Move GATKRunReport tests from private to public
-Hide AWS downloader credentials in a private properties file -Remove references to private ActiveRegion walker Allows phone home functionality to be tested at release time when we are running tests on the release jar.
This commit is contained in:
David Roazen
parent
6b3320f067
commit
d5e38ec39b
|
|
@ -0,0 +1,310 @@
|
|||
/*
|
||||
* 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.gatk.phonehome;
|
||||
|
||||
import org.broadinstitute.sting.BaseTest;
|
||||
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
|
||||
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
|
||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
|
||||
import org.broadinstitute.sting.gatk.walkers.Walker;
|
||||
import org.broadinstitute.sting.gatk.walkers.qc.CountLoci;
|
||||
import org.broadinstitute.sting.gatk.walkers.qc.CountRODs;
|
||||
import org.broadinstitute.sting.gatk.walkers.qc.CountReads;
|
||||
import org.broadinstitute.sting.utils.Utils;
|
||||
import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
|
||||
import org.broadinstitute.sting.utils.activeregion.ActivityProfileState;
|
||||
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
import org.jets3t.service.S3Service;
|
||||
import org.jets3t.service.S3ServiceException;
|
||||
import org.jets3t.service.ServiceException;
|
||||
import org.jets3t.service.model.S3Object;
|
||||
import org.testng.Assert;
|
||||
import org.testng.annotations.BeforeClass;
|
||||
import org.testng.annotations.DataProvider;
|
||||
import org.testng.annotations.Test;
|
||||
|
||||
import java.io.ByteArrayInputStream;
|
||||
import java.io.ByteArrayOutputStream;
|
||||
import java.io.FileInputStream;
|
||||
import java.io.InputStream;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.Properties;
|
||||
|
||||
public class GATKRunReportUnitTest extends BaseTest {
|
||||
private final static boolean DEBUG = false;
|
||||
private static final long S3_PUT_TIMEOUT_IN_MILLISECONDS_FOR_TESTING = 30 * 1000;
|
||||
private static final String AWS_DOWNLOADER_CREDENTIALS_PROPERTIES_FILE = privateTestDir + "phonehome/awsDownloaderCredentials.properties";
|
||||
|
||||
private Walker walker;
|
||||
private Exception exception;
|
||||
private GenomeAnalysisEngine engine;
|
||||
private String downloaderAccessKey;
|
||||
private String downloaderSecretKey;
|
||||
|
||||
@BeforeClass
|
||||
public void setup() throws Exception {
|
||||
walker = new CountReads();
|
||||
exception = new IllegalArgumentException("javaException");
|
||||
engine = new GenomeAnalysisEngine();
|
||||
engine.setArguments(new GATKArgumentCollection());
|
||||
|
||||
Properties awsProperties = new Properties();
|
||||
awsProperties.load(new FileInputStream(AWS_DOWNLOADER_CREDENTIALS_PROPERTIES_FILE));
|
||||
downloaderAccessKey = awsProperties.getProperty("accessKey");
|
||||
downloaderSecretKey = awsProperties.getProperty("secretKey");
|
||||
}
|
||||
|
||||
@Test(enabled = ! DEBUG)
|
||||
public void testAWSKeysAreValid() {
|
||||
// throws an exception if they aren't
|
||||
GATKRunReport.checkAWSAreValid();
|
||||
}
|
||||
|
||||
@Test(enabled = ! DEBUG)
|
||||
public void testAccessKey() throws Exception {
|
||||
testAWSKey(GATKRunReport.getAWSUploadAccessKey(), GATKRunReport.AWS_ACCESS_KEY_MD5);
|
||||
}
|
||||
|
||||
@Test(enabled = ! DEBUG)
|
||||
public void testSecretKey() throws Exception {
|
||||
testAWSKey(GATKRunReport.getAWSUploadSecretKey(), GATKRunReport.AWS_SECRET_KEY_MD5);
|
||||
}
|
||||
|
||||
private void testAWSKey(final String accessKey, final String expectedMD5) throws Exception {
|
||||
Assert.assertNotNull(accessKey, "AccessKey should not be null");
|
||||
final String actualmd5 = Utils.calcMD5(accessKey);
|
||||
Assert.assertEquals(actualmd5, expectedMD5);
|
||||
}
|
||||
|
||||
@DataProvider(name = "GATKReportCreationTest")
|
||||
public Object[][] makeGATKReportCreationTest() {
|
||||
List<Object[]> tests = new ArrayList<Object[]>();
|
||||
|
||||
final Walker readWalker = new CountReads();
|
||||
final Walker lociWalker = new CountLoci();
|
||||
final Walker rodWalker = new CountRODs();
|
||||
final Walker artWalker = new RunReportDummyActiveRegionWalker();
|
||||
|
||||
final Exception noException = null;
|
||||
final Exception javaException = new IllegalArgumentException("javaException");
|
||||
final Exception stingException = new ReviewedStingException("StingException");
|
||||
final Exception userException = new UserException("userException");
|
||||
|
||||
final GenomeAnalysisEngine engine = new GenomeAnalysisEngine();
|
||||
engine.setArguments(new GATKArgumentCollection());
|
||||
|
||||
for ( final Walker walker : Arrays.asList(readWalker, lociWalker, rodWalker, artWalker) ) {
|
||||
for ( final Exception exception : Arrays.asList(noException, javaException, stingException, userException) ) {
|
||||
tests.add(new Object[]{walker, exception, engine});
|
||||
}
|
||||
}
|
||||
|
||||
return tests.toArray(new Object[][]{});
|
||||
}
|
||||
|
||||
@Test(enabled = !DEBUG, dataProvider = "GATKReportCreationTest")
|
||||
public void testGATKReportCreationReadingAndWriting(final Walker walker, final Exception exception, final GenomeAnalysisEngine engine) throws Exception {
|
||||
final GATKRunReport report = new GATKRunReport(walker, exception, engine, GATKRunReport.PhoneHomeOption.STDOUT);
|
||||
final ByteArrayOutputStream captureStream = new ByteArrayOutputStream();
|
||||
final boolean succeeded = report.postReportToStream(captureStream);
|
||||
Assert.assertTrue(succeeded, "Failed to write report to stream");
|
||||
Assert.assertFalse(report.exceptionOccurredDuringPost(), "Post succeeded but report says it failed");
|
||||
Assert.assertNull(report.getErrorMessage(), "Post succeeded but there was an error message");
|
||||
Assert.assertNull(report.getErrorThrown(), "Post succeeded but there was an error message");
|
||||
final InputStream readStream = new ByteArrayInputStream(captureStream.toByteArray());
|
||||
|
||||
GATKRunReport deserialized = null;
|
||||
try {
|
||||
deserialized = GATKRunReport.deserializeReport(readStream);
|
||||
} catch ( Exception e ) {
|
||||
final String reportString = new String(captureStream.toByteArray());
|
||||
Assert.fail("Failed to deserialize GATK report " + reportString + " with exception " + e);
|
||||
}
|
||||
|
||||
if ( deserialized != null )
|
||||
Assert.assertEquals(report, deserialized);
|
||||
}
|
||||
|
||||
@DataProvider(name = "GATKAWSReportMode")
|
||||
public Object[][] makeGATKAWSReportMode() {
|
||||
List<Object[]> tests = new ArrayList<Object[]>();
|
||||
|
||||
for ( final GATKRunReport.AWSMode mode : GATKRunReport.AWSMode.values() ) {
|
||||
tests.add(new Object[]{mode});
|
||||
}
|
||||
|
||||
return tests.toArray(new Object[][]{});
|
||||
}
|
||||
|
||||
// Will fail with timeout if AWS time out isn't working
|
||||
// Will fail with exception if AWS doesn't protect itself from errors
|
||||
@Test(enabled = ! DEBUG, dataProvider = "GATKAWSReportMode", timeOut = S3_PUT_TIMEOUT_IN_MILLISECONDS_FOR_TESTING * 2)
|
||||
public void testAWS(final GATKRunReport.AWSMode awsMode) {
|
||||
logger.warn("Starting testAWS mode=" + awsMode);
|
||||
|
||||
// Use a shorter timeout than usual when we're testing GATKRunReport.AWSMode.TIMEOUT
|
||||
final long thisTestS3Timeout = awsMode == GATKRunReport.AWSMode.TIMEOUT ? 30 * 1000 : S3_PUT_TIMEOUT_IN_MILLISECONDS_FOR_TESTING;
|
||||
final GATKRunReport report = new GATKRunReport(walker, exception, engine, GATKRunReport.PhoneHomeOption.AWS, thisTestS3Timeout);
|
||||
report.sendAWSToTestBucket();
|
||||
report.setAwsMode(awsMode);
|
||||
final S3Object s3Object = report.postReportToAWSS3();
|
||||
|
||||
if ( awsMode == GATKRunReport.AWSMode.NORMAL ) {
|
||||
Assert.assertNotNull(s3Object, "Upload to AWS failed, s3Object was null. error was " + report.formatError());
|
||||
Assert.assertFalse(report.exceptionOccurredDuringPost(), "The upload should have succeeded but the report says it didn't. Error was " + report.formatError());
|
||||
Assert.assertNull(report.getErrorMessage(), "Report succeeded but an error message was found");
|
||||
Assert.assertNull(report.getErrorThrown(), "Report succeeded but an thrown error was found");
|
||||
try {
|
||||
final GATKRunReport deserialized = GATKRunReport.deserializeReport(downloaderAccessKey, downloaderSecretKey, report.getS3ReportBucket(), s3Object);
|
||||
Assert.assertEquals(report, deserialized);
|
||||
deleteFromS3(report);
|
||||
} catch ( Exception e ) {
|
||||
Assert.fail("Failed to read, deserialize, or delete GATK report " + s3Object.getName() + " with exception " + e);
|
||||
}
|
||||
} else {
|
||||
Assert.assertNull(s3Object, "AWS upload should have failed for mode " + awsMode + " but got non-null s3 object back " + s3Object + " error was " + report.formatError());
|
||||
Assert.assertTrue(report.exceptionOccurredDuringPost(), "S3 object was null but the report says that the upload succeeded");
|
||||
Assert.assertNotNull(report.getErrorMessage(), "Report succeeded but an error message wasn't found");
|
||||
if ( awsMode == GATKRunReport.AWSMode.FAIL_WITH_EXCEPTION )
|
||||
Assert.assertNotNull(report.getErrorThrown());
|
||||
}
|
||||
}
|
||||
|
||||
private void deleteFromS3(final GATKRunReport report) throws Exception {
|
||||
final S3Service s3Service = GATKRunReport.initializeAWSService(downloaderAccessKey, downloaderSecretKey);
|
||||
// Retrieve the whole data object we created previously
|
||||
s3Service.deleteObject(report.getS3ReportBucket(), report.getReportFileName());
|
||||
}
|
||||
|
||||
@DataProvider(name = "PostReportByType")
|
||||
public Object[][] makePostReportByType() {
|
||||
List<Object[]> tests = new ArrayList<Object[]>();
|
||||
|
||||
for ( final GATKRunReport.PhoneHomeOption et : GATKRunReport.PhoneHomeOption.values() ) {
|
||||
tests.add(new Object[]{et});
|
||||
}
|
||||
|
||||
return tests.toArray(new Object[][]{});
|
||||
}
|
||||
|
||||
@Test(enabled = ! DEBUG, dataProvider = "PostReportByType", timeOut = S3_PUT_TIMEOUT_IN_MILLISECONDS_FOR_TESTING * 2)
|
||||
public void testPostReportByType(final GATKRunReport.PhoneHomeOption type) {
|
||||
final GATKRunReport report = new GATKRunReport(walker, exception, engine, GATKRunReport.PhoneHomeOption.AWS, S3_PUT_TIMEOUT_IN_MILLISECONDS_FOR_TESTING);
|
||||
Assert.assertFalse(report.exceptionOccurredDuringPost(), "An exception occurred during posting the report");
|
||||
final boolean succeeded = report.postReport(type);
|
||||
|
||||
if ( type == GATKRunReport.PhoneHomeOption.NO_ET )
|
||||
Assert.assertFalse(succeeded, "NO_ET option shouldn't write a report");
|
||||
else {
|
||||
Assert.assertTrue(succeeded, "Any non NO_ET option should succeed in writing a report");
|
||||
|
||||
if ( type == GATKRunReport.PhoneHomeOption.STDOUT ) {
|
||||
// nothing to do
|
||||
} else {
|
||||
// must have gone to AWS
|
||||
try {
|
||||
Assert.assertTrue(report.wentToAWS(), "The report should have gone to AWS but the report says it wasn't");
|
||||
deleteFromS3(report);
|
||||
} catch ( Exception e ) {
|
||||
Assert.fail("Failed delete GATK report " + report.getReportFileName() + " with exception " + e);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
public interface S3Op {
|
||||
public void apply() throws ServiceException;
|
||||
}
|
||||
|
||||
// Will fail with timeout if AWS time out isn't working
|
||||
// Will fail with exception if AWS doesn't protect itself from errors
|
||||
@Test(timeOut = S3_PUT_TIMEOUT_IN_MILLISECONDS_FOR_TESTING * 2)
|
||||
public void testAWSPublicKeyHasAccessControls() throws Exception {
|
||||
final GATKRunReport report = new GATKRunReport(walker, exception, engine, GATKRunReport.PhoneHomeOption.AWS, S3_PUT_TIMEOUT_IN_MILLISECONDS_FOR_TESTING);
|
||||
report.sendAWSToTestBucket();
|
||||
final S3Object s3Object = report.postReportToAWSS3();
|
||||
Assert.assertNotNull(s3Object, "Upload to AWS failed, s3Object was null. error was " + report.formatError());
|
||||
|
||||
// create a service with the public key, and make sure it cannot list or delete
|
||||
final S3Service s3Service = GATKRunReport.initializeAWSService(GATKRunReport.getAWSUploadAccessKey(), GATKRunReport.getAWSUploadSecretKey());
|
||||
assertOperationNotAllowed("listAllBuckets", new S3Op() {
|
||||
@Override
|
||||
public void apply() throws S3ServiceException {
|
||||
s3Service.listAllBuckets();
|
||||
}
|
||||
});
|
||||
assertOperationNotAllowed("listBucket", new S3Op() {
|
||||
@Override
|
||||
public void apply() throws S3ServiceException { s3Service.listObjects(report.getS3ReportBucket()); }
|
||||
});
|
||||
assertOperationNotAllowed("createBucket", new S3Op() {
|
||||
@Override
|
||||
public void apply() throws S3ServiceException { s3Service.createBucket("ShouldNotCreate"); }
|
||||
});
|
||||
assertOperationNotAllowed("deleteObject", new S3Op() {
|
||||
@Override
|
||||
public void apply() throws ServiceException { s3Service.deleteObject(report.getS3ReportBucket(), report.getReportFileName()); }
|
||||
});
|
||||
}
|
||||
|
||||
private void assertOperationNotAllowed(final String name, final S3Op op) {
|
||||
try {
|
||||
op.apply();
|
||||
// only gets here if the operation was successful
|
||||
Assert.fail("Operation " + name + " ran successfully but we expected to it fail");
|
||||
} catch ( ServiceException e ) {
|
||||
Assert.assertEquals(e.getErrorCode(), "AccessDenied");
|
||||
}
|
||||
}
|
||||
|
||||
class RunReportDummyActiveRegionWalker extends ActiveRegionWalker<Integer, Integer> {
|
||||
@Override
|
||||
public ActivityProfileState isActive(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
return new ActivityProfileState(ref.getLocus(), 0.0);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Integer map(ActiveRegion activeRegion, RefMetaDataTracker metaDataTracker) {
|
||||
return 0;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Integer reduceInit() {
|
||||
return 0;
|
||||
}
|
||||
|
||||
@Override
|
||||
public Integer reduce(Integer value, Integer sum) {
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue