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More aggressive checking of AWS key quality upon startup in the GATK

This commit is contained in:
Mark DePristo 2013-01-31 09:08:26 -05:00
parent b875ff4c8d
commit 404ee9a6e4
5 changed files with 77 additions and 48 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -47,6 +47,7 @@ import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.gatk.io.stubs.Stub; import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.gatk.iterators.ReadTransformer; import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
import org.broadinstitute.sting.gatk.iterators.ReadTransformersMode; import org.broadinstitute.sting.gatk.iterators.ReadTransformersMode;
import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation; import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
@ -222,6 +223,9 @@ public class GenomeAnalysisEngine {
* @return the value of this traversal. * @return the value of this traversal.
*/ */
public Object execute() { public Object execute() {
// first thing is to make sure the AWS keys can be decrypted
GATKRunReport.checkAWSAreValid();
//HeapSizeMonitor monitor = new HeapSizeMonitor(); //HeapSizeMonitor monitor = new HeapSizeMonitor();
//monitor.start(); //monitor.start();
setStartTime(new java.util.Date()); setStartTime(new java.util.Date());

25
public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
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@ -73,6 +73,9 @@ import java.util.zip.GZIPOutputStream;
* GATK run report database. * GATK run report database.
*/ */
public class GATKRunReport { public class GATKRunReport {
protected final static String AWS_ACCESS_KEY_MD5 = "c0f0afa1ff5ba41d9bf216cfcdbf26bf";
protected final static String AWS_SECRET_KEY_MD5 = "db2f13b3a7c98ad24e28783733ec4a62";
/** /**
* The root file system directory where we keep common report data * The root file system directory where we keep common report data
*/ */
@ -358,6 +361,28 @@ public class GATKRunReport {
return getAWSKey("GATK_AWS_secret.key"); return getAWSKey("GATK_AWS_secret.key");
} }
/**
* Check that the AWS keys can be decrypted and are what we expect them to be
*
* @throws ReviewedStingException if anything goes wrong
*/
public static void checkAWSAreValid() {
try {
final String accessKeyMD5 = Utils.calcMD5(getAWSAccessKey());
final String secretKeyMD5 = Utils.calcMD5(getAWSSecretKey());
if ( ! AWS_ACCESS_KEY_MD5.equals(accessKeyMD5) ) {
throw new ReviewedStingException("Invalid AWS access key found, expected MD5 " + AWS_ACCESS_KEY_MD5 + " but got " + accessKeyMD5);
}
if ( ! AWS_SECRET_KEY_MD5.equals(secretKeyMD5) ) {
throw new ReviewedStingException("Invalid AWS secret key found, expected MD5 " + AWS_SECRET_KEY_MD5 + " but got " + secretKeyMD5);
}
} catch ( Exception e ) {
throw new ReviewedStingException("Couldn't decrypt AWS keys, something is wrong with the GATK distribution");
}
}
private class S3PutRunnable implements Runnable { private class S3PutRunnable implements Runnable {
public AtomicBoolean isSuccess; public AtomicBoolean isSuccess;

4
public/java/test/org/broadinstitute/sting/gatk/phonehome/GATKRunReportUnitTest.java
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@ -36,12 +36,12 @@ import java.security.NoSuchAlgorithmException;
public class GATKRunReportUnitTest extends BaseTest { public class GATKRunReportUnitTest extends BaseTest {
@Test @Test
public void testAccessKey() throws Exception { public void testAccessKey() throws Exception {
testAWSKey(GATKRunReport.getAWSAccessKey(), "c0f0afa1ff5ba41d9bf216cfcdbf26bf"); testAWSKey(GATKRunReport.getAWSAccessKey(), GATKRunReport.AWS_ACCESS_KEY_MD5);
} }
@Test @Test
public void testSecretKey() throws Exception { public void testSecretKey() throws Exception {
testAWSKey(GATKRunReport.getAWSSecretKey(), "db2f13b3a7c98ad24e28783733ec4a62"); testAWSKey(GATKRunReport.getAWSSecretKey(), GATKRunReport.AWS_SECRET_KEY_MD5);
} }
private void testAWSKey(final String accessKey, final String expectedMD5) throws Exception { private void testAWSKey(final String accessKey, final String expectedMD5) throws Exception {