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Merge pull request #222 from broadinstitute/dr_convenient_diff_engine_md5_display_in_bamboo_GSA-915 

Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements
This commit is contained in:
Mark DePristo 2013-05-11 10:58:42 -07:00
parent 111e8cef0f 639030bd6d
commit cb49b8cc71
7 changed files with 270 additions and 102 deletions
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3
build.xml
View File

@ -1031,6 +1031,7 @@
<delete dir="${staging.dir}"/> <delete dir="${staging.dir}"/>
<delete dir="${dist.dir}"/> <delete dir="${dist.dir}"/>
<delete dir="${pipelinetest.dir}"/> <delete dir="${pipelinetest.dir}"/>
<delete dir="${integration.tests.dir}"/>
</target> </target>
<!-- Depend on this target if your target requires a clean working directory but you don't want to depend on clean directly --> <!-- Depend on this target if your target requires a clean working directory but you don't want to depend on clean directly -->
@ -1043,6 +1044,7 @@
<available file="${staging.dir}" /> <available file="${staging.dir}" />
<available file="${dist.dir}" /> <available file="${dist.dir}" />
<available file="${pipelinetest.dir}" /> <available file="${pipelinetest.dir}" />
<available file="${integration.tests.dir}" />
<available file="${javadoc.dir}" /> <available file="${javadoc.dir}" />
<available file="${scaladoc.dir}" /> <available file="${scaladoc.dir}" />
<available file="${gatkdocs.dir}" /> <available file="${gatkdocs.dir}" />
@ -1078,6 +1080,7 @@
<property name="scala.public.test.sources" value="${public.dir}/scala/test"/> <property name="scala.public.test.sources" value="${public.dir}/scala/test"/>
<property name="scala.private.test.sources" value="${private.dir}/scala/test"/> <property name="scala.private.test.sources" value="${private.dir}/scala/test"/>
<property name="scala.protected.test.sources" value="${protected.dir}/scala/test"/> <property name="scala.protected.test.sources" value="${protected.dir}/scala/test"/>
<property name="integration.tests.dir" value="integrationtests" />
<property name="pipelinetest.dir" value="pipelinetests" /> <property name="pipelinetest.dir" value="pipelinetests" />
<property name="report" value="${build.dir}/report"/> <property name="report" value="${build.dir}/report"/>
<property name="iwww.report.dir" value="${user.home}/private_html/report"/> <property name="iwww.report.dir" value="${user.home}/private_html/report"/>

58
public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
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@ -248,4 +248,62 @@ public class JVMUtils {
interfaces.add(interfaceClass.getSimpleName()); interfaces.add(interfaceClass.getSimpleName());
return Utils.join(", ", interfaces); return Utils.join(", ", interfaces);
} }
/**
* Returns the Class that invoked the specified "callee" class by examining the runtime stack.
* The calling class is defined as the first class below the callee class on the stack.
*
* For example, given callee == MyClass and the following runtime stack:
*
* JVMUtils.getCallingClass(MyClass) <-- top
* MyClass.foo()
* MyClass.bar()
* OtherClass.foo()
* OtherClass.bar()
* etc.
*
* this method would return OtherClass, since its methods invoked the methods in MyClass.
*
* Considers only the occurrence of the callee class on the stack that is closest to the top
* (even if there are multiple, non-contiguous occurrences).
*
* @param callee Class object for the class whose calling class we want to locate
* @return Class object for the class that invoked the callee class, or null if
* no calling class was found
* @throws IllegalArgumentException if the callee class is not found on the runtime stack
* @throws IllegalStateException if we get an error while trying to load the Class object for the calling
* class reported on the runtime stack
*/
public static Class getCallingClass( final Class callee ) {
final StackTraceElement[] stackTrace = new Throwable().getStackTrace();
final String calleeClassName = callee.getName();
// Start examining the stack at the second-from-the-top position, to remove
// this method call (ie., the call to getCallingClass() itself) from consideration.
int stackTraceIndex = 1;
// Find the first occurrence of the callee on the runtime stack. Need to use String comparison
// unfortunately, due to limitations of the StackTraceElement class.
while ( stackTraceIndex < stackTrace.length && ! stackTrace[stackTraceIndex].getClassName().equals(calleeClassName) ) {
stackTraceIndex++;
}
// Make sure we actually found the callee class on the stack
if ( stackTraceIndex == stackTrace.length ) {
throw new IllegalArgumentException(String.format("Specified callee %s is not present on the call stack", callee.getSimpleName()));
}
// Now find the caller class, which will be the class below the callee on the stack
while ( stackTraceIndex < stackTrace.length && stackTrace[stackTraceIndex].getClassName().equals(calleeClassName) ) {
stackTraceIndex++;
}
try {
return stackTraceIndex < stackTrace.length ? Class.forName(stackTrace[stackTraceIndex].getClassName()) : null;
}
catch ( ClassNotFoundException e ) {
throw new IllegalStateException(String.format("Could not find caller class %s from the runtime stack in the classpath",
stackTrace[stackTraceIndex].getClassName()));
}
}
} }

151
public/java/test/org/broadinstitute/sting/MD5DB.java
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@ -97,7 +97,12 @@ public class MD5DB {
if ( ! dir.exists() ) { if ( ! dir.exists() ) {
System.out.printf("##### Creating MD5 db %s%n", LOCAL_MD5_DB_DIR); System.out.printf("##### Creating MD5 db %s%n", LOCAL_MD5_DB_DIR);
if ( ! dir.mkdir() ) { if ( ! dir.mkdir() ) {
throw new ReviewedStingException("Infrastructure failure: failed to create md5 directory " + LOCAL_MD5_DB_DIR); // Need to check AGAIN whether the dir exists, because we might be doing multi-process parallelism
// within the same working directory, and another GATK instance may have come along and created the
// directory between the calls to exists() and mkdir() above.
if ( ! dir.exists() ) {
throw new ReviewedStingException("Infrastructure failure: failed to create md5 directory " + LOCAL_MD5_DB_DIR);
}
} }
} }
} }
@ -203,98 +208,106 @@ public class MD5DB {
} }
public static class MD5Match { public static class MD5Match {
final String actualMD5, expectedMD5; public final String actualMD5, expectedMD5;
final String failMessage; public final String failMessage;
boolean failed; public final String diffEngineOutput;
public final boolean failed;
public MD5Match(final String actualMD5, final String expectedMD5, final String failMessage, final boolean failed) { public MD5Match(final String actualMD5, final String expectedMD5, final String failMessage, final String diffEngineOutput, final boolean failed) {
this.actualMD5 = actualMD5; this.actualMD5 = actualMD5;
this.expectedMD5 = expectedMD5; this.expectedMD5 = expectedMD5;
this.failMessage = failMessage; this.failMessage = failMessage;
this.diffEngineOutput = diffEngineOutput;
this.failed = failed; this.failed = failed;
} }
} }
/** /**
* Tests a file MD5 against an expected value, returning the MD5. NOTE: This function WILL throw an exception if the MD5s are different. * Tests a file MD5 against an expected value, returning an MD5Match object containing a description of the
* @param name Name of the test. * match or mismatch. In case of a mismatch, outputs a description of the mismatch to various log files/streams.
*
* NOTE: This function WILL NOT throw an exception if the MD5s are different.
*
* @param testName Name of the test.
* @param testClassName Name of the class that contains the test.
* @param resultsFile File to MD5. * @param resultsFile File to MD5.
* @param expectedMD5 Expected MD5 value. * @param expectedMD5 Expected MD5 value.
* @param parameterize If true or if expectedMD5 is an empty string, will print out the calculated MD5 instead of error text. * @param parameterize If true or if expectedMD5 is an empty string, will print out the calculated MD5 instead of error text.
* @return The calculated MD5. * @return an MD5Match object containing a description of the match/mismatch. Will have its "failed" field set
* to true if there was a mismatch (unless we're using the "parameterize" argument)
*/ */
public MD5Match assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5, final boolean parameterize) { public MD5Match testFileMD5(final String testName, final String testClassName, final File resultsFile, final String expectedMD5, final boolean parameterize) {
final String actualMD5 = testFileMD5(name, resultsFile, expectedMD5, parameterize); final String actualMD5 = calculateFileMD5(resultsFile);
String failMessage = null; String diffEngineOutput = "";
String failMessage = "";
boolean failed = false; boolean failed = false;
// copy md5 to integrationtests
updateMD5Db(actualMD5, resultsFile);
if (parameterize || expectedMD5.equals("")) { if (parameterize || expectedMD5.equals("")) {
// Don't assert BaseTest.log(String.format("PARAMETERIZATION: file %s has md5 = %s", resultsFile, actualMD5));
} else if ( actualMD5.equals(expectedMD5) ) { } else if ( ! expectedMD5.equals(actualMD5) ) {
//BaseTest.log(String.format(" => %s PASSED (expected=%s)", name, expectedMD5));
} else {
failed = true; failed = true;
failMessage = String.format("%s has mismatching MD5s: expected=%s observed=%s", name, expectedMD5, actualMD5); failMessage = String.format("%s:%s has mismatching MD5s: expected=%s observed=%s", testClassName, testName, expectedMD5, actualMD5);
diffEngineOutput = logMD5MismatchAndGetDiffEngineOutput(testName, testClassName, expectedMD5, actualMD5);
} }
return new MD5Match(actualMD5, expectedMD5, failMessage, failed); return new MD5Match(actualMD5, expectedMD5, failMessage, diffEngineOutput, failed);
} }
/** /**
* Tests a file MD5 against an expected value, returning the MD5. NOTE: This function WILL NOT throw an exception if the MD5s are different. * Calculates the MD5 for the specified file and returns it as a String
* @param name Name of the test. *
* @param resultsFile File to MD5. * @param file file whose MD5 to calculate
* @param expectedMD5 Expected MD5 value. * @return file's MD5 in String form
* @param parameterize If true or if expectedMD5 is an empty string, will print out the calculated MD5 instead of error text. * @throws RuntimeException if the file could not be read
* @return The calculated MD5.
*/ */
public String testFileMD5(final String name, final File resultsFile, final String expectedMD5, final boolean parameterize) { public String calculateFileMD5( final File file ) {
try { try {
final String filemd5sum = Utils.calcMD5(getBytesFromFile(resultsFile)); return Utils.calcMD5(getBytesFromFile(file));
}
// catch ( Exception e ) {
// copy md5 to integrationtests throw new RuntimeException("Failed to read bytes from file: " + file + " for MD5 calculation", e);
//
updateMD5Db(filemd5sum, resultsFile);
if (parameterize || expectedMD5.equals("")) {
BaseTest.log(String.format("PARAMETERIZATION: file %s has md5 = %s", resultsFile, filemd5sum));
} else {
//System.out.println(String.format("Checking MD5 for %s [calculated=%s, expected=%s]", resultsFile, filemd5sum, expectedMD5));
//System.out.flush();
if ( ! expectedMD5.equals(filemd5sum) ) {
// we are going to fail for real in assertEquals (so we are counted by the testing framework).
// prepare ourselves for the comparison
System.out.printf("##### Test %s is going to fail #####%n", name);
String pathToExpectedMD5File = getMD5FilePath(expectedMD5, "[No DB file found]");
String pathToFileMD5File = getMD5FilePath(filemd5sum, "[No DB file found]");
BaseTest.log(String.format("expected %s", expectedMD5));
BaseTest.log(String.format("calculated %s", filemd5sum));
BaseTest.log(String.format("diff %s %s", pathToExpectedMD5File, pathToFileMD5File));
md5MismatchStream.printf("%s\t%s\t%s%n", expectedMD5, filemd5sum, name);
md5MismatchStream.flush();
// inline differences
final ByteArrayOutputStream baos = new ByteArrayOutputStream();
final PrintStream ps = new PrintStream(baos);
DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(ps, 20, 10, 0, MAX_RAW_DIFFS_TO_SUMMARIZE, false);
boolean success = DiffEngine.simpleDiffFiles(new File(pathToExpectedMD5File), new File(pathToFileMD5File), MAX_RECORDS_TO_READ, params);
if ( success ) {
final String content = baos.toString();
BaseTest.log(content);
System.out.printf("Note that the above list is not comprehensive. At most 20 lines of output, and 10 specific differences will be listed. Please use -T DiffObjects -R public/testdata/exampleFASTA.fasta -m %s -t %s to explore the differences more freely%n",
pathToExpectedMD5File, pathToFileMD5File);
}
ps.close();
}
}
return filemd5sum;
} catch (Exception e) {
throw new RuntimeException("Failed to read bytes from calls file: " + resultsFile, e);
} }
} }
/**
* Logs a description (including diff engine output) of the MD5 mismatch between the expectedMD5
* and actualMD5 to a combination of BaseTest.log(), the md5MismatchStream, and stdout, then returns
* the diff engine output.
*
* @param testName name of the test that generated the mismatch
* @param testClassName name of the class containing the test that generated the mismatch
* @param expectedMD5 the MD5 we were expecting from this test
* @param actualMD5 the MD5 we actually calculated from the test output
* @return the diff engine output produced while logging the description of the mismatch
*/
private String logMD5MismatchAndGetDiffEngineOutput(final String testName, final String testClassName, final String expectedMD5, final String actualMD5) {
System.out.printf("##### Test %s:%s is going to fail #####%n", testClassName, testName);
String pathToExpectedMD5File = getMD5FilePath(expectedMD5, "[No DB file found]");
String pathToFileMD5File = getMD5FilePath(actualMD5, "[No DB file found]");
BaseTest.log(String.format("expected %s", expectedMD5));
BaseTest.log(String.format("calculated %s", actualMD5));
BaseTest.log(String.format("diff %s %s", pathToExpectedMD5File, pathToFileMD5File));
md5MismatchStream.printf("%s\t%s\t%s%n", expectedMD5, actualMD5, testName);
md5MismatchStream.flush();
// inline differences
String diffEngineOutput = "";
final ByteArrayOutputStream baos = new ByteArrayOutputStream();
final PrintStream ps = new PrintStream(baos);
DiffEngine.SummaryReportParams params = new DiffEngine.SummaryReportParams(ps, 20, 10, 0, MAX_RAW_DIFFS_TO_SUMMARIZE, false);
boolean success = DiffEngine.simpleDiffFiles(new File(pathToExpectedMD5File), new File(pathToFileMD5File), MAX_RECORDS_TO_READ, params);
if ( success ) {
diffEngineOutput = baos.toString();
BaseTest.log(diffEngineOutput);
System.out.printf("Note that the above list is not comprehensive. At most 20 lines of output, and 10 specific differences will be listed. Please use -T DiffObjects -R public/testdata/exampleFASTA.fasta -m %s -t %s to explore the differences more freely%n",
pathToExpectedMD5File, pathToFileMD5File);
}
ps.close();
return diffEngineOutput;
}
} }

19
public/java/test/org/broadinstitute/sting/MD5Mismatch.java
View File

@ -35,29 +35,32 @@ import java.util.List;
* @since Date created * @since Date created
*/ */
public class MD5Mismatch extends Exception { public class MD5Mismatch extends Exception {
final List<String> actuals, expecteds; final List<String> actuals, expecteds, diffEngineOutputs;
public MD5Mismatch(final String actual, final String expected) { public MD5Mismatch(final String actual, final String expected, final String diffEngineOutput) {
this(Collections.singletonList(actual), Collections.singletonList(expected)); this(Collections.singletonList(actual), Collections.singletonList(expected), Collections.singletonList(diffEngineOutput));
} }
public MD5Mismatch(final List<String> actuals, final List<String> expecteds) { public MD5Mismatch(final List<String> actuals, final List<String> expecteds, final List<String> diffEngineOutputs) {
super(formatMessage(actuals, expecteds)); super(formatMessage(actuals, expecteds, diffEngineOutputs));
this.actuals = actuals; this.actuals = actuals;
this.expecteds = expecteds; this.expecteds = expecteds;
this.diffEngineOutputs = diffEngineOutputs;
} }
@Override @Override
public String toString() { public String toString() {
return formatMessage(actuals, expecteds); return formatMessage(actuals, expecteds, diffEngineOutputs);
} }
private final static String formatMessage(final List<String> actuals, final List<String> expecteds) { private static String formatMessage(final List<String> actuals, final List<String> expecteds, final List<String> diffEngineOutputs) {
final StringBuilder b = new StringBuilder("MD5 mismatch: "); final StringBuilder b = new StringBuilder("MD5 mismatch: ");
for ( int i = 0; i < actuals.size(); i++ ) { for ( int i = 0; i < actuals.size(); i++ ) {
if ( i > 1 ) b.append("\t\t\n"); if ( i >= 1 ) b.append("\t\t\n\n");
b.append("actual ").append(actuals.get(i)); b.append("actual ").append(actuals.get(i));
b.append(" expected ").append(expecteds.get(i)); b.append(" expected ").append(expecteds.get(i));
b.append("\nDiff Engine Output:\n");
b.append(diffEngineOutputs.get(i));
} }
return b.toString(); return b.toString();
} }

64
public/java/test/org/broadinstitute/sting/WalkerTest.java
View File

@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport; import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.variant.bcf2.BCF2Utils; import org.broadinstitute.variant.bcf2.BCF2Utils;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.variant.vcf.VCFCodec; import org.broadinstitute.variant.vcf.VCFCodec;
@ -73,10 +74,6 @@ public class WalkerTest extends BaseTest {
return md5DB; return md5DB;
} }
public MD5DB.MD5Match assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5) {
return getMd5DB().assertMatchingMD5(name, resultsFile, expectedMD5, parameterize());
}
public void validateOutputBCFIfPossible(final String name, final File resultFile) { public void validateOutputBCFIfPossible(final String name, final File resultFile) {
final File bcfFile = BCF2Utils.shadowBCF(resultFile); final File bcfFile = BCF2Utils.shadowBCF(resultFile);
if ( bcfFile != null && bcfFile.exists() ) { if ( bcfFile != null && bcfFile.exists() ) {
@ -114,15 +111,15 @@ public class WalkerTest extends BaseTest {
} }
} }
public List<String> assertMatchingMD5s(final String name, List<File> resultFiles, List<String> expectedMD5s) { public List<String> assertMatchingMD5s(final String testName, final String testClassName, List<File> resultFiles, List<String> expectedMD5s) {
List<String> md5s = new ArrayList<String>(); List<String> md5s = new ArrayList<String>();
List<MD5DB.MD5Match> fails = new ArrayList<MD5DB.MD5Match>(); List<MD5DB.MD5Match> fails = new ArrayList<MD5DB.MD5Match>();
for (int i = 0; i < resultFiles.size(); i++) { for (int i = 0; i < resultFiles.size(); i++) {
MD5DB.MD5Match result = assertMatchingMD5(name, resultFiles.get(i), expectedMD5s.get(i)); MD5DB.MD5Match result = getMd5DB().testFileMD5(testName, testClassName, resultFiles.get(i), expectedMD5s.get(i), parameterize());
validateOutputBCFIfPossible(name, resultFiles.get(i)); validateOutputBCFIfPossible(testName, resultFiles.get(i));
if ( ! result.failed ) { if ( ! result.failed ) {
validateOutputIndex(name, resultFiles.get(i)); validateOutputIndex(testName, resultFiles.get(i));
md5s.add(result.expectedMD5); md5s.add(result.expectedMD5);
} else { } else {
fails.add(result); fails.add(result);
@ -132,14 +129,17 @@ public class WalkerTest extends BaseTest {
if ( ! fails.isEmpty() ) { if ( ! fails.isEmpty() ) {
List<String> actuals = new ArrayList<String>(); List<String> actuals = new ArrayList<String>();
List<String> expecteds = new ArrayList<String>(); List<String> expecteds = new ArrayList<String>();
List<String> diffEngineOutputs = new ArrayList<String>();
for ( final MD5DB.MD5Match fail : fails ) { for ( final MD5DB.MD5Match fail : fails ) {
actuals.add(fail.actualMD5); actuals.add(fail.actualMD5);
expecteds.add(fail.expectedMD5); expecteds.add(fail.expectedMD5);
diffEngineOutputs.add(fail.diffEngineOutput);
logger.warn("Fail: " + fail.failMessage); logger.warn("Fail: " + fail.failMessage);
} }
final MD5Mismatch failure = new MD5Mismatch(actuals, expecteds); final MD5Mismatch failure = new MD5Mismatch(actuals, expecteds, diffEngineOutputs);
Assert.fail(failure.toString(), failure); Assert.fail(failure.toString());
} }
return md5s; return md5s;
@ -170,6 +170,9 @@ public class WalkerTest extends BaseTest {
boolean includeImplicitArgs = true; boolean includeImplicitArgs = true;
boolean includeShadowBCF = true; boolean includeShadowBCF = true;
// Name of the test class that created this test case
private Class testClass;
// the default output path for the integration test // the default output path for the integration test
private File outputFileLocation = null; private File outputFileLocation = null;
@ -183,6 +186,7 @@ public class WalkerTest extends BaseTest {
this.args = args; this.args = args;
this.nOutputFiles = md5s.size(); this.nOutputFiles = md5s.size();
this.md5s = md5s; this.md5s = md5s;
this.testClass = getCallingTestClass();
} }
public WalkerTestSpec(String args, List<String> exts, List<String> md5s) { public WalkerTestSpec(String args, List<String> exts, List<String> md5s) {
@ -194,12 +198,22 @@ public class WalkerTest extends BaseTest {
this.nOutputFiles = md5s.size(); this.nOutputFiles = md5s.size();
this.md5s = md5s; this.md5s = md5s;
this.exts = exts; this.exts = exts;
this.testClass = getCallingTestClass();
} }
public WalkerTestSpec(String args, int nOutputFiles, Class expectedException) { public WalkerTestSpec(String args, int nOutputFiles, Class expectedException) {
this.args = args; this.args = args;
this.nOutputFiles = nOutputFiles; this.nOutputFiles = nOutputFiles;
this.expectedException = expectedException; this.expectedException = expectedException;
this.testClass = getCallingTestClass();
}
private Class getCallingTestClass() {
return JVMUtils.getCallingClass(getClass());
}
public String getTestClassName() {
return testClass.getSimpleName();
} }
public String getArgsWithImplicitArgs() { public String getArgsWithImplicitArgs() {
@ -306,7 +320,7 @@ public class WalkerTest extends BaseTest {
if ( spec.expectsException() ) { if ( spec.expectsException() ) {
// this branch handles the case were we are testing that a walker will fail as expected // this branch handles the case were we are testing that a walker will fail as expected
return executeTest(name, spec.getOutputFileLocation(), null, tmpFiles, args, spec.getExpectedException()); return executeTest(name, spec.getTestClassName(), spec.getOutputFileLocation(), null, tmpFiles, args, spec.getExpectedException());
} else { } else {
List<String> md5s = new LinkedList<String>(); List<String> md5s = new LinkedList<String>();
md5s.addAll(spec.md5s); md5s.addAll(spec.md5s);
@ -316,7 +330,7 @@ public class WalkerTest extends BaseTest {
md5s.add(md5); md5s.add(md5);
tmpFiles.add(spec.auxillaryFiles.get(md5)); tmpFiles.add(spec.auxillaryFiles.get(md5));
} }
return executeTest(name, spec.getOutputFileLocation(), md5s, tmpFiles, args, null); return executeTest(name, spec.getTestClassName(), spec.getOutputFileLocation(), md5s, tmpFiles, args, null);
} }
} }
@ -337,35 +351,37 @@ public class WalkerTest extends BaseTest {
/** /**
* execute the test, given the following: * execute the test, given the following:
* @param name the name of the test * @param testName the name of the test
* @param testClassName the name of the class that contains the test
* @param md5s the list of md5s * @param md5s the list of md5s
* @param tmpFiles the temp file corresponding to the md5 list * @param tmpFiles the temp file corresponding to the md5 list
* @param args the argument list * @param args the argument list
* @param expectedException the expected exception or null * @param expectedException the expected exception or null
* @return a pair of file and string lists * @return a pair of file and string lists
*/ */
private Pair<List<File>, List<String>> executeTest(String name, File outputFileLocation, List<String> md5s, List<File> tmpFiles, String args, Class expectedException) { private Pair<List<File>, List<String>> executeTest(String testName, String testClassName, File outputFileLocation, List<String> md5s, List<File> tmpFiles, String args, Class expectedException) {
if ( md5s != null ) qcMD5s(name, md5s); if ( md5s != null ) qcMD5s(testName, md5s);
if (outputFileLocation != null) if (outputFileLocation != null)
args += " -o " + outputFileLocation.getAbsolutePath(); args += " -o " + outputFileLocation.getAbsolutePath();
executeTest(name, args, expectedException); executeTest(testName, testClassName, args, expectedException);
if ( expectedException != null ) { if ( expectedException != null ) {
return null; return null;
} else { } else {
// we need to check MD5s // we need to check MD5s
return new Pair<List<File>, List<String>>(tmpFiles, assertMatchingMD5s(name, tmpFiles, md5s)); return new Pair<List<File>, List<String>>(tmpFiles, assertMatchingMD5s(testName, testClassName, tmpFiles, md5s));
} }
} }
/** /**
* execute the test, given the following: * execute the test, given the following:
* @param name the name of the test * @param testName the name of the test
* @param args the argument list * @param testClassName the name of the class that contains the test
* @param args the argument list
* @param expectedException the expected exception or null * @param expectedException the expected exception or null
*/ */
private void executeTest(String name, String args, Class expectedException) { private void executeTest(String testName, String testClassName, String args, Class expectedException) {
CommandLineGATK instance = new CommandLineGATK(); CommandLineGATK instance = new CommandLineGATK();
String[] command = Utils.escapeExpressions(args); String[] command = Utils.escapeExpressions(args);
@ -374,7 +390,7 @@ public class WalkerTest extends BaseTest {
try { try {
final String now = new SimpleDateFormat("HH:mm:ss").format(new Date()); final String now = new SimpleDateFormat("HH:mm:ss").format(new Date());
final String cmdline = Utils.join(" ",command); final String cmdline = Utils.join(" ",command);
System.out.println(String.format("[%s] Executing test %s with GATK arguments: %s", now, name, cmdline)); System.out.println(String.format("[%s] Executing test %s:%s with GATK arguments: %s", now, testClassName, testName, cmdline));
// also write the command line to the HTML log for convenient follow-up // also write the command line to the HTML log for convenient follow-up
// do the replaceAll so paths become relative to the current // do the replaceAll so paths become relative to the current
BaseTest.log(cmdline.replaceAll(publicTestDirRoot, "").replaceAll(privateTestDirRoot, "")); BaseTest.log(cmdline.replaceAll(publicTestDirRoot, "").replaceAll(privateTestDirRoot, ""));
@ -388,8 +404,8 @@ public class WalkerTest extends BaseTest {
// it's the type we expected // it's the type we expected
//System.out.println(String.format(" => %s PASSED", name)); //System.out.println(String.format(" => %s PASSED", name));
} else { } else {
final String message = String.format("Test %s expected exception %s but instead got %s with error message %s", final String message = String.format("Test %s:%s expected exception %s but instead got %s with error message %s",
name, expectedException, e.getClass(), e.getMessage()); testClassName, testName, expectedException, e.getClass(), e.getMessage());
if ( e.getCause() != null ) { if ( e.getCause() != null ) {
final ByteArrayOutputStream baos = new ByteArrayOutputStream(); final ByteArrayOutputStream baos = new ByteArrayOutputStream();
final PrintStream ps = new PrintStream(baos); final PrintStream ps = new PrintStream(baos);
@ -409,7 +425,7 @@ public class WalkerTest extends BaseTest {
if ( expectedException != null ) { if ( expectedException != null ) {
if ( ! gotAnException ) if ( ! gotAnException )
// we expected an exception but didn't see it // we expected an exception but didn't see it
Assert.fail(String.format("Test %s expected exception %s but none was thrown", name, expectedException.toString())); Assert.fail(String.format("Test %s:%s expected exception %s but none was thrown", testClassName, testName, expectedException.toString()));
} else { } else {
if ( CommandLineExecutable.result != 0) { if ( CommandLineExecutable.result != 0) {
throw new RuntimeException("Error running the GATK with arguments: " + args); throw new RuntimeException("Error running the GATK with arguments: " + args);

75
public/java/test/org/broadinstitute/sting/utils/classloader/JVMUtilsUnitTest.java 100644
View File

@ -0,0 +1,75 @@
/*
* 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.sting.utils.classloader;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
public class JVMUtilsUnitTest {
// Test classes used by the tests for JVMUtils.getCallingClass():
private static class DummyTestClass1 {
public static Class getCaller( final Class callee ) {
return DummyTestClass2.getCaller(callee);
}
}
private static class DummyTestClass2 {
public static Class getCaller( final Class callee ) {
return DummyTestClass3.getCaller(callee);
}
}
private static class DummyTestClass3 {
public static Class getCaller( final Class callee ) {
return JVMUtils.getCallingClass(callee);
}
}
@DataProvider( name = "TestGetCallingClassDataProvider" )
public Object[][] getTestCallingClassTestData() {
return new Object[][] {
{ DummyTestClass1.class, JVMUtilsUnitTest.class },
{ DummyTestClass2.class, DummyTestClass1.class },
{ DummyTestClass3.class, DummyTestClass2.class }
};
}
@Test( dataProvider = "TestGetCallingClassDataProvider" )
public void testGetCallingClass( final Class callee, final Class expectedCaller ) {
final Class reportedCaller = DummyTestClass1.getCaller(callee);
Assert.assertEquals(reportedCaller, expectedCaller,
String.format("Wrong calling class returned from DummyTestClass1.getCaller(%s)", callee.getSimpleName()));
}
@Test( expectedExceptions = IllegalArgumentException.class )
public void testGetCallingClassCalleeNotFound() {
// Trying to get the calling class of a class not on the runtime stack should produce an exception.
JVMUtils.getCallingClass(DummyTestClass1.class);
}
}

2
public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
View File

@ -113,7 +113,7 @@ object PipelineTest extends BaseTest with Logging {
private def assertMatchingMD5s(name: String, fileMD5s: Traversable[(File, String)], parameterize: Boolean) { private def assertMatchingMD5s(name: String, fileMD5s: Traversable[(File, String)], parameterize: Boolean) {
var failed = 0 var failed = 0
for ((file, expectedMD5) <- fileMD5s) { for ((file, expectedMD5) <- fileMD5s) {
val calculatedMD5 = md5DB.testFileMD5(name, file, expectedMD5, parameterize) val calculatedMD5 = md5DB.testFileMD5(name, "", file, expectedMD5, parameterize).actualMD5
if (!parameterize && expectedMD5 != "" && expectedMD5 != calculatedMD5) if (!parameterize && expectedMD5 != "" && expectedMD5 != calculatedMD5)
failed += 1 failed += 1
} }