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More extensive testing of type of error thrown in multi-threaded walker test 

-- Unfortunately the result of the multi-threaded test is non-deterministic so run the test 10x times to see if the right expection is always thrown
-- Now prints the stack trace and exception message of the caught exception of the wrong type, if this occurs
This commit is contained in:
Mark DePristo 2012-04-12 14:42:40 -04:00
parent 0dd571928d
commit e85e9a8cf5
2 changed files with 17 additions and 14 deletions
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15
public/java/test/org/broadinstitute/sting/WalkerTest.java
View File

@ -26,18 +26,17 @@
package org.broadinstitute.sting;
import org.apache.commons.lang.StringUtils;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.Tribble;
import org.broad.tribble.index.Index;
import org.broad.tribble.index.IndexFactory;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.gatk.CommandLineExecutable;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.testng.Assert;
import org.testng.annotations.BeforeMethod;
@ -315,9 +314,9 @@ public class WalkerTest extends BaseTest {
// it's the type we expected
System.out.println(String.format(" => %s PASSED", name));
} else {
e.printStackTrace();
Assert.fail(String.format("Test %s expected exception %s but got %s instead",
name, expectedException, e.getClass()));
e.printStackTrace(System.out); // must print to stdout to see the message
Assert.fail(String.format("Test %s expected exception %s but instead got %s with error message %s",
name, expectedException, e.getClass(), e.getMessage()));
}
} else {
// we didn't expect an exception but we got one :-(

16
public/java/test/org/broadinstitute/sting/gatk/EngineFeaturesIntegrationTest.java
View File

@ -86,13 +86,15 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
// --------------------------------------------------------------------------------
private class EngineErrorHandlingTestProvider extends TestDataProvider {
Class expectedException;
boolean multiThreaded;
final Class expectedException;
final boolean multiThreaded;
final int iterationsToTest;
public EngineErrorHandlingTestProvider(Class exceptedException, final boolean multiThreaded) {
super(EngineErrorHandlingTestProvider.class);
this.expectedException = exceptedException;
this.multiThreaded = multiThreaded;
this.iterationsToTest = multiThreaded ? 10 : 1;
setName(String.format("Engine error handling: expected %s, is-multithreaded %b", exceptedException, multiThreaded));
}
}
@ -113,9 +115,11 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
//
@Test(dataProvider = "EngineErrorHandlingTestProvider")
public void testEngineErrorHandlingTestProvider(EngineErrorHandlingTestProvider cfg) {
final String root = "-T ErrorThrowing -R " + b37KGReference;
final String args = root + (cfg.multiThreaded ? " -nt 2" : "") + " -E " + cfg.expectedException.getSimpleName();
WalkerTestSpec spec = new WalkerTestSpec(args, 0, cfg.expectedException);
executeTest(cfg.toString(), spec);
for ( int i = 0; i < cfg.iterationsToTest; i++ ) {
final String root = "-T ErrorThrowing -R " + b37KGReference;
final String args = root + (cfg.multiThreaded ? " -nt 2" : "") + " -E " + cfg.expectedException.getSimpleName();
WalkerTestSpec spec = new WalkerTestSpec(args, 0, cfg.expectedException);
executeTest(cfg.toString(), spec);
}
}
}