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Personal MD5 database system now live. WalkerTest now maintains a database of result files associated with MD5 results in integrationtest/, and provides command lines for diff-ing expected to current md5 results when encountering failed intergration tests. The suite currently takes 200Mb to store. Update and run intergrationtest to build your very own expectation database for future development work. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3466 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-05-31 16:06:16 +00:00
parent 2b02324587
commit 21427211c0
1 changed files with 67 additions and 0 deletions
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67
java/test/org/broadinstitute/sting/WalkerTest.java
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@ -32,6 +32,7 @@ import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.Utils;
import org.junit.Test;
import org.apache.commons.io.FileUtils;
import java.io.File;
import java.io.FileInputStream;
@ -45,10 +46,54 @@ public class WalkerTest extends BaseTest {
// the default output path for the integration test
private File outputFileLocation = null;
/**
* Subdirectory under the ant build directory where we store integration test md5 results
*/
public static final String MD5_FILE_DB_SUBDIR = "integrationtests";
public void setOutputFileLocation(File outputFileLocation) {
this.outputFileLocation = outputFileLocation;
}
private static void ensureMd5DbDirectory() {
// todo -- make path
File dir = new File(MD5_FILE_DB_SUBDIR);
if ( ! dir.exists() ) {
System.out.printf("##### Creating MD5 db %s%n", MD5_FILE_DB_SUBDIR);
if ( ! dir.mkdir() ) {
throw new StingException("Infrastructure failure: failed to create md5 directory " + MD5_FILE_DB_SUBDIR);
}
}
}
private static File getFileForMD5(final String md5) {
final String basename = String.format("%s.integrationtest", md5);
return new File(MD5_FILE_DB_SUBDIR + "/" + basename);
}
private static void updateMD5Db(final String md5, final File resultsFile) {
// todo -- copy results file to DB dir if needed under filename for md5
final File dbFile = getFileForMD5(md5);
if ( ! dbFile.exists() ) {
// the file isn't already in the db, copy it over
System.out.printf("##### Updating MD5 file: %s%n", dbFile.getPath());
try {
FileUtils.copyFile(resultsFile, dbFile);
} catch ( IOException e ) {
throw new StingException(e.getMessage());
}
} else {
System.out.printf("##### MD5 file is up to date: %s%n", dbFile.getPath());
}
}
private static String getMD5Path(final String md5, final String valueIfNotFound) {
// todo -- look up the result in the directory and return the path if it exists
final File dbFile = getFileForMD5(md5);
return dbFile.exists() ? dbFile.getPath() : valueIfNotFound;
}
public String assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5) {
try {
byte[] bytesOfMessage = getBytesFromFile(resultsFile);
@ -56,12 +101,32 @@ public class WalkerTest extends BaseTest {
BigInteger bigInt = new BigInteger(1, thedigest);
String filemd5sum = bigInt.toString(16);
while (filemd5sum.length() < 32) filemd5sum = "0" + filemd5sum; // pad to length 32
//
// copy md5 to integrationtests
//
updateMD5Db(filemd5sum, resultsFile);
if (parameterize() || expectedMD5.equals("")) {
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();
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 fail #####%n", name);
String pathToExpectedMD5File = getMD5Path(expectedMD5, "[No DB file found]");
String pathToFileMD5File = getMD5Path(filemd5sum, "[No DB file found]");
System.out.printf("##### Path to expected file (MD5=%s): %s%n", expectedMD5, pathToExpectedMD5File);
System.out.printf("##### Path to expected file (MD5=%s): %s%n", filemd5sum, pathToFileMD5File);
System.out.printf("##### Diff command: diff %s %s%n", pathToExpectedMD5File, pathToFileMD5File);
// todo -- add support for simple inline display of the first N differences for text file
}
Assert.assertEquals(name + " Mismatching MD5s", expectedMD5, filemd5sum);
System.out.println(String.format(" => %s PASSED", name));
}
@ -145,6 +210,8 @@ public class WalkerTest extends BaseTest {
}
protected Pair<List<File>, List<String>> executeTest(final String name, WalkerTestSpec spec) {
ensureMd5DbDirectory(); // ensure the md5 directory exists
List<File> tmpFiles = new ArrayList<File>();
for (int i = 0; i < spec.nOutputFiles; i++) {
String ext = spec.exts == null ? ".tmp" : "." + spec.exts.get(i);