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Commit dcfc6456 authored by Clement Frainay's avatar Clement Frainay
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write log in output dir

provide a filewritter to the logger. Logs are duplicated
parent 16a652a5
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......@@ -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();
......
<?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>
......
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