Update Log4J Version

Previous version was incompatible with ahead of time compilation, however, this version of Log4J allows for native compilation.
virtualcell · Feb 18, 2025 · 8b066ab · 8b066ab
1 parent 7ba479d
commit 8b066ab
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Showing 4 changed files with 81 additions and 31 deletions.
diff --git a/pom.xml b/pom.xml
@@ -152,20 +152,20 @@
 		<jung-graph-impl.version>2.1.1</jung-graph-impl.version>
 		<jung-samples.version>2.1.1</jung-samples.version>
 		<junit-jupiter.version>5.10.1</junit-jupiter.version>
-		<log4j-slf4j2-impl.version>2.22.1</log4j-slf4j2-impl.version>
-		<log4j-1.2-api.version>2.22.1</log4j-1.2-api.version>
-		<log4j-api.version>2.22.1</log4j-api.version>
-		<log4j-core.version>2.22.1</log4j-core.version>
-		<log4j-jul.version>2.22.1</log4j-jul.version>
+		<log4j-slf4j2-impl.version>2.24.0</log4j-slf4j2-impl.version>
+		<log4j-1.2-api.version>2.24.0</log4j-1.2-api.version>
+		<log4j-api.version>2.24.0</log4j-api.version>
+		<log4j-core.version>2.24.0</log4j-core.version>
+		<log4j-jul.version>2.24.0</log4j-jul.version>
 		<log4j2-jboss-logmanager.version>1.1.2.Final</log4j2-jboss-logmanager.version>
-		<log4j-layout-template-json.version>2.22.1</log4j-layout-template-json.version>
+		<log4j-layout-template-json.version>2.24.0</log4j-layout-template-json.version>
 		<lz4.version>1.8.0</lz4.version>
 		<mongodb-driver-sync.version>5.0.0</mongodb-driver-sync.version>
 		<n5.version>3.0.0</n5.version>
 		<netcdf.version>4.3.22</netcdf.version>
 		<nitrite.version>2.1.1</nitrite.version>
 		<ojdbc-bom.version>23.3.0.23.09</ojdbc-bom.version>
-		<ome-common.version>6.0.22</ome-common.version>
+		<ome-common.version>6.0.24</ome-common.version>
 		<opencsv.version>5.7.1</opencsv.version>
 		<picocli.version>4.6.3</picocli.version>
 		<postgresql.version>42.6.0</postgresql.version>
@@ -175,7 +175,7 @@
 		<sesame-rio-api.version>2.9.0</sesame-rio-api.version>
 		<sesame-rio-rdfxml.version>2.9.0</sesame-rio-rdfxml.version>
 		<sesame-rio-n3.version>2.9.0</sesame-rio-n3.version>
-		<slf4j-api.version>2.0.9</slf4j-api.version>
+		<slf4j-api.version>2.0.16</slf4j-api.version>
 		<sshj.version>0.35.0</sshj.version>
 		<thrift.version>0.18.0</thrift.version>
 		<xercesImpl.version>2.8.1</xercesImpl.version>

diff --git a/vcell-core/pom.xml b/vcell-core/pom.xml
@@ -117,6 +117,12 @@
 			<groupId>com.google.guava</groupId>
 			<artifactId>guava</artifactId>
 			<version>${guava.version}</version>
+			<exclusions>
+				<exclusion>
+					<groupId>com.google.errorprone</groupId>
+					<artifactId>error_prone_annotations</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>javax.media.jai</groupId>
@@ -299,6 +305,10 @@
 					<groupId>com.google.guava</groupId>
 					<artifactId>guava</artifactId>
 				</exclusion>
+				<exclusion>
+					<groupId>org.slf4j</groupId>
+					<artifactId>slf4j-api</artifactId>
+				</exclusion>
 			</exclusions>
 		</dependency>
 		<!-- https://mvnrepository.com/artifact/com.github.ome.bioformats/formats-bsd -->

diff --git a/vcell-nativelib/pom.xml b/vcell-nativelib/pom.xml
@@ -19,7 +19,7 @@
         <maven.compiler.source>${java.specification.version}</maven.compiler.source>
         <maven.compiler.target>${java.specification.version}</maven.compiler.target>
         <imageName>sbml_to_fvsolver</imageName>
-        <mainClass>org.vcell.pyvcell.SBMLSpatialTest</mainClass>
+        <mainClass>org.vcell.Main</mainClass>
     </properties>
 
     <dependencies>
@@ -28,34 +28,68 @@
             <artifactId>vcell-core</artifactId>
             <version>0.0.1-SNAPSHOT</version>
             <scope>compile</scope>
-<!--            <exclusions>-->
-<!--                <exclusion>-->
-<!--                    <groupId>org.slf4j</groupId>-->
-<!--                    <artifactId>slf4j-api</artifactId>-->
-<!--                </exclusion>-->
-<!--                <exclusion>-->
-<!--                    <groupId>org.apache.logging.log4j</groupId>-->
-<!--                    <artifactId>log4j-1.2-api</artifactId>-->
-<!--                </exclusion>-->
-<!--                <exclusion>-->
-<!--                    <groupId>org.apache.logging.log4j</groupId>-->
-<!--                    <artifactId>log4j-api</artifactId>-->
-<!--                </exclusion>-->
-<!--                <exclusion>-->
-<!--                    <groupId>org.apache.logging.log4j</groupId>-->
-<!--                    <artifactId>log4j-core</artifactId>-->
-<!--                </exclusion>-->
-<!--                <exclusion>-->
-<!--                    <groupId>com.lowagie</groupId>-->
-<!--                    <artifactId>itext</artifactId>-->
-<!--                </exclusion>-->
-<!--            </exclusions>-->
+            <exclusions>
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-api</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.apache.logging.log4j</groupId>
+                    <artifactId>log4j-core</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.apache.logging.log4j</groupId>
+                    <artifactId>log4j-api</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.apache.logging.log4j</groupId>
+                    <artifactId>log4j-1.2-api</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>com.google.errorprone</groupId>
+                    <artifactId>error_prone_annotations</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+        <dependency>
+            <groupId>org.sbml.jsbml</groupId>
+            <artifactId>jsbml-core</artifactId>
+            <version>${jsbml.version}</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-api</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.apache.logging.log4j</groupId>
+                    <artifactId>log4j-core</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.apache.logging.log4j</groupId>
+                    <artifactId>log4j-1.2-api</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>com.thoughtworks.xstream</groupId>
+                    <artifactId>xstream</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+        <dependency>
+            <groupId>org.sbml.jsbml.ext</groupId>
+            <artifactId>jsbml-spatial</artifactId>
+            <version>${jsbml.version}</version>
         </dependency>
         <dependency>
             <groupId>org.junit.jupiter</groupId>
             <artifactId>junit-jupiter</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-api</artifactId>
+            <version>2.24.0</version>
+            <scope>compile</scope>
+        </dependency>
     </dependencies>
 
     <build>

diff --git a/vcell-server/pom.xml b/vcell-server/pom.xml
@@ -128,6 +128,12 @@
 			<groupId>org.apache.activemq</groupId>
 			<artifactId>activemq-client</artifactId>
 			<version>${activemq-client.version}</version>
+			<exclusions>
+				<exclusion>
+					<groupId>org.slf4j</groupId>
+					<artifactId>slf4j-api</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.activemq</groupId>