write log in output dir

provide a filewritter to the logger. Logs are duplicated

src/main/java/groupId/IsoMet/ParseSbml.java

@@ -10,8 +10,15 @@ import groupId.IsoMet.utils.FilterBuilder;
 import groupId.IsoMet.utils.Flag;
 import groupId.IsoMet.utils.ReactionFilter;
 import groupId.IsoMet.utils.TransitionComputor;
+import org.apache.logging.log4j.Level;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.core.Appender;
+import org.apache.logging.log4j.core.Filter;
+import org.apache.logging.log4j.core.appender.WriterAppender;
+import org.apache.logging.log4j.core.config.Configuration;
+import org.apache.logging.log4j.core.config.LoggerConfig;
+import org.apache.logging.log4j.core.layout.PatternLayout;
 import org.openscience.cdk.exception.CDKException;
 import org.sbml.jsbml.*;
 
@@ -140,7 +147,28 @@ public class ParseSbml {
 
 
 
-	public static void main(String[] args) {
+	private static void addAppender(final Writer writer, final String writerName, final String pattern) {
+		final org.apache.logging.log4j.core.LoggerContext context = (org.apache.logging.log4j.core.LoggerContext) LogManager.getContext(false);
+		final Configuration config = context.getConfiguration();
+		final PatternLayout layout = PatternLayout.newBuilder()
+				.withPattern(pattern)
+				.build();
+		final Appender appender = WriterAppender.createAppender(layout, null, writer, writerName, false, true);
+		appender.start();
+		config.addAppender(appender);
+		updateLoggers(appender, config);
+	}
+
+	private static void  updateLoggers(final Appender appender, final Configuration config) {
+		final Level level = null;
+		final Filter filter = null;
+		for (final LoggerConfig loggerConfig : config.getLoggers().values()) {
+			loggerConfig.addAppender(appender, level, filter);
+		}
+		config.getRootLogger().addAppender(appender, level, filter);
+	}
+
+	public static void main(String[] args) throws IOException {
 		//PARAMS
 		//----------------
 		// input parameters
@@ -153,14 +181,17 @@ public class ParseSbml {
 		String outputDir = args[2];
 		boolean atomCountOnly = true;
 		//----------------
+
+
+		//set logger
+		addAppender(new BufferedWriter(new FileWriter(new File(outputDir, "gsam.log"))),"ParseSbml","%d{yyy-MM-dd HH:mm} %logger{1}, %-5level - %msg%n");
+
 		logger.info("[INPUT] SBML: "+sbmlPath);
 		logger.info("[INPUT] SMILES: "+smilesPath);
 		logger.info("[PARAM] Atom tracked: "+atomTracked);
 		logger.info("[PARAM] Max total number of atoms in reaction: "+maxAtoms);
 		logger.info("[PARAM] "+sbmlPath);
 
-
-
 		ParseSbml parser = new ParseSbml();
 
 		Instant start = Instant.now();

src/main/resources/log4j2.xml

 <?xml version="1.0" encoding="UTF-8"?>
-<Configuration status="ALL">
+<Configuration status="WARN" packages="groupId.IsoMet">
     <Appenders>
         <Console name="Console" target="SYSTEM_OUT">
             <PatternLayout pattern="%d{HH:mm} %logger{1} : %highlight{%-5level} - %msg%n" />
@@ -12,6 +12,9 @@
         <Logger name="groupId.IsoMet" level="debug" additivity="false">
             <AppenderRef ref="GSAMLOG"/>
         </Logger>
+       <!-- <Logger name="org.sbml.jsbml" level="error" additivity="false">
+            <AppenderRef ref="GSAMLOG"/>
+        </Logger> -->
         <Root level="warn">
             <AppenderRef ref="Console"/>
         </Root>