247 lines
8.0 KiB
Java
247 lines
8.0 KiB
Java
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package org.broadinstitute.sting.utils.cmdLine;
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import org.apache.log4j.*;
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import java.io.IOException;
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import java.text.DateFormat;
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import java.text.SimpleDateFormat;
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/**
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* User: aaron
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* Date: Mar 19, 2009
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* Time: 3:54:56 PM
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* <p/>
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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* <p/>
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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* <p/>
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* <p/>
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* This class is our implementation of the command line parser, similar to Pickard's. We instead
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* support GNU style command line arguements, and use this class to setup the global parser.
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*/
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public abstract class CommandLineProgram {
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/**
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* Our Argument parser, which handles parsing the command line in GNU format
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*/
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protected ArgumentParser m_parser;
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/**
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* our log, which we want to capture anything from org.broadinstitute.sting
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*/
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private static Logger logger = Logger.getRootLogger();// .getLogger(CommandLineProgram.class);
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/**
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* the default log level
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*/
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public String logging_level = "ERROR";
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/**
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* where to send the output of our logger
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*/
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public String toFile = null;
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/**
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* do we want to silence the command line output
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*/
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public Boolean quietMode = false;
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/**
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* do we want to generate debugging information with the logs
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*/
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public Boolean debugMode = false;
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/**
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* our logging output patterns
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*/
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private static String patternString = "%p %m %n";
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private static String debugPatternString = "%n[level] %p%n[date]\t\t %d{dd MMM yyyy HH:mm:ss,SSS} %n[class]\t\t %C %n[location]\t %l %n[line number]\t %L %n[message]\t %m %n";
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/**
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* the contract for the inheriting class is that they have a setupArgs()
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* function which sets up the args to the specific program.
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*/
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protected abstract void setupArgs();
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/**
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* this is the function that the inheriting class can expect to have called
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* when all the argument processing is done
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*
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* @return the return code to exit the program with
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*/
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protected abstract int execute();
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/**
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* this is used to indicate if they've asked for help
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*/
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public Boolean help = false;
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/**
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* This function is called to start processing the command line, and kick
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* off the execute message of the program.
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*
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* @param clp the command line program to execute
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* @param args the command line arguments passed in
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*/
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public static void start(CommandLineProgram clp, String[] args) {
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try {
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// setup a basic log configuration
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BasicConfigurator.configure();
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// setup our log layout
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PatternLayout layout = new PatternLayout();
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// setup the parser
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clp.m_parser = new ArgumentParser(clp.getClass().getName(), clp);
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// setup the default help and logging args controlled by the base class
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clp.setupDefaultArgs();
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// setup the args
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clp.setupArgs();
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// process the args
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clp.m_parser.processArgs(args);
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// if we're in debug mode, set the mode up
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if (clp.debugMode) {
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//logger.info("Setting debug");
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layout.setConversionPattern(debugPatternString);
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} else {
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//logger.info("not Setting debug");
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layout.setConversionPattern(patternString);
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}
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// if they set the mode to quiet
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if (clp.quietMode) {
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// the only appender we should have is stdout, the following meathod is
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// deprecated, but the standard remove all appenders doesn't seem to work
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// TODO: find the right function
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//Category root = Category.getRoot();
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//root.removeAllAppenders();
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//logger.removeAllAppenders();
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}
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// they asked for help, give it to them
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if (clp.help) {
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clp.m_parser.printHelp();
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System.exit(1);
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}
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// if they specify a log location, output our data there
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if (clp.toFile != null) {
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FileAppender appender = null;
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try {
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appender = new FileAppender(layout, clp.toFile, false);
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logger.addAppender(appender);
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} catch (IOException e) {
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throw new RuntimeException("Unable to re-route log output to " + clp.toFile + " make sure the destination exists");
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}
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}
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// regardless of what happens next, generate the header information
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generateHeaderInformation(clp, args);
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// set the default logger level
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clp.setupLoggerLevel();
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// call the execute
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int result = clp.execute();
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// return the result
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System.exit(result);
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}
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catch (Exception e) {
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// we catch all exceptions here. if it makes it to this level, we're in trouble. Let's bail!
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// TODO: what if the logger is the exception? hmm...
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logger.fatal("Exception caught by base Command Line Program, with message: " + e.getMessage());
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logger.fatal("with cause: " + e.getCause());
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e.printStackTrace();
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throw new RuntimeException(e.getMessage());
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}
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}
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/**
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* generateHeaderInformation
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* <p/>
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*
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* Generate a standard header for the logger
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* @param clp the command line program to execute
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* @param args the command line arguments passed in
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*
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**/
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protected static void generateHeaderInformation(CommandLineProgram clp, String[] args) {
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DateFormat dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss");
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java.util.Date date = new java.util.Date();
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logger.info("-------------------------------------------------------");
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logger.info("Program Name: " + clp.getClass().getName());
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String output = "";
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for (String str : args) {
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output = output + str + " ";
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}
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logger.info("Program Args: " + output);
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logger.info("Time/Date: " + dateFormat.format(date));
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logger.info("-------------------------------------------------------");
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}
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/**
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* this function checks the logger level passed in on the command line, taking the lowest
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* level that was provided.
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*/
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private void setupLoggerLevel() {
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Level par = Level.ERROR;
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if (logging_level.equals("DEBUG")) {
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par = Level.DEBUG;
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}
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if (logging_level.equals("ERROR")) {
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par = Level.ERROR;
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}
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if (logging_level.equals("FATAL")) {
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par = Level.FATAL;
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}
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if (logging_level.equals("INFO")) {
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par = Level.INFO;
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}
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if (logging_level.equals("WARN")) {
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par = Level.WARN;
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}
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if (logging_level.equals("OFF")) {
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par = Level.OFF;
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}
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logger.setLevel(par);
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}
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/**
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* we have some default options that should always get checked for in the
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* arguments provided to the program
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*/
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private void setupDefaultArgs() {
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m_parser.addOptionalFlag("help", "h", "Generate this help message", "help");
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m_parser.addOptionalArg("logging_level", "l", "Set the logging level", "logging_level");
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m_parser.addOptionalArg("log_to_file", "log", "Set the logging location", "toFile");
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m_parser.addOptionalFlag("quiet_output_mode", "quiet", "Set the logging to quiet mode, no output to stdout", "quietMode");
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m_parser.addOptionalFlag("debug_mode", "debug", "Set the logging file string to include a lot of debugging information (SLOW!)", "debugMode");
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}
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}
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