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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
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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.iterators.ReadTransformer;
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.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
@ -222,6 +223,9 @@ public class GenomeAnalysisEngine {
* @return the value of this traversal.
*/
public Object execute() {
// first thing is to make sure the AWS keys can be decrypted
GATKRunReport.checkAWSAreValid();
//HeapSizeMonitor monitor = new HeapSizeMonitor();
//monitor.start();
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.
*/
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
*/
@ -358,6 +361,28 @@ public class GATKRunReport {
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 {
public AtomicBoolean isSuccess;

46
public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
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@ -1,27 +1,27 @@
/*
* 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.
*/
* 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;

4
public/java/test/org/broadinstitute/sting/gatk/phonehome/GATKRunReportUnitTest.java
View File

@ -36,12 +36,12 @@ import java.security.NoSuchAlgorithmException;
public class GATKRunReportUnitTest extends BaseTest {
@Test
public void testAccessKey() throws Exception {
testAWSKey(GATKRunReport.getAWSAccessKey(), "c0f0afa1ff5ba41d9bf216cfcdbf26bf");
testAWSKey(GATKRunReport.getAWSAccessKey(), GATKRunReport.AWS_ACCESS_KEY_MD5);
}
@Test
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 {

46
public/java/test/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java
View File

@ -1,27 +1,27 @@
/*
* 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.
*/
* 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;