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All MD5 mismatches for test are shown 

-- Now for tests like DoC, with 20 output md5s, you see all of the differences before failing.
This commit is contained in:
Mark DePristo 2011-10-04 15:53:52 -07:00
parent e1d6c7a50a
commit 463eab7604
2 changed files with 40 additions and 12 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

31
public/java/test/org/broadinstitute/sting/MD5DB.java
View File

@ -129,7 +129,7 @@ public class MD5DB {
System.out.printf("##### Skipping update, cannot write file %s%n", dbFile);
}
} else {
System.out.printf("##### MD5 file is up to date: %s%n", dbFile.getPath());
//System.out.printf("##### MD5 file is up to date: %s%n", dbFile.getPath());
}
}
@ -170,6 +170,18 @@ public class MD5DB {
return bytes;
}
public static class MD5Match {
final String md5;
final String failMessage;
boolean failed;
public MD5Match(final String md5, final String failMessage, final boolean failed) {
this.md5 = md5;
this.failMessage = failMessage;
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.
@ -178,18 +190,21 @@ public class MD5DB {
* @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.
*/
public static String assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5, final boolean parameterize) {
String filemd5sum = testFileMD5(name, resultsFile, expectedMD5, parameterize);
public static MD5Match assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5, final boolean parameterize) {
final String filemd5sum = testFileMD5(name, resultsFile, expectedMD5, parameterize);
String failMessage = null;
boolean failed = false;
if (parameterize || expectedMD5.equals("")) {
// Don't assert
} else if ( filemd5sum.equals(expectedMD5) ) {
System.out.println(String.format(" => %s PASSED", name));
System.out.println(String.format(" => %s PASSED (expected=%s)", name, expectedMD5));
} else {
Assert.fail(String.format("%s has mismatching MD5s: expected=%s observed=%s", name, expectedMD5, filemd5sum));
failed = true;
failMessage = String.format("%s has mismatching MD5s: expected=%s observed=%s", name, expectedMD5, filemd5sum);
}
return filemd5sum;
return new MD5Match(filemd5sum, failMessage, failed);
}
@ -218,8 +233,8 @@ public class MD5DB {
System.out.println(String.format("PARAMETERIZATION[%s]: file %s has md5 = %s, stated expectation is %s, equal? = %b",
name, resultsFile, filemd5sum, expectedMD5, filemd5sum.equals(expectedMD5)));
} else {
System.out.println(String.format("Checking MD5 for %s [calculated=%s, expected=%s]", resultsFile, filemd5sum, expectedMD5));
System.out.flush();
//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).

21
public/java/test/org/broadinstitute/sting/WalkerTest.java
View File

@ -52,7 +52,7 @@ public class WalkerTest extends BaseTest {
GenomeAnalysisEngine.resetRandomGenerator();
}
public String assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5) {
public MD5DB.MD5Match assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5) {
return MD5DB.assertMatchingMD5(name, resultsFile, expectedMD5, parameterize());
}
@ -84,10 +84,23 @@ public class WalkerTest extends BaseTest {
public List<String> assertMatchingMD5s(final String name, List<File> resultFiles, List<String> expectedMD5s) {
List<String> md5s = new ArrayList<String>();
List<MD5DB.MD5Match> fails = new ArrayList<MD5DB.MD5Match>();
for (int i = 0; i < resultFiles.size(); i++) {
String md5 = assertMatchingMD5(name, resultFiles.get(i), expectedMD5s.get(i));
maybeValidateSupplementaryFile(name, resultFiles.get(i));
md5s.add(i, md5);
MD5DB.MD5Match result = assertMatchingMD5(name, resultFiles.get(i), expectedMD5s.get(i));
if ( ! result.failed ) {
maybeValidateSupplementaryFile(name, resultFiles.get(i));
md5s.add(result.md5);
} else {
fails.add(result);
}
}
if ( ! fails.isEmpty() ) {
for ( final MD5DB.MD5Match fail : fails ) {
logger.warn("Fail: " + fail.failMessage);
}
Assert.fail("Test failed: " + name);
}
return md5s;