diff --git a/build.xml b/build.xml
index 56bf4f0cd..2e9df4d5e 100644
--- a/build.xml
+++ b/build.xml
@@ -1031,6 +1031,7 @@
+
@@ -1043,6 +1044,7 @@
+
@@ -1078,6 +1080,7 @@
+
diff --git a/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java b/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
index 2f5115dfa..8f4958f6c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
@@ -248,4 +248,62 @@ public class JVMUtils {
interfaces.add(interfaceClass.getSimpleName());
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()));
+ }
+ }
}
diff --git a/public/java/test/org/broadinstitute/sting/MD5DB.java b/public/java/test/org/broadinstitute/sting/MD5DB.java
index 2b0d52a11..7bd6f7bc4 100644
--- a/public/java/test/org/broadinstitute/sting/MD5DB.java
+++ b/public/java/test/org/broadinstitute/sting/MD5DB.java
@@ -97,7 +97,12 @@ public class MD5DB {
if ( ! dir.exists() ) {
System.out.printf("##### Creating MD5 db %s%n", LOCAL_MD5_DB_DIR);
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 {
- final String actualMD5, expectedMD5;
- final String failMessage;
- boolean failed;
+ public final String actualMD5, expectedMD5;
+ public final String failMessage;
+ 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.expectedMD5 = expectedMD5;
this.failMessage = failMessage;
+ this.diffEngineOutput = diffEngineOutput;
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.
- * @param name Name of the test.
+ * Tests a file MD5 against an expected value, returning an MD5Match object containing a description of the
+ * 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 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.
- * @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) {
- final String actualMD5 = testFileMD5(name, resultsFile, expectedMD5, parameterize);
- String failMessage = null;
+ public MD5Match testFileMD5(final String testName, final String testClassName, final File resultsFile, final String expectedMD5, final boolean parameterize) {
+ final String actualMD5 = calculateFileMD5(resultsFile);
+ String diffEngineOutput = "";
+ String failMessage = "";
boolean failed = false;
+ // copy md5 to integrationtests
+ updateMD5Db(actualMD5, resultsFile);
+
if (parameterize || expectedMD5.equals("")) {
- // Don't assert
- } else if ( actualMD5.equals(expectedMD5) ) {
- //BaseTest.log(String.format(" => %s PASSED (expected=%s)", name, expectedMD5));
- } else {
+ BaseTest.log(String.format("PARAMETERIZATION: file %s has md5 = %s", resultsFile, actualMD5));
+ } else if ( ! expectedMD5.equals(actualMD5) ) {
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.
- * @param name Name of the test.
- * @param resultsFile File to MD5.
- * @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.
- * @return The calculated MD5.
+ * Calculates the MD5 for the specified file and returns it as a String
+ *
+ * @param file file whose MD5 to calculate
+ * @return file's MD5 in String form
+ * @throws RuntimeException if the file could not be read
*/
- public String testFileMD5(final String name, final File resultsFile, final String expectedMD5, final boolean parameterize) {
+ public String calculateFileMD5( final File file ) {
try {
- final String filemd5sum = Utils.calcMD5(getBytesFromFile(resultsFile));
-
- //
- // copy md5 to integrationtests
- //
- 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);
+ return Utils.calcMD5(getBytesFromFile(file));
+ }
+ catch ( Exception e ) {
+ throw new RuntimeException("Failed to read bytes from file: " + file + " for MD5 calculation", 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;
+ }
}
diff --git a/public/java/test/org/broadinstitute/sting/MD5Mismatch.java b/public/java/test/org/broadinstitute/sting/MD5Mismatch.java
index e459a24ce..56acedaf0 100644
--- a/public/java/test/org/broadinstitute/sting/MD5Mismatch.java
+++ b/public/java/test/org/broadinstitute/sting/MD5Mismatch.java
@@ -35,29 +35,32 @@ import java.util.List;
* @since Date created
*/
public class MD5Mismatch extends Exception {
- final List actuals, expecteds;
+ final List actuals, expecteds, diffEngineOutputs;
- public MD5Mismatch(final String actual, final String expected) {
- this(Collections.singletonList(actual), Collections.singletonList(expected));
+ public MD5Mismatch(final String actual, final String expected, final String diffEngineOutput) {
+ this(Collections.singletonList(actual), Collections.singletonList(expected), Collections.singletonList(diffEngineOutput));
}
- public MD5Mismatch(final List actuals, final List expecteds) {
- super(formatMessage(actuals, expecteds));
+ public MD5Mismatch(final List actuals, final List expecteds, final List diffEngineOutputs) {
+ super(formatMessage(actuals, expecteds, diffEngineOutputs));
this.actuals = actuals;
this.expecteds = expecteds;
+ this.diffEngineOutputs = diffEngineOutputs;
}
@Override
public String toString() {
- return formatMessage(actuals, expecteds);
+ return formatMessage(actuals, expecteds, diffEngineOutputs);
}
- private final static String formatMessage(final List actuals, final List expecteds) {
+ private static String formatMessage(final List actuals, final List expecteds, final List diffEngineOutputs) {
final StringBuilder b = new StringBuilder("MD5 mismatch: ");
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(" expected ").append(expecteds.get(i));
+ b.append("\nDiff Engine Output:\n");
+ b.append(diffEngineOutputs.get(i));
}
return b.toString();
}
diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java
index dd5a2b0a7..40f1f7bcd 100644
--- a/public/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.variant.bcf2.BCF2Utils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.variant.vcf.VCFCodec;
@@ -73,10 +74,6 @@ public class WalkerTest extends BaseTest {
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) {
final File bcfFile = BCF2Utils.shadowBCF(resultFile);
if ( bcfFile != null && bcfFile.exists() ) {
@@ -114,15 +111,15 @@ public class WalkerTest extends BaseTest {
}
}
- public List assertMatchingMD5s(final String name, List resultFiles, List expectedMD5s) {
+ public List assertMatchingMD5s(final String testName, final String testClassName, List resultFiles, List expectedMD5s) {
List md5s = new ArrayList();
List fails = new ArrayList();
for (int i = 0; i < resultFiles.size(); i++) {
- MD5DB.MD5Match result = assertMatchingMD5(name, resultFiles.get(i), expectedMD5s.get(i));
- validateOutputBCFIfPossible(name, resultFiles.get(i));
+ MD5DB.MD5Match result = getMd5DB().testFileMD5(testName, testClassName, resultFiles.get(i), expectedMD5s.get(i), parameterize());
+ validateOutputBCFIfPossible(testName, resultFiles.get(i));
if ( ! result.failed ) {
- validateOutputIndex(name, resultFiles.get(i));
+ validateOutputIndex(testName, resultFiles.get(i));
md5s.add(result.expectedMD5);
} else {
fails.add(result);
@@ -132,14 +129,17 @@ public class WalkerTest extends BaseTest {
if ( ! fails.isEmpty() ) {
List actuals = new ArrayList();
List expecteds = new ArrayList();
+ List diffEngineOutputs = new ArrayList();
+
for ( final MD5DB.MD5Match fail : fails ) {
actuals.add(fail.actualMD5);
expecteds.add(fail.expectedMD5);
+ diffEngineOutputs.add(fail.diffEngineOutput);
logger.warn("Fail: " + fail.failMessage);
}
- final MD5Mismatch failure = new MD5Mismatch(actuals, expecteds);
- Assert.fail(failure.toString(), failure);
+ final MD5Mismatch failure = new MD5Mismatch(actuals, expecteds, diffEngineOutputs);
+ Assert.fail(failure.toString());
}
return md5s;
@@ -170,6 +170,9 @@ public class WalkerTest extends BaseTest {
boolean includeImplicitArgs = 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
private File outputFileLocation = null;
@@ -183,6 +186,7 @@ public class WalkerTest extends BaseTest {
this.args = args;
this.nOutputFiles = md5s.size();
this.md5s = md5s;
+ this.testClass = getCallingTestClass();
}
public WalkerTestSpec(String args, List exts, List md5s) {
@@ -194,12 +198,22 @@ public class WalkerTest extends BaseTest {
this.nOutputFiles = md5s.size();
this.md5s = md5s;
this.exts = exts;
+ this.testClass = getCallingTestClass();
}
public WalkerTestSpec(String args, int nOutputFiles, Class expectedException) {
this.args = args;
this.nOutputFiles = nOutputFiles;
this.expectedException = expectedException;
+ this.testClass = getCallingTestClass();
+ }
+
+ private Class getCallingTestClass() {
+ return JVMUtils.getCallingClass(getClass());
+ }
+
+ public String getTestClassName() {
+ return testClass.getSimpleName();
}
public String getArgsWithImplicitArgs() {
@@ -306,7 +320,7 @@ public class WalkerTest extends BaseTest {
if ( spec.expectsException() ) {
// 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 {
List md5s = new LinkedList();
md5s.addAll(spec.md5s);
@@ -316,7 +330,7 @@ public class WalkerTest extends BaseTest {
md5s.add(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:
- * @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 tmpFiles the temp file corresponding to the md5 list
* @param args the argument list
* @param expectedException the expected exception or null
* @return a pair of file and string lists
*/
- private Pair, List> executeTest(String name, File outputFileLocation, List md5s, List tmpFiles, String args, Class expectedException) {
- if ( md5s != null ) qcMD5s(name, md5s);
+ private Pair, List> executeTest(String testName, String testClassName, File outputFileLocation, List md5s, List tmpFiles, String args, Class expectedException) {
+ if ( md5s != null ) qcMD5s(testName, md5s);
if (outputFileLocation != null)
args += " -o " + outputFileLocation.getAbsolutePath();
- executeTest(name, args, expectedException);
+ executeTest(testName, testClassName, args, expectedException);
if ( expectedException != null ) {
return null;
} else {
// we need to check MD5s
- return new Pair, List>(tmpFiles, assertMatchingMD5s(name, tmpFiles, md5s));
+ return new Pair, List>(tmpFiles, assertMatchingMD5s(testName, testClassName, tmpFiles, md5s));
}
}
/**
* execute the test, given the following:
- * @param name the name of the test
- * @param args the argument list
+ * @param testName the name of the test
+ * @param testClassName the name of the class that contains the test
+ * @param args the argument list
* @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();
String[] command = Utils.escapeExpressions(args);
@@ -374,7 +390,7 @@ public class WalkerTest extends BaseTest {
try {
final String now = new SimpleDateFormat("HH:mm:ss").format(new Date());
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
// do the replaceAll so paths become relative to the current
BaseTest.log(cmdline.replaceAll(publicTestDirRoot, "").replaceAll(privateTestDirRoot, ""));
@@ -388,8 +404,8 @@ public class WalkerTest extends BaseTest {
// it's the type we expected
//System.out.println(String.format(" => %s PASSED", name));
} else {
- final String message = String.format("Test %s expected exception %s but instead got %s with error message %s",
- name, expectedException, e.getClass(), e.getMessage());
+ final String message = String.format("Test %s:%s expected exception %s but instead got %s with error message %s",
+ testClassName, testName, expectedException, e.getClass(), e.getMessage());
if ( e.getCause() != null ) {
final ByteArrayOutputStream baos = new ByteArrayOutputStream();
final PrintStream ps = new PrintStream(baos);
@@ -409,7 +425,7 @@ public class WalkerTest extends BaseTest {
if ( expectedException != null ) {
if ( ! gotAnException )
// 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 {
if ( CommandLineExecutable.result != 0) {
throw new RuntimeException("Error running the GATK with arguments: " + args);
diff --git a/public/java/test/org/broadinstitute/sting/utils/classloader/JVMUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/classloader/JVMUtilsUnitTest.java
new file mode 100644
index 000000000..6ffd47f37
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/utils/classloader/JVMUtilsUnitTest.java
@@ -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);
+ }
+}
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
index 03b38ffe9..6741e4107 100644
--- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
+++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
@@ -113,7 +113,7 @@ object PipelineTest extends BaseTest with Logging {
private def assertMatchingMD5s(name: String, fileMD5s: Traversable[(File, String)], parameterize: Boolean) {
var failed = 0
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)
failed += 1
}