Output a summary of WARN messages
This commit is contained in:
Ron Levine
parent
ea615f8918
commit
edc1b20132
|
|
@ -53,7 +53,6 @@ package org.broadinstitute.gatk.tools.walkers.annotator;
|
|||
|
||||
import htsjdk.tribble.readers.LineIterator;
|
||||
import htsjdk.tribble.readers.PositionalBufferedStream;
|
||||
import htsjdk.variant.variantcontext.Genotype;
|
||||
import htsjdk.variant.vcf.VCFHeader;
|
||||
import htsjdk.variant.vcf.VCFHeaderLine;
|
||||
import org.broadinstitute.gatk.engine.walkers.WalkerTest;
|
||||
|
|
|
|||
|
|
@ -40,6 +40,8 @@ import java.util.*;
|
|||
|
||||
public abstract class CommandLineProgram {
|
||||
|
||||
private static final int NUM_WARN_MESSAGES = 10;
|
||||
|
||||
/** The command-line program and the arguments it returned. */
|
||||
public ParsingEngine parser = null;
|
||||
|
||||
|
|
@ -169,15 +171,21 @@ public abstract class CommandLineProgram {
|
|||
|
||||
try {
|
||||
// setup our log layout
|
||||
PatternLayout layout = new PatternLayout();
|
||||
PatternLayout layout = new PatternLayout(patternString);
|
||||
|
||||
Logger logger = CommandLineUtils.getStingLogger();
|
||||
|
||||
// Appender for saving logging messages to a list
|
||||
final ListAppender listAppender = new ListAppender(layout, NUM_WARN_MESSAGES, Level.WARN);
|
||||
|
||||
// add appender for saving logging messages to a list
|
||||
logger.addAppender(listAppender);
|
||||
|
||||
// now set the layout of all the loggers to our layout
|
||||
CommandLineUtils.setLayout(logger, layout);
|
||||
|
||||
// Initialize the logger using the defaults.
|
||||
clp.setupLoggerLevel(layout);
|
||||
clp.setupLoggerLevel();
|
||||
|
||||
// setup the parser
|
||||
ParsingEngine parser = clp.parser = new ParsingEngine(clp);
|
||||
|
|
@ -200,7 +208,7 @@ public abstract class CommandLineProgram {
|
|||
parser.loadArgumentsIntoObject(clp);
|
||||
|
||||
// Initialize the logger using the loaded command line.
|
||||
clp.setupLoggerLevel(layout);
|
||||
clp.setupLoggerLevel();
|
||||
|
||||
Class[] argumentSources = clp.getArgumentSources();
|
||||
for (Class argumentSource : argumentSources)
|
||||
|
|
@ -226,15 +234,14 @@ public abstract class CommandLineProgram {
|
|||
parser.loadArgumentsIntoObject(clp);
|
||||
|
||||
// Initialize the logger using the loaded command line.
|
||||
clp.setupLoggerLevel(layout);
|
||||
clp.setupLoggerLevel();
|
||||
}
|
||||
|
||||
if ( ! dryRun ) {
|
||||
// if they specify a log location, output our data there
|
||||
if (clp.toFile != null) {
|
||||
FileAppender appender;
|
||||
try {
|
||||
appender = new FileAppender(layout, clp.toFile, false);
|
||||
final FileAppender appender = new FileAppender(layout, clp.toFile, false);
|
||||
logger.addAppender(appender);
|
||||
} catch (IOException e) {
|
||||
throw new RuntimeException("Unable to re-route log output to " + clp.toFile + " make sure the destination exists");
|
||||
|
|
@ -246,6 +253,12 @@ public abstract class CommandLineProgram {
|
|||
|
||||
// call the execute
|
||||
CommandLineProgram.result = clp.execute();
|
||||
|
||||
// write logging events
|
||||
printDoneAndLogMessages(listAppender);
|
||||
|
||||
// clear saved logging events
|
||||
listAppender.close();
|
||||
}
|
||||
}
|
||||
catch (ArgumentException e) {
|
||||
|
|
@ -266,13 +279,10 @@ public abstract class CommandLineProgram {
|
|||
}
|
||||
|
||||
/**
|
||||
* this function checks the logger level passed in on the command line, taking the lowest
|
||||
* level that was provided.
|
||||
* @param layout Pattern layout to format based on the logger level.
|
||||
* this function takes the logger level passed in on the command line and uses it to set the level of the logger
|
||||
* @throws ArgumentException if the logging level is not valid (DEBUG, INFO, WARN, ERROR, FATAL, OFF)
|
||||
*/
|
||||
private void setupLoggerLevel(PatternLayout layout) {
|
||||
layout.setConversionPattern(patternString);
|
||||
|
||||
private void setupLoggerLevel() {
|
||||
// set the default logger level
|
||||
Level par;
|
||||
if (logging_level.toUpperCase().equals("DEBUG")) {
|
||||
|
|
@ -347,6 +357,18 @@ public abstract class CommandLineProgram {
|
|||
return parser.isArgumentPresent("version");
|
||||
}
|
||||
|
||||
/**
|
||||
* Print done and log messages saved in a list.
|
||||
*
|
||||
* @param listAppender Appender for saving logging messages to a list
|
||||
*/
|
||||
private static void printDoneAndLogMessages(final ListAppender listAppender) {
|
||||
System.out.println("------------------------------------------------------------------------------------------");
|
||||
System.out.print("Done. ");
|
||||
listAppender.write();
|
||||
System.out.println("------------------------------------------------------------------------------------------");
|
||||
}
|
||||
|
||||
/**
|
||||
* Print help and exit.
|
||||
*/
|
||||
|
|
@ -376,7 +398,7 @@ public abstract class CommandLineProgram {
|
|||
* @param t the error
|
||||
*/
|
||||
public static void exitSystemWithError(String msg, final Throwable t) {
|
||||
errorPrintf("------------------------------------------------------------------------------------------%n");
|
||||
errorPrintf("--%n");
|
||||
errorPrintf("stack trace %n");
|
||||
t.printStackTrace();
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,146 @@
|
|||
/*
|
||||
* Copyright 2012-2016 Broad Institute, Inc.
|
||||
*
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
* copies of the Software, and to permit persons to whom the
|
||||
* Software is furnished to do so, subject to the following
|
||||
* conditions:
|
||||
*
|
||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
*
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
|
||||
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
|
||||
package org.broadinstitute.gatk.utils.commandline;
|
||||
|
||||
import org.apache.log4j.AppenderSkeleton;
|
||||
import org.apache.log4j.Layout;
|
||||
import org.apache.log4j.Level;
|
||||
import org.apache.log4j.spi.LoggingEvent;
|
||||
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
* Appender for saving logging loggingEvents to a list
|
||||
*/
|
||||
public class ListAppender extends AppenderSkeleton {
|
||||
/**
|
||||
* List of logging events
|
||||
*
|
||||
*/
|
||||
protected final List<LoggingEvent> loggingEvents = new ArrayList<>();
|
||||
|
||||
/**
|
||||
* number of logging events to keep
|
||||
*/
|
||||
protected int loggingEventsToKeep = 0;
|
||||
|
||||
/**
|
||||
* number of logging events to keep
|
||||
*/
|
||||
protected int numLoggingEvents = 0;
|
||||
|
||||
/**
|
||||
* Log warning level to keep
|
||||
*/
|
||||
protected Level logLevelToKeep = Level.WARN;
|
||||
|
||||
/**
|
||||
* Constructor
|
||||
*
|
||||
* @param layout output layout
|
||||
* @param loggingEventsToKeep number of warnings to keep
|
||||
* @param logLevelToKeep logging logLevelToKeep ( TRACE, DEBUG, INFO, WARN, ERROR, FATAL, OFF )
|
||||
*/
|
||||
public ListAppender(final Layout layout, final int loggingEventsToKeep, final Level logLevelToKeep) {
|
||||
this.layout = layout;
|
||||
this.loggingEventsToKeep = loggingEventsToKeep;
|
||||
this.logLevelToKeep = logLevelToKeep;
|
||||
}
|
||||
|
||||
/**
|
||||
* Constructor
|
||||
*
|
||||
* Hide from use
|
||||
*/
|
||||
private ListAppender() {}
|
||||
|
||||
/**
|
||||
* Close the appender
|
||||
*
|
||||
* Clear out the logging events
|
||||
*/
|
||||
@Override
|
||||
public synchronized void close() {
|
||||
loggingEvents.clear();
|
||||
numLoggingEvents = 0;
|
||||
}
|
||||
|
||||
/**
|
||||
* Is a message layout required?
|
||||
*
|
||||
* @return true
|
||||
*/
|
||||
@Override
|
||||
public boolean requiresLayout() {
|
||||
return true;
|
||||
}
|
||||
|
||||
/**
|
||||
* Append log event to the list of logging events
|
||||
*
|
||||
* @param loggingEvent The logging events
|
||||
*/
|
||||
@Override
|
||||
protected synchronized void append(final LoggingEvent loggingEvent) {
|
||||
if ( loggingEvent.getLevel().equals(logLevelToKeep) ) {
|
||||
numLoggingEvents++;
|
||||
if ( numLoggingEvents <= loggingEventsToKeep )
|
||||
loggingEvents.add(loggingEvent);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* The string representation for the class data
|
||||
*
|
||||
* @return string containing the logging events
|
||||
* @throws ReviewedGATKException if layout is null
|
||||
*/
|
||||
public synchronized String toString() {
|
||||
final String msgType = logLevelToKeep.toString() + " messages";
|
||||
if ( loggingEvents.isEmpty() ) {
|
||||
return "There were no " + new String(msgType).toLowerCase() + ".\n";
|
||||
} else {
|
||||
String out = "There were " + Integer.toString(numLoggingEvents) + " " + msgType;
|
||||
if ( layout == null )
|
||||
throw new ReviewedGATKException("layout cannot be null");
|
||||
out += ", the first " + loggingEvents.size() + " are repeated below.\n";
|
||||
for ( LoggingEvent event : loggingEvents ) {
|
||||
out += layout.format(event);
|
||||
}
|
||||
return out;
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Write class data to standard out
|
||||
*/
|
||||
public void write() {
|
||||
System.out.print(this);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,95 @@
|
|||
/*
|
||||
* Copyright 2012-2016 Broad Institute, Inc.
|
||||
*
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
* copies of the Software, and to permit persons to whom the
|
||||
* Software is furnished to do so, subject to the following
|
||||
* conditions:
|
||||
*
|
||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
*
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
|
||||
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
|
||||
package org.broadinstitute.gatk.utils.commandline;
|
||||
|
||||
import org.apache.log4j.Level;
|
||||
import org.apache.log4j.Logger;
|
||||
import org.apache.log4j.PatternLayout;
|
||||
import org.apache.commons.lang.StringUtils;
|
||||
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
|
||||
import org.testng.Assert;
|
||||
import org.testng.annotations.Test;
|
||||
|
||||
public class ListAppenderUnitTest {
|
||||
|
||||
private final static int EVENTS_TO_KEEP = 10;
|
||||
private final static int EVENTS = 200;
|
||||
private final static String MSG_TO_LOG = ": All work and no play makes Jack a dull boy.";
|
||||
private final static String MSG_TOO_LONG = ": Don't write this one.";
|
||||
private final static Logger LOGGER = Logger.getLogger(ListAppenderUnitTest.class);
|
||||
|
||||
@Test
|
||||
public void testListAppender() {
|
||||
|
||||
LOGGER.removeAllAppenders();
|
||||
final ListAppender listAppender = new ListAppender(new PatternLayout(PatternLayout.DEFAULT_CONVERSION_PATTERN), EVENTS_TO_KEEP, Level.WARN);
|
||||
LOGGER.addAppender(listAppender);
|
||||
|
||||
for ( int i = 0; i < EVENTS; i++ ) {
|
||||
LOGGER.warn(i + MSG_TO_LOG);
|
||||
LOGGER.info(i + MSG_TOO_LONG);
|
||||
}
|
||||
|
||||
final String listAppenderString = listAppender.toString();
|
||||
listAppender.write();
|
||||
|
||||
Assert.assertEquals(StringUtils.countMatches(listAppenderString, MSG_TO_LOG), EVENTS_TO_KEEP);
|
||||
Assert.assertFalse(listAppenderString.contains(MSG_TOO_LONG));
|
||||
Assert.assertTrue(listAppenderString.contains(Integer.toString(EVENTS_TO_KEEP)));
|
||||
Assert.assertTrue(listAppenderString.contains(listAppender.logLevelToKeep.toString()));
|
||||
Assert.assertEquals(listAppender.numLoggingEvents, EVENTS);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testListAppenderNoWarnMsgs() {
|
||||
|
||||
LOGGER.removeAllAppenders();
|
||||
final ListAppender listAppender = new ListAppender(new PatternLayout(PatternLayout.DEFAULT_CONVERSION_PATTERN), EVENTS_TO_KEEP, Level.WARN);
|
||||
LOGGER.addAppender(listAppender);
|
||||
|
||||
for ( int i = 0; i < EVENTS; i++ ) {
|
||||
LOGGER.info(i + MSG_TOO_LONG);
|
||||
}
|
||||
|
||||
final String listAppenderString = listAppender.toString();
|
||||
Assert.assertEquals(StringUtils.countMatches(listAppenderString, MSG_TO_LOG), 0);
|
||||
Assert.assertFalse(listAppenderString.contains(MSG_TOO_LONG));
|
||||
Assert.assertFalse(listAppenderString.contains(Integer.toString(EVENTS_TO_KEEP)));
|
||||
Assert.assertTrue(listAppenderString.contains(listAppender.logLevelToKeep.toString().toLowerCase()));
|
||||
Assert.assertEquals(listAppender.numLoggingEvents, 0);
|
||||
}
|
||||
|
||||
@Test(expectedExceptions = ReviewedGATKException.class)
|
||||
public void testListAppenderMissingLayout() {
|
||||
|
||||
LOGGER.removeAllAppenders();
|
||||
final ListAppender listAppender = new ListAppender(null, 1, Level.WARN);
|
||||
LOGGER.addAppender(listAppender);
|
||||
LOGGER.warn("Warning");
|
||||
|
||||
final String listAppenderString = listAppender.toString();
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue