Update deps

MPDL · Apr 19, 2024 · bc35f98 · bc35f98
1 parent 2d970b2
commit bc35f98
Show file tree

Hide file tree

Showing 13 changed files with 183 additions and 194 deletions.
diff --git a/pom.xml b/pom.xml
@@ -74,7 +74,7 @@
 	<properties>
 		<!-- the jdk version to use -->
 		<jdk.version>17</jdk.version>
-		<jersey.version>2.39</jersey.version>
+		<jersey.version>2.42</jersey.version>
 
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<!-- Used by Tomcat to trip version Nr when deploy WAR package, e.g., imeji_1.0_screenshot->imeji -->
@@ -389,7 +389,7 @@
 			<groupId>org.apache.jena</groupId>
 			<artifactId>apache-jena-libs</artifactId>
 			<type>pom</type>
-			<version>4.10.0</version>
+			<version>5.0.0</version>
 			<exclusions>
 				<exclusion>
 					<groupId>com.fasterxml.jackson.core</groupId>
@@ -411,17 +411,17 @@
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-1.2-api</artifactId>
-			<version>2.20.0</version>
+			<version>2.23.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-api</artifactId>
-			<version>2.20.0</version>
+			<version>2.23.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-core</artifactId>
-			<version>2.20.0</version>
+			<version>2.23.1</version>
 		</dependency>
 		<!-- USED during compile, e.g. javax.mail -->
 		<dependency>
@@ -449,7 +449,7 @@
 		<dependency>
 			<groupId>org.junit.vintage</groupId>
 			<artifactId>junit-vintage-engine</artifactId>
-			<version>5.9.1</version>
+			<version>5.10.2</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
@@ -461,7 +461,7 @@
 		<dependency>
 	      <groupId>org.awaitility</groupId>
 	      <artifactId>awaitility</artifactId>
-	      <version>4.0.1</version>
+	      <version>4.2.1</version>
 	      <scope>test</scope>
 		</dependency>
 		<!-- START JSF 2 -->
@@ -509,13 +509,13 @@
 		<dependency>
 			<groupId>org.apache.tika</groupId>
 			<artifactId>tika-core</artifactId>
-			<version>2.9.1</version>
+			<version>2.9.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>org.apache.tika</groupId>
 			<artifactId>tika-parsers-standard-package</artifactId>
-			<version>2.9.1</version>
+			<version>2.9.2</version>
 		</dependency>
 
 		<!--
@@ -578,19 +578,19 @@
 		<dependency>
 			<groupId>org.bitbucket.b_c</groupId>
 			<artifactId>jose4j</artifactId>
-			<version>0.9.3</version>
+			<version>0.9.4</version>
 		</dependency>
 
 		<dependency>
 			<groupId>io.swagger.core.v3</groupId>
 			<artifactId>swagger-jaxrs2</artifactId>
-			<version>2.2.18</version>
+			<version>2.2.21</version>
 		</dependency>
 
 		<dependency>
 			<groupId>co.elastic.clients</groupId>
 			<artifactId>elasticsearch-java</artifactId>
-			<version>8.11.2</version>
+			<version>8.11.4</version>
 		</dependency>
 
 
@@ -633,19 +633,19 @@
 		<dependency>
 		    <groupId>org.testcontainers</groupId>
 		    <artifactId>elasticsearch</artifactId>
-		    <version>1.19.1</version>
+		    <version>1.19.7</version>
 		    <scope>test</scope>
 		</dependency>
 		<!-- Add slf4j-Dependency to get the TestContainers Log (Solves: 'SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".') -->		
 		<dependency>
 	       <groupId>org.slf4j</groupId>
 	       <artifactId>slf4j-api</artifactId>
-	       <version>2.0.5</version>
+	       <version>2.0.12</version>
 	   </dependency>
 	   	<dependency>
 	       <groupId>org.apache.logging.log4j</groupId>
 	       <artifactId>log4j-slf4j-impl</artifactId>
-	       <version>2.20.0</version>
+	       <version>2.23.1</version>
 	   </dependency>
 		<dependency>
 			<groupId>org.mapdb</groupId>
@@ -660,7 +660,7 @@
 		<dependency>
 		    <groupId>org.jsoup</groupId>
 		    <artifactId>jsoup</artifactId>
-		    <version>1.15.3</version>
+		    <version>1.17.2</version>
 		</dependency>
 		<dependency>
 			<groupId>com.googlecode.json-simple</groupId>
@@ -676,7 +676,7 @@
 		<dependency>
 			<groupId>com.google.guava</groupId>
 			<artifactId>guava</artifactId>
-			<version>32.1.3-jre</version>
+			<version>33.1.0-jre</version>
 		</dependency>
 
 		<dependency>

diff --git a/src/main/java/de/mpg/imeji/j2j/queries/Queries.java b/src/main/java/de/mpg/imeji/j2j/queries/Queries.java
@@ -34,7 +34,7 @@ public static LinkedList<String> executeSPARQLQueryAndGetResults(String sparqlQu
     // set the model for more efficient handling
     final QueryExecution qexec = QueryExecutionFactory.create(q, dataset.getNamedModel(modelName));
     qexec.getContext().set(TDB.symUnionDefaultGraph, true);
-    qexec.setTimeout(-1);
+    //qexec.setTimeout(-1);
 
     LinkedList<String> resultURIs = new LinkedList<String>();
     try {

diff --git a/src/main/java/de/mpg/imeji/j2j/transaction/SearchTransaction.java b/src/main/java/de/mpg/imeji/j2j/transaction/SearchTransaction.java
@@ -52,7 +52,7 @@ protected void execute(Dataset ds) throws ImejiException {
     final Query q = QueryFactory.create(searchQuery, Syntax.syntaxARQ);
     final QueryExecution qexec = initQueryExecution(ds, q);
     qexec.getContext().set(TDB.symUnionDefaultGraph, true);
-    qexec.setTimeout(-1);
+    //qexec.setTimeout(-1);
     try {
       final ResultSet rs = qexec.execSelect();
       setResults(rs);

diff --git a/src/main/java/de/mpg/imeji/logic/init/ImejiInitializer.java b/src/main/java/de/mpg/imeji/logic/init/ImejiInitializer.java
@@ -8,10 +8,11 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import de.mpg.imeji.logic.storage.Storage;
 import de.mpg.imeji.logic.util.StorageUtils;
 import org.apache.jena.atlas.lib.AlarmClock;
-import org.apache.jena.tdb.StoreConnection;
+
+import org.apache.jena.tdb1.base.file.Location;
+import org.apache.jena.tdb1.sys.StoreConnection;
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
 import org.jose4j.lang.JoseException;
@@ -22,8 +23,6 @@
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.tdb.TDB;
 import org.apache.jena.tdb.TDBFactory;
-import org.apache.jena.tdb.base.file.Location;
-import org.apache.jena.tdb.sys.TDBMaker;
 
 import de.mpg.imeji.exceptions.AlreadyExistsException;
 import de.mpg.imeji.exceptions.ImejiException;
@@ -57,6 +56,8 @@
 import de.mpg.imeji.logic.security.user.UserService.USER_TYPE;
 import de.mpg.imeji.logic.util.StringHelper;
 
+
+
 /**
  * Initialize imeji
  *

diff --git a/src/main/java/de/mpg/imeji/presentation/admin/mode/ModeFilter.java b/src/main/java/de/mpg/imeji/presentation/admin/mode/ModeFilter.java
@@ -16,7 +16,6 @@
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
-
 import de.mpg.imeji.presentation.rewrite.RequestHelper;
 import de.mpg.imeji.logic.config.Imeji;
 import de.mpg.imeji.presentation.navigation.Navigation;
@@ -110,9 +109,9 @@ private boolean isPrivateModus() {
   }
 
   private void redirectToLogin(ServletRequest serv, ServletResponse resp) throws UnsupportedEncodingException, IOException {
-    final String url = navigation.getApplicationUri() + RequestHelper.getCurrentInstance((HttpServletRequest) serv).getPrettyRequestURL().toString();
-    final Map<String, List<String>> params =
-        RequestHelper.getCurrentInstance((HttpServletRequest) serv).getRequestQueryParameters();
+    final String url =
+        navigation.getApplicationUri() + RequestHelper.getCurrentInstance((HttpServletRequest) serv).getPrettyRequestURL().toString();
+    final Map<String, List<String>> params = RequestHelper.getCurrentInstance((HttpServletRequest) serv).getRequestQueryParameters();
     ((HttpServletResponse) resp).sendRedirect(navigation.getApplicationUrl() + "login?" + REDIRECT_AFTER_LOGIN_PARAM + "="
         + URLEncoder.encode(url + HistoryUtil.paramsMapToString(params), "UTF-8"));
   }

diff --git a/src/main/java/de/mpg/imeji/presentation/collection/share/ShareBean.java b/src/main/java/de/mpg/imeji/presentation/collection/share/ShareBean.java
@@ -123,7 +123,8 @@ public void init() throws ImejiException {
     input = new ShareInput(uri.toString(), ownersEmail, getSessionUser(), getLocale(), instanceName);
     shareList = new ShareList(owner, uri.toString(), getSessionUser(), getLocale());
     isAdmin = SecurityUtil.authorization().administrate(getSessionUser(), shareTo);
-    pageUrl = RequestHelper.getCurrentInstance().getPrettyRequestURL().toString() + RequestHelper.getCurrentInstance().getRequestQueryString();
+    pageUrl =
+        RequestHelper.getCurrentInstance().getPrettyRequestURL().toString() + RequestHelper.getCurrentInstance().getRequestQueryString();
     pageUrl = pageUrl.split("[&\\?]group=")[0];
   }
 

diff --git a/src/main/java/de/mpg/imeji/presentation/item/details/ItemBean.java b/src/main/java/de/mpg/imeji/presentation/item/details/ItemBean.java
@@ -91,8 +91,7 @@ public class ItemBean extends SuperBean {
    *
    * @
    */
-  public ItemBean() {
-  }
+  public ItemBean() {}
 
   public void preRenderView() throws IOException {
     if (FacesContext.getCurrentInstance().getPartialViewContext().isAjaxRequest()) {

diff --git a/src/main/java/de/mpg/imeji/presentation/navigation/history/HistoryFilter.java b/src/main/java/de/mpg/imeji/presentation/navigation/history/HistoryFilter.java
@@ -28,7 +28,6 @@
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
 
-
 import de.mpg.imeji.exceptions.AuthenticationError;
 import de.mpg.imeji.exceptions.BadRequestException;
 import de.mpg.imeji.exceptions.NotAllowedError;