/*
* Copyright (c) 2012 The Broad Institute
*
* 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.engine;
import org.broadinstitute.gatk.engine.walkers.WalkerTest;
import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.Output;
import org.broadinstitute.gatk.engine.contexts.AlignmentContext;
import org.broadinstitute.gatk.engine.contexts.ReferenceContext;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.engine.walkers.LocusWalker;
import org.broadinstitute.gatk.utils.SimpleTimer;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.concurrent.TimeUnit;
/**
*
*/
public class MaxRuntimeIntegrationTest extends WalkerTest {
public static class SleepingWalker extends LocusWalker<Integer, Integer> {
@Output PrintStream out;
@Argument(fullName="sleepTime",shortName="sleepTime",doc="x", required=false)
public int sleepTime = 100;
@Override
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
try {Thread.sleep(sleepTime);} catch (InterruptedException e) {};
return 1;
}
@Override public Integer reduceInit() { return 0; }
@Override public Integer reduce(Integer value, Integer sum) { return sum + value; }
@Override
public void onTraversalDone(Integer result) {
out.println(result);
}
}
private static final long STARTUP_TIME = TimeUnit.NANOSECONDS.convert(60, TimeUnit.SECONDS);
private class MaxRuntimeTestProvider extends TestDataProvider {
final long maxRuntime;
final TimeUnit unit;
public MaxRuntimeTestProvider(final long maxRuntime, final TimeUnit unit) {
super(MaxRuntimeTestProvider.class);
this.maxRuntime = maxRuntime;
this.unit = unit;
setName(String.format("Max runtime test : %d of %s", maxRuntime, unit));
}
public long expectedMaxRuntimeNano() {
return TimeUnit.NANOSECONDS.convert(maxRuntime, unit) + STARTUP_TIME;
}
}
@DataProvider(name = "MaxRuntimeProvider")
public Object[][] makeMaxRuntimeProvider() {
for ( final TimeUnit requestedUnits : Arrays.asList(TimeUnit.NANOSECONDS, TimeUnit.MILLISECONDS, TimeUnit.SECONDS, TimeUnit.MINUTES) )
new MaxRuntimeTestProvider(requestedUnits.convert(30, TimeUnit.SECONDS), requestedUnits);
return MaxRuntimeTestProvider.getTests(MaxRuntimeTestProvider.class);
}
//
// Loop over errors to throw, make sure they are the errors we get back from the engine, regardless of NT type
//
@Test(enabled = true, dataProvider = "MaxRuntimeProvider", timeOut = 120 * 1000)
public void testMaxRuntime(final MaxRuntimeTestProvider cfg) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T PrintReads -R " + hg18Reference
+ " -I " + validationDataLocation + "NA12878.WEx.downsampled20x.bam -o /dev/null"
+ " -maxRuntime " + cfg.maxRuntime + " -maxRuntimeUnits " + cfg.unit, 0,
Collections.<String>emptyList());
final SimpleTimer timer = new SimpleTimer().start();
executeTest("Max runtime " + cfg, spec);
final long actualRuntimeNano = timer.getElapsedTimeNano();
Assert.assertTrue(actualRuntimeNano < cfg.expectedMaxRuntimeNano(),
"Actual runtime " + TimeUnit.SECONDS.convert(actualRuntimeNano, TimeUnit.NANOSECONDS)
+ " exceeded max. tolerated runtime " + TimeUnit.SECONDS.convert(cfg.expectedMaxRuntimeNano(), TimeUnit.NANOSECONDS)
+ " given requested runtime " + cfg.maxRuntime + " " + cfg.unit);
}
@DataProvider(name = "SubshardProvider")
public Object[][] makeSubshardProvider() {
List<Object[]> tests = new ArrayList<Object[]>();
// this functionality can be adapted to provide input data for whatever you might want in your data
tests.add(new Object[]{10});
tests.add(new Object[]{100});
tests.add(new Object[]{500});
tests.add(new Object[]{1000});
tests.add(new Object[]{2000});
return tests.toArray(new Object[][]{});
}
@Test(enabled = true, dataProvider = "SubshardProvider", timeOut = 120 * 1000)
public void testSubshardTimeout(final int sleepTime) throws Exception {
final int maxRuntime = 5000;
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T SleepingWalker -R " + b37KGReference
+ " -I " + privateTestDir + "NA12878.100kb.BQSRv2.example.bam -o %s"
+ " -maxRuntime " + maxRuntime + " -maxRuntimeUnits MILLISECONDS -sleepTime " + sleepTime, 1,
Collections.singletonList(""));
final File result = executeTest("Subshard max runtime ", spec).getFirst().get(0);
final int cycle = Integer.valueOf(new BufferedReader(new FileReader(result)).readLine());
final int maxCycles = (int)Math.ceil((maxRuntime * 5) / sleepTime);
logger.warn(String.format("Max cycles %d saw %d in file %s with sleepTime %d and maxRuntime %d", maxCycles, cycle, result, sleepTime, maxRuntime));
Assert.assertTrue(cycle < maxCycles, "Too many cycles seen -- saw " + cycle + " in file " + result + " but max should have been " + maxCycles);
}
}