			</dependency>
 
+			<!-- Also declares versions for sub groups such as
+			org.glassfish.jersey.containers -->
+			<dependency>
+				<groupId>org.glassfish.jersey</groupId>
+				<artifactId>jersey-bom</artifactId>
+				<version>${jersey.version}</version>
+				<scope>import</scope>
+				<type>pom</type>
+			</dependency>
+
 			<dependency>
 				<groupId>javax.ws.rs</groupId>
 				<artifactId>javax.ws.rs-api</artifactId>
@@ -197,39 +223,11 @@
 				<version>${hadoop.version}</version>
 			</dependency>
 
-			<!-- Also declares versions for sub groups such as
-			org.glassfish.jersey.containers -->
-			<dependency>
-				<groupId>org.glassfish.jersey</groupId>
-				<artifactId>jersey-bom</artifactId>
-				<version>${jersey.version}</version>
-				<scope>import</scope>
-				<type>pom</type>
-			</dependency>
-
-			<!--
-                        <dependency>
-                                <groupId>jakarta.servlet</groupId>
-                                <artifactId>jakarta.servlet-api</artifactId>
-                                <version>${jakarta.servlet-api.version}</version>
-			</dependency>
-			-->
-
 			<dependency>
 				<groupId>org.aksw.conjure</groupId>
 				<artifactId>conjure-datasources</artifactId>
 				<version>${conjure.version}</version>
 				<exclusions>
-<!--
-					<exclusion>
-						<groupId>org.apache.spark</groupId>
-						<artifactId>spark-sql_2.13</artifactId>
-					</exclusion>
-					<exclusion>
-						<groupId>org.apache.spark</groupId>
-						<artifactId>spark-core_2.13</artifactId>
-					</exclusion>
--->
 				</exclusions>
 			</dependency>
 			<dependency>
@@ -257,13 +255,6 @@
 				<artifactId>picocli</artifactId>
 				<version>${picocli.version}</version>
 			</dependency>
-			<dependency>
-				<groupId>org.aksw.jenax</groupId>
-				<artifactId>jenax-bom</artifactId>
-				<version>${jenax.version}</version>
-				<type>pom</type>
-				<scope>import</scope>
-			</dependency>
 			<dependency>
 				<groupId>org.slf4j</groupId>
 				<artifactId>slf4j-bom</artifactId>
@@ -303,122 +294,19 @@
 					</exclusion>
 				</exclusions>
 			</dependency>
-			<!--
-			<dependency>
-				<groupId>org.aksw.jenax</groupId>
-				<artifactId>jenax-rx-ops-syscall</artifactId>
-				<version>${jenax.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.aksw.jenax</groupId>
-				<artifactId>jenax-arq-connection-virtuoso</artifactId>
-				<version>${jenax.version}</version>
-			</dependency>
 
-			<dependency>
-				<groupId>org.aksw.jenax</groupId>
-				<artifactId>jenax-arq-algebra</artifactId>
-				<version>${jenax.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.aksw.jenax</groupId>
-				<artifactId>jenax-arq-hdt</artifactId>
-				<version>${jenax.version}</version>
-			</dependency>
--->
 			<dependency>
 				<groupId>org.aksw.rdf-processing-toolkit</groupId>
 				<artifactId>rdf-processing-toolkit-cli</artifactId>
 				<version>${project.version}</version>
 			</dependency>
-			<!-- <dependency> <groupId>org.aksw.rdf-processing-toolkit</groupId>
-			<artifactId>rdf-processing-toolkit-bundle</artifactId> 
-				<version>${project.version}</version> </dependency> -->
+
 			<dependency>
 				<groupId>org.locationtech.jts.io</groupId>
 				<artifactId>jts-io-common</artifactId>
 				<version>1.18.1</version>
 			</dependency>
 
-
-			<!-- <dependency> <groupId>org.aksw.sparql-integrate</groupId>
-			<artifactId>sparql-integrate-ckan-core</artifactId> 
-				<version>${project.version}</version> </dependency> <dependency>
-			<groupId>org.aksw.sparql-integrate</groupId> 
-				<artifactId>sparql-integrate-ckan-cli</artifactId>
-			<version>${project.version}</version> 
-			</dependency> -->
-			<!--
-			<dependency>
-				<groupId>org.aksw.jenax</groupId>
-				<artifactId>jenax-arq-plugins-bundle</artifactId>
-				<version>${jenax.version}</version>
-			-->
-			<!-- <exclusions> <exclusion>
-			<groupId>org.locationtech.jts</groupId> 
-					<artifactId>jts-core</artifactId> </exclusion> <exclusion>
-			<groupId>com.vividsolutions</groupId> 
-					<artifactId>jts-core</artifactId> </exclusion> <exclusion>
-			<groupId>com.vividsolutions</groupId> 
-					<artifactId>jts-io</artifactId> </exclusion> <exclusion>
-			<groupId>org.geotools</groupId> 
-					<artifactId>gt-epsg-hsql</artifactId> </exclusion> <exclusion>
-			<groupId>org.geotools</groupId> 
-					<artifactId>gt-geometry</artifactId> </exclusion> <exclusion>
-			<groupId>org.geotools</groupId> 
-					<artifactId>gt-referencing</artifactId> </exclusion> <exclusion>
-			<groupId>org.codehaus.plexus</groupId> 
-					<artifactId>plexus-utils</artifactId> </exclusion> </exclusions> -->
-			<!-- </dependency> -->
-			<!--
-			<dependency>
-				<groupId>org.aksw.jenax</groupId>
-				<artifactId>jenax-rx-dataaccess</artifactId>
-				<version>${jenax.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.aksw.jenax</groupId>
-				<artifactId>jenax-io-core</artifactId>
-				<version>${jenax.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.aksw.jenax</groupId>
-				<artifactId>jenax-arq-json</artifactId>
-				<version>${jenax.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.aksw.jenax</groupId>
-				<artifactId>jenax-server-standalone</artifactId>
-				<version>${jenax.version}</version>
-				</dependency>
-			-->
-			<!-- <dependency> <groupId>io.github.galbiston</groupId>
-			<artifactId>geosparql-jena</artifactId> 
-				<version>1.1.1</version> </dependency> <dependency>
-			<groupId>org.apache.sis.non-free</groupId> 
-				<artifactId>sis-embedded-data</artifactId> <version>0.8</version> </dependency> -->
-			<!-- <dependency> -->
-			<!-- <groupId>com.beust</groupId> -->
-			<!-- <artifactId>jcommander</artifactId> -->
-			<!-- <version>1.78</version> -->
-			<!-- </dependency> -->
-			<!-- <dependency> <groupId>org.springframework.boot</groupId>
-			<artifactId>spring-boot</artifactId> 
-				<version>${spring-boot.version}</version> </dependency> <dependency>
-			<groupId>org.springframework.boot</groupId> 
-				<artifactId>spring-boot-autoconfigure</artifactId>
-			<version>${spring-boot.version}</version> 
-				</dependency> <dependency> <groupId>org.springframework.boot</groupId>
-			<artifactId>spring-boot-loader</artifactId> 
-				<version>${spring-boot.version}</version> </dependency> -->
-			<!-- <dependency> <groupId>eu.trentorise.opendata</groupId>
-			<artifactId>jackan</artifactId> 
-				<version>0.4.2</version> </dependency> -->
 			<dependency>
 				<groupId>org.eclipse.jgit</groupId>
 				<artifactId>org.eclipse.jgit</artifactId>
@@ -439,32 +327,13 @@
 				<artifactId>jsch.agentproxy.sshagent</artifactId>
 				<version>0.0.9</version>
 			</dependency>
-			<!--
-			<dependency>
-                                <groupId>log4j</groupId>
-				<artifactId>log4j</artifactId>
-				<version>1.2.17</version>
-				<scope>provided</scope>
-			</dependency>
 
-			<dependency>
-                                <groupId>org.apache.logging.log4j</groupId>
-                                <artifactId>log4j-1.2-api</artifactId>
-                                <version>2.17.2</version>
-                                <scope>provided</scope>
-			</dependency>
-			-->
-			<!-- <dependency> -->
-			<!-- <groupId>org.slf4j</groupId> -->
-			<!-- <artifactId>slf4j-api</artifactId> -->
-			<!-- <version>${slf4j.version}</version> -->
-			<!-- </dependency> -->
-			<!-- Virtual FileSystem -->
 			<dependency>
 				<groupId>org.aksw.thirdparty.com.sshtools</groupId>
 				<artifactId>vfs2nio</artifactId>
 				<version>0.0.1-3-SNAPSHOT</version>
 			</dependency>
+
 			<dependency>
 				<groupId>org.apache.commons</groupId>
 				<artifactId>commons-vfs2</artifactId>
@@ -487,85 +356,7 @@
 					</exclusion>
 				</exclusions>
 			</dependency>
-			<!-- explicit jetty dependencies to pin version conflict with
-			hadoop-client -->
-			<!--
-			<dependency>
-				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>jetty-client</artifactId>
-				<version>${jetty.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>jetty-util</artifactId>
-				<version>${jetty.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>jetty-io</artifactId>
-				<version>${jetty.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>jetty-http</artifactId>
-				<version>${jetty.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>jetty-servlets</artifactId>
-				<version>${jetty.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>jetty-servlet</artifactId>
-				<version>${jetty.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>jetty-server</artifactId>
-				<version>${jetty.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>jetty-webapp</artifactId>
-				<version>${jetty.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>jetty-xml</artifactId>
-				<version>${jetty.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>jetty-security</artifactId>
-				<version>${jetty.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>jetty-util-ajax</artifactId>
-				<version>${jetty.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>jetty-annotations</artifactId>
-				<version>${jetty.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>jetty-plus</artifactId>
-				<version>${jetty.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>jetty-jndi</artifactId>
-				<version>${jetty.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.eclipse.jetty</groupId>
-				<artifactId>apache-jsp</artifactId>
-				<version>${jetty.version}</version>
-			</dependency>
-			-->
+
 			<dependency>
 				<groupId>junit</groupId>
 				<artifactId>junit</artifactId>
diff --git a/rdf-processing-toolkit-cli/pom.xml b/rdf-processing-toolkit-cli/pom.xml
index f89d704..6160d28 100644
--- a/rdf-processing-toolkit-cli/pom.xml
+++ b/rdf-processing-toolkit-cli/pom.xml
@@ -11,6 +11,58 @@
 	<artifactId>rdf-processing-toolkit-cli</artifactId>
 	<dependencies>
 
+		<dependency>
+			<groupId>org.aksw.jenax</groupId>
+			<artifactId>jenax-server-standalone</artifactId>
+		</dependency>
+
+		<dependency>
+			<groupId>org.aksw.jenax</groupId>
+			<artifactId>jenax-arq-picocli</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.aksw.jenax</groupId>
+			<artifactId>jenax-conjure-core</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.aksw.jenax</groupId>
+			<artifactId>jenax-rx-ops-syscall</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.aksw.jenax</groupId>
+			<artifactId>jenax-arq-algebra</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.aksw.jenax</groupId>
+			<artifactId>jenax-arq-hdt</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.aksw.jenax</groupId>
+			<artifactId>jenax-arq-json</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.aksw.jenax</groupId>
+			<artifactId>jenax-arq-plugins-bundle</artifactId>
+		</dependency>
+		<!-- TODO sparql-generate ships with its own log4j.properties file which
+		may break logging-->
+		<dependency>
+			<groupId>org.aksw.jenax</groupId>
+			<artifactId>jenax-arq-plugins-generate</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.aksw.jenax</groupId>
+			<artifactId>jenax-arq-plugins-qudtlib</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.aksw.jenax</groupId>
+			<artifactId>jenax-rx-dataaccess</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>org.aksw.jenax</groupId>
+			<artifactId>jenax-io-core</artifactId>
+		</dependency>
+
 		<dependency>
 			<groupId>javax.ws.rs</groupId>
 			<artifactId>javax.ws.rs-api</artifactId>
@@ -28,7 +80,7 @@
 			<groupId>net.sansa-stack</groupId>
 			<artifactId>sansa-cmds-picocli_2.13</artifactId>
 			<exclusions>
-<!--
+				<!--
 				<exclusion>
 					<groupId>org.apache.hadoop</groupId>
 					<artifactId>hadoop-client-runtime</artifactId>
@@ -90,10 +142,10 @@
 			<groupId>org.apache.hadoop</groupId>
 			<artifactId>hadoop-common</artifactId>
 		</dependency>
-                        <dependency>
-                                <groupId>org.apache.hadoop</groupId>
-                                <artifactId>hadoop-hdfs-client</artifactId>
-                        </dependency>
+		<dependency>
+			<groupId>org.apache.hadoop</groupId>
+			<artifactId>hadoop-hdfs-client</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>org.aksw.conjure</groupId>
 			<artifactId>conjure-datasources</artifactId>
@@ -106,56 +158,7 @@
 			<groupId>info.picocli</groupId>
 			<artifactId>picocli</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.aksw.jenax</groupId>
-			<artifactId>jenax-arq-picocli</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.aksw.jenax</groupId>
-			<artifactId>jenax-conjure-core</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.aksw.jenax</groupId>
-			<artifactId>jenax-rx-ops-syscall</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.aksw.jenax</groupId>
-			<artifactId>jenax-arq-algebra</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.aksw.jenax</groupId>
-			<artifactId>jenax-arq-hdt</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.aksw.jenax</groupId>
-			<artifactId>jenax-arq-json</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.aksw.jenax</groupId>
-			<artifactId>jenax-arq-plugins-bundle</artifactId>
-		</dependency>
-		<!-- TODO sparql-generate ships with its own log4j.properties file which
-		may break logging-->
-		<dependency>
-			<groupId>org.aksw.jenax</groupId>
-			<artifactId>jenax-arq-plugins-generate</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.aksw.jenax</groupId>
-			<artifactId>jenax-arq-plugins-qudtlib</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.aksw.jenax</groupId>
-			<artifactId>jenax-rx-dataaccess</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.aksw.jenax</groupId>
-			<artifactId>jenax-io-core</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>org.aksw.jenax</groupId>
-			<artifactId>jenax-server-standalone</artifactId>
-		</dependency>
+
 		<dependency>
 			<groupId>org.locationtech.jts.io</groupId>
 			<artifactId>jts-io-common</artifactId>
@@ -198,7 +201,7 @@
 			<artifactId>junit</artifactId>
 			<scope>test</scope>
 		</dependency>
-<!--
+		<!--
 		<dependency>
 			<groupId>org.aksw.rmltk</groupId>
 			<artifactId>rml-testsuite-processor-core</artifactId>
diff --git a/rdf-processing-toolkit-cli/src/main/resources/log4j2.properties b/rdf-processing-toolkit-cli/src/main/resources/log4j2.properties
index e780b9d..da6eeef 100644
--- a/rdf-processing-toolkit-cli/src/main/resources/log4j2.properties
+++ b/rdf-processing-toolkit-cli/src/main/resources/log4j2.properties
@@ -6,7 +6,7 @@ appender.console.name = STDERR
 appender.console.target = SYSTEM_ERR
 appender.console.layout.type = PatternLayout
 # appender.console.layout.pattern = [%p] %m%n
-appender.console.layout.pattern = %d{HH:mm:ss} [%p] [%c{1.}:%L] - %m%n
+appender.console.layout.pattern = %d{HH:mm:ss} %t [%p] [%c{1.}:%L] - %m%n
 # appender.console.layout.pattern = %d{yyyy-MM-dd HH:mm:ss} [%p] [%c:%L] - %m%n
 
 rootLogger.level = info