Bumping up to slf4j2 and log4j2. Logging doesn't work correctly yet, at least in some modules

josemduarte · josemduarte · commit 1be0260ebfd4 · 2024-04-24T16:21:15.000-07:00
diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml
@@ -86,7 +86,7 @@
 		<!-- binding for log4j2, scope=runTime set in parent pom -->
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
-			<artifactId>log4j-slf4j-impl</artifactId>
+			<artifactId>log4j-slf4j2-impl</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
@@ -63,7 +63,7 @@
     	<!-- binding for log4j2, scope=runTime set in parent pom -->
  		<dependency>
     		<groupId>org.apache.logging.log4j</groupId>
-    		<artifactId>log4j-slf4j-impl</artifactId>
+    		<artifactId>log4j-slf4j2-impl</artifactId>
   		</dependency>
   		<dependency>
     		<groupId>org.apache.logging.log4j</groupId>
diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml
@@ -63,7 +63,7 @@
 		<!-- binding for log4j2, scope=runTime set in parent pom -->
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
-			<artifactId>log4j-slf4j-impl</artifactId>
+			<artifactId>log4j-slf4j2-impl</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml
@@ -103,7 +103,7 @@
     	<!-- binding for log4j2, scope=runTime set in parent pom -->
  		<dependency>
     		<groupId>org.apache.logging.log4j</groupId>
-    		<artifactId>log4j-slf4j-impl</artifactId>
+    		<artifactId>log4j-slf4j2-impl</artifactId>
   		</dependency>
   		<dependency>
     		<groupId>org.apache.logging.log4j</groupId>
diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml
@@ -50,7 +50,7 @@
     	<!-- binding for log4j2, scope=runTime set in parent pom -->
  		<dependency>
     		<groupId>org.apache.logging.log4j</groupId>
-    		<artifactId>log4j-slf4j-impl</artifactId>
+    		<artifactId>log4j-slf4j2-impl</artifactId>
   		</dependency>
   		<dependency>
     		<groupId>org.apache.logging.log4j</groupId>
diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml
@@ -43,7 +43,7 @@
 		<!-- binding for log4j2, scope=runTime set in parent pom -->
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
-			<artifactId>log4j-slf4j-impl</artifactId>
+			<artifactId>log4j-slf4j2-impl</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml
@@ -33,7 +33,7 @@
     	<!-- binding for log4j2, scope=runTime set in parent pom -->
  		<dependency>
     		<groupId>org.apache.logging.log4j</groupId>
-    		<artifactId>log4j-slf4j-impl</artifactId>
+    		<artifactId>log4j-slf4j2-impl</artifactId>
   		</dependency>
   		<dependency>
     		<groupId>org.apache.logging.log4j</groupId>
diff --git a/biojava-protein-comparison-tool/pom.xml b/biojava-protein-comparison-tool/pom.xml
@@ -67,7 +67,7 @@
 		<!-- binding for log4j2, scope=runTime set in parent pom -->
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
-			<artifactId>log4j-slf4j-impl</artifactId>
+			<artifactId>log4j-slf4j2-impl</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml
@@ -74,7 +74,7 @@
 		<!-- binding for log4j2, scope=runTime set in parent pom -->
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
-			<artifactId>log4j-slf4j-impl</artifactId>
+			<artifactId>log4j-slf4j2-impl</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml
@@ -53,7 +53,7 @@
         <!-- binding for log4j2, scope=runTime set in parent pom -->
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-slf4j-impl</artifactId>
+            <artifactId>log4j-slf4j2-impl</artifactId>
         </dependency>
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml
@@ -91,7 +91,7 @@
 		<!-- binding for log4j2, scope=runTime set in parent pom -->
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
-			<artifactId>log4j-slf4j-impl</artifactId>
+			<artifactId>log4j-slf4j2-impl</artifactId>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml
@@ -37,7 +37,7 @@
     	<!-- binding for log4j2, scope=runTime set in parent pom -->
  		<dependency>
     		<groupId>org.apache.logging.log4j</groupId>
-    		<artifactId>log4j-slf4j-impl</artifactId>
+    		<artifactId>log4j-slf4j2-impl</artifactId>
   		</dependency>
   		<dependency>
     		<groupId>org.apache.logging.log4j</groupId>
diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml
@@ -41,7 +41,7 @@
     	<!-- binding for log4j2, scope=runTime set in parent pom -->
  		<dependency>
     		<groupId>org.apache.logging.log4j</groupId>
-    		<artifactId>log4j-slf4j-impl</artifactId>
+    		<artifactId>log4j-slf4j2-impl</artifactId>
   		</dependency>
   		<dependency>
     		<groupId>org.apache.logging.log4j</groupId>
diff --git a/pom.xml b/pom.xml
@@ -40,8 +40,8 @@
     	<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 		<maxmem>512M</maxmem>
 		<mmtf.version>1.0.11</mmtf.version>
-		<slf4j.version>1.7.36</slf4j.version>
-		<log4j.version>2.22.0</log4j.version>
+		<slf4j.version>2.0.12</slf4j.version>
+		<log4j.version>2.23.1</log4j.version>
 		<junit-jupiter.version>5.10.1</junit-jupiter.version>
 		<ciftools.artifact>ciftools-java</ciftools.artifact>
 		<ciftools.version>5.0.1</ciftools.version>
@@ -436,7 +436,7 @@
 			<!-- binding for log4j 2 -->
 			<dependency>
 				<groupId>org.apache.logging.log4j</groupId>
-				<artifactId>log4j-slf4j-impl</artifactId>
+				<artifactId>log4j-slf4j2-impl</artifactId>
 				<version>${log4j.version}</version>
 				<!-- runtime scope includes the test scope as well -->
 				<scope>runtime</scope>
