public static synchronized void createLoggers(boolean reinit) {
if (m_initialized == true && reinit == false) {
return;
}
if (!m_initialized) {
Logger.getLogger("").removeHandler(Logger.getLogger("").getHandlers()[0]);
}
if (m_initialized) {
m_severeLogger.removeHandler(m_severeLogger.getHandlers()[0]);
m_nonSevereLogger.removeHandler(m_nonSevereLogger.getHandlers()[0]);
}
Handler severeHandler = new AMyConsoleHandler(System.err);
severeHandler.setFormatter(new SingleLineFormatter());
m_severeLogger.addHandler(severeHandler);
m_severeLogger.setLevel(getLoggingLevel());
Handler nonSevereHandler = new AMyConsoleHandler(System.out);
nonSevereHandler.setFormatter(new SingleLineFormatter());
m_nonSevereLogger.addHandler(nonSevereHandler);
m_nonSevereLogger.setLevel(getLoggingLevel());
m_initialized = true;
}
public static synchronized void setLoggingLevel(String loggingLevel) {
if (loggingLevel.toLowerCase().equals("severe")) {
m_loggingLevel = Level.SEVERE;
} else if (loggingLevel.toLowerCase().equals("warning")) {
m_loggingLevel = Level.WARNING;
} else if (loggingLevel.toLowerCase().equals("info")) {
m_loggingLevel = Level.INFO;
} else if (loggingLevel.toLowerCase().equals("config")) {
m_loggingLevel = Level.CONFIG;
} else if (loggingLevel.toLowerCase().equals("fine")) {
m_loggingLevel = Level.FINE;
} else if (loggingLevel.toLowerCase().equals("finer")) {
m_loggingLevel = Level.FINER;
} else if (loggingLevel.toLowerCase().equals("finest")) {
m_loggingLevel = Level.FINEST;
} else {
m_loggingLevel = Level.WARNING;
}
if (m_initialized) {
m_severeLogger.setLevel(m_loggingLevel);
m_nonSevereLogger.setLevel(m_loggingLevel);
}
}
public void preprocess(Run run) {
File logFile = new File(getRunDir(run), "genetik.log");
try {
SimpleFileHandler fh = new SimpleFileHandler(logFile);
fh.setFormatter(new CompactFormatter());
Logger logger = Logger.getLogger(GenetikConstants.LOGGER);
logger.setLevel(Level.INFO);
logger.setUseParentHandlers(false);
Handler handlers[] = logger.getHandlers();
logger.addHandler(fh);
for (Handler h : handlers) {
logger.removeHandler(h);
if (h instanceof SimpleFileHandler) h.close(); // close our old one
}
} catch (Exception exp) {
throw new IllegalArgumentException(
"Unable to create log file at " + logFile.getAbsolutePath());
}
super.preprocess(run);
}
public void setUp() throws Exception {
super.setUp();
log.setLevel(Logger.LEVEL_DEBUG);
if (dig == null) {
dig = MessageDigest.getInstance(hashAlgorithm);
}
mau = new MockArchivalUnit(new MockPlugin());
cus = new MockCachedUrlSet(mau, null);
cus.setHashItSource(Collections.EMPTY_LIST);
TimeBase.setSimulated();
}
// Private method to reset an invidual target logger.
private void resetLogger(String name) {
Logger logger = getLogger(name);
if (logger == null) {
return;
}
// Close all the Logger's handlers.
Handler[] targets = logger.getHandlers();
for (int i = 0; i < targets.length; i++) {
Handler h = targets[i];
logger.removeHandler(h);
try {
h.close();
} catch (Exception ex) {
// Problems closing a handler? Keep going...
}
}
if (name != null && name.equals("")) {
// This is the root logger.
logger.setLevel(defaultLevel);
} else {
logger.setLevel(null);
}
}
public static Logger initLogger() {
Logger initlogger = Logger.getLogger(settings.getMainClass());
initlogger.setLevel(settings.getLogLevel());
boolean addconsole = false;
if (settings.getLogToFile()) {
try {
Handler handler = new FileHandler(settings.getLogFile(), true);
handler.setFormatter(new SimpleFormatter());
initlogger.addHandler(handler);
} catch (Exception e) {
Logger().warning("Could not set logfile " + settings.getLogFile() + ": " + e.getMessage());
addconsole = true;
}
}
addconsole = settings.getLogToConsole() || addconsole;
if (addconsole) {
initlogger.addHandler(new ConsoleHandler());
}
// restore original log state
logger.setLevel(templevel);
templevel = null;
return initlogger;
}
// Private method to set a level on a logger.
// If necessary, we raise privilege before doing the call.
private static void doSetLevel(final Logger logger, final Level level) {
SecurityManager sm = System.getSecurityManager();
if (sm == null) {
// There is no security manager, so things are easy.
logger.setLevel(level);
return;
}
// There is a security manager. Raise privilege before
// calling setLevel.
AccessController.doPrivileged(new PrivilegedAction() {
public Object run() {
logger.setLevel(level);
return null;
}});
}
public UkkonenSuffixTree() {
logger =
Logger.getLogger(
"edu.psu.compbio.seqcode.gse.projects.chipseq.assembler.UkkonenSuffixTree");
isLogging = true;
minLogLevel = Level.SEVERE;
logger.setFilter(new LoggingFilter());
logger.addHandler(new LoggingHandler(System.err, false));
logger.setUseParentHandlers(false);
logger.setLevel(Level.SEVERE);
logger.log(Level.FINE, "Logger setup complete.");
strings = new Vector<TreeString>();
terminal = '$';
root = new TreeNode(null);
totalStringEdges = new Vector<TreeEdge>();
extState = null;
}
// Private method to be called when the configuration has
// changed to apply any level settings to any pre-existing loggers.
synchronized private void setLevelsOnExistingLoggers() {
Enumeration enum = props.propertyNames();
while (enum.hasMoreElements()) {
String key = (String)enum.nextElement();
if (!key.endsWith(".level")) {
// Not a level definition.
continue;
}
int ix = key.length() - 6;
String name = key.substring(0, ix);
Level level = getLevelProperty(key, null);
if (level == null) {
System.err.println("Bad level value for property: " + key);
continue;
}
Logger l = getLogger(name);
if (l == null) {
continue;
}
l.setLevel(level);
}
}
private void initLogger() {
ConsoleHandler consoleHandler = null;
Logger rootLogger = LogManager.getLogManager().getLogger("");
Handler[] handlers = rootLogger.getHandlers();
for (Handler handler : handlers) {
if (handler instanceof ConsoleHandler) {
consoleHandler = (ConsoleHandler) handler;
rootLogger.removeHandler(handler);
}
}
logger = Logger.getLogger(contextId);
logger.setLevel(logLevel);
if (!logLevel.equals(Level.OFF)) {
LogFormatter formatter = new LogFormatter();
if (consoleLog) {
if (consoleHandler == null) {
consoleHandler = new ConsoleHandler();
}
consoleHandler.setFormatter(formatter);
consoleHandler.setLevel(logLevel);
logger.addHandler(consoleHandler);
}
String userHomePath = getProperty("user.home", ".");
File logDir = new File(userHomePath, '.' + contextId + "/log");
logDir.mkdirs();
String logFilePattern = new File(logDir, contextId + "-%g.log").getPath();
try {
FileHandler fileHandler = new FileHandler(logFilePattern);
fileHandler.setFormatter(formatter);
fileHandler.setLevel(logLevel);
logger.addHandler(fileHandler);
} catch (IOException e) {
System.err.println("Error: Failed to create log file: " + logFilePattern);
}
}
}
static {
// Use anonymous logger (System.err), until settings read, set initial level to WARNING
logger = Logger.getAnonymousLogger();
templevel = logger.getLevel();
logger.setLevel(Level.WARNING);
}
static {
_libraryLogger.setLevel(Level.INFO);
}