Restoring key-related unit/integration tests

The recent GATKReport commit accidentally clobbered a few tests -- this
restores them.

public/java/test/org/broadinstitute/sting/utils/crypt/CryptUtilsUnitTest.java

@@ -27,9 +27,10 @@ package org.broadinstitute.sting.utils.crypt;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.testng.Assert;
+import org.testng.SkipException;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
+import org.testng.Assert;
 
 import java.io.File;
 import java.io.FileInputStream;
@@ -40,7 +41,6 @@ import java.security.PrivateKey;
 import java.security.PublicKey;
 import java.util.Arrays;
 
-@Test(enabled = false)
 public class CryptUtilsUnitTest extends BaseTest {
 
     @Test
@@ -65,11 +65,21 @@ public class CryptUtilsUnitTest extends BaseTest {
 
     @Test
     public void testGATKMasterKeyPairMutualDecryption() {
+        if ( gatkPrivateKeyExistsButReadPermissionDenied() ) {
+            throw new SkipException(String.format("Skipping test %s because we do not have permission to read the GATK private key",
+                                    "testGATKMasterKeyPairMutualDecryption"));
+        }
+
         Assert.assertTrue(CryptUtils.keysDecryptEachOther(CryptUtils.loadGATKMasterPrivateKey(), CryptUtils.loadGATKMasterPublicKey()));
     }
 
     @Test
     public void testGATKMasterPrivateKeyWithDistributedPublicKeyMutualDecryption() {
+        if ( gatkPrivateKeyExistsButReadPermissionDenied() ) {
+            throw new SkipException(String.format("Skipping test %s because we do not have permission to read the GATK private key",
+                                    "testGATKMasterPrivateKeyWithDistributedPublicKeyMutualDecryption"));
+        }
+
         Assert.assertTrue(CryptUtils.keysDecryptEachOther(CryptUtils.loadGATKMasterPrivateKey(), CryptUtils.loadGATKDistributedPublicKey()));
     }
 
@@ -157,6 +167,11 @@ public class CryptUtilsUnitTest extends BaseTest {
 
     @Test
     public void testLoadGATKMasterPrivateKey() {
+        if ( gatkPrivateKeyExistsButReadPermissionDenied() ) {
+            throw new SkipException(String.format("Skipping test %s because we do not have permission to read the GATK private key",
+                                    "testLoadGATKMasterPrivateKey"));
+        }
+
         PrivateKey gatkMasterPrivateKey = CryptUtils.loadGATKMasterPrivateKey();
     }
 
@@ -175,4 +190,9 @@ public class CryptUtilsUnitTest extends BaseTest {
         Assert.assertEquals(originalKey.getAlgorithm(), keyFromDisk.getAlgorithm());
         Assert.assertEquals(originalKey.getFormat(), keyFromDisk.getFormat());
     }
+
+    private boolean gatkPrivateKeyExistsButReadPermissionDenied() {
+        File gatkPrivateKey = new File(CryptUtils.GATK_MASTER_PRIVATE_KEY_FILE);
+        return gatkPrivateKey.exists() && ! gatkPrivateKey.canRead();
+    }
 }

public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java

@@ -32,7 +32,6 @@ import org.testng.annotations.Test;
 
 import java.util.Arrays;
 
-@Test(enabled = false)
 public class GATKKeyIntegrationTest extends WalkerTest {
 
     public static final String BASE_COMMAND = String.format("-T PrintReads -R %s -I %s -o %%s",

public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyUnitTest.java

@@ -27,19 +27,24 @@ package org.broadinstitute.sting.utils.crypt;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.testng.Assert;
+import org.testng.SkipException;
 import org.testng.annotations.Test;
+import org.testng.Assert;
 
 import java.io.File;
 import java.security.KeyPair;
 import java.security.PrivateKey;
 import java.security.PublicKey;
 
-@Test(enabled = false)
 public class GATKKeyUnitTest extends BaseTest {
 
     @Test
     public void testCreateGATKKeyUsingMasterKeyPair() {
+        if ( gatkPrivateKeyExistsButReadPermissionDenied() ) {
+            throw new SkipException(String.format("Skipping test %s because we do not have permission to read the GATK private key",
+                                    "testCreateGATKKeyUsingMasterKeyPair"));
+        }
+
         PrivateKey masterPrivateKey = CryptUtils.loadGATKMasterPrivateKey();
         PublicKey masterPublicKey = CryptUtils.loadGATKMasterPublicKey();
 
@@ -50,6 +55,11 @@ public class GATKKeyUnitTest extends BaseTest {
 
     @Test
     public void testCreateGATKKeyUsingMasterPrivateKeyAndDistributedPublicKey() {
+        if ( gatkPrivateKeyExistsButReadPermissionDenied() ) {
+            throw new SkipException(String.format("Skipping test %s because we do not have permission to read the GATK private key",
+                                    "testCreateGATKKeyUsingMasterPrivateKeyAndDistributedPublicKey"));
+        }
+
         PrivateKey masterPrivateKey = CryptUtils.loadGATKMasterPrivateKey();
         PublicKey distributedPublicKey = CryptUtils.loadGATKDistributedPublicKey();
 
@@ -83,8 +93,7 @@ public class GATKKeyUnitTest extends BaseTest {
         KeyPair keyPair = CryptUtils.generateKeyPair();
 
         // Email addresses cannot contain the NUL byte, since it's used as a sectional delimiter in the key file:
-        GATKKey key = new GATKKey(CryptUtils.loadGATKMasterPrivateKey(), CryptUtils.loadGATKDistributedPublicKey(),
+        GATKKey key = new GATKKey(keyPair.getPrivate(), keyPair.getPublic(), emailAddressWithNulByte);
-                                  emailAddressWithNulByte);
     }
 
     @Test
@@ -111,4 +120,9 @@ public class GATKKeyUnitTest extends BaseTest {
 
         GATKKey key = new GATKKey(CryptUtils.loadGATKDistributedPublicKey(), nonExistentFile);
     }
+
+    private boolean gatkPrivateKeyExistsButReadPermissionDenied() {
+        File gatkPrivateKey = new File(CryptUtils.GATK_MASTER_PRIVATE_KEY_FILE);
+        return gatkPrivateKey.exists() && ! gatkPrivateKey.canRead();
+    }
 }