diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml
index c4c8a691c..fea1e93e3 100644
--- a/public/external-example/pom.xml
+++ b/public/external-example/pom.xml
@@ -204,6 +204,10 @@
**/*UnitTest.class
+
+ ${gatk.basedir}
+ unit
+
@@ -236,6 +240,10 @@
**/*IntegrationTest.class
+
+ ${gatk.basedir}
+ integrationtest
+
diff --git a/public/gatk-root/pom.xml b/public/gatk-root/pom.xml
index b0adc4cc9..a7e720acb 100644
--- a/public/gatk-root/pom.xml
+++ b/public/gatk-root/pom.xml
@@ -424,6 +424,10 @@
**/*UnitTest.class
+
+ ${gatk.basedir}
+ unit
+
@@ -474,6 +478,10 @@
**/*IntegrationTest.class
+
+ ${gatk.basedir}
+ integration
+
@@ -491,6 +499,10 @@
**/*QueueTest.class
+
+ ${gatk.basedir}
+ queue
+
@@ -507,6 +519,10 @@
**/*LargeScaleTest.class
+
+ ${gatk.basedir}
+ largescale
+
@@ -523,6 +539,10 @@
**/*KnowledgeBaseTest.class
+
+ ${gatk.basedir}
+ knowledgebasetests
+
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
index 1c78574df..0f73d9002 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/BaseTest.java
@@ -88,7 +88,10 @@ public abstract class BaseTest {
public static final Logger logger = CommandLineUtils.getStingLogger();
private static final String CURRENT_DIRECTORY = System.getProperty("user.dir");
+ public static final String gatkDirectory = System.getProperty("gatkdir", CURRENT_DIRECTORY) + "/";
public static final String baseDirectory = System.getProperty("basedir", CURRENT_DIRECTORY) + "/";
+ public static final String testType = System.getProperty("testType"); // May be null
+ public static final String testTypeSubDirectory = testType == null ? "" : ("/" + testType); // May be empty
public static final String hg18Reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta";
public static final String hg19Reference = "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta";
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
index 218906fdd..0313ad3e9 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/MD5DB.java
@@ -49,7 +49,7 @@ public class MD5DB {
*/
private static final int MAX_RECORDS_TO_READ = 1000000;
private static final int MAX_RAW_DIFFS_TO_SUMMARIZE = -1;
- public static final String LOCAL_MD5_DB_DIR = BaseTest.baseDirectory + "integrationtests";
+ public static final String LOCAL_MD5_DB_DIR = BaseTest.gatkDirectory + "integrationtests";
public static final String GLOBAL_MD5_DB_DIR = "/humgen/gsa-hpprojects/GATK/data/integrationtests";
// tracking and emitting a data file of origina and new md5s
@@ -65,14 +65,26 @@ public class MD5DB {
ensureMd5DbDirectory();
- logger.debug("Creating md5 mismatch db at " + MD5MismatchesFile);
+ boolean exists = MD5MismatchesFile.exists();
+
+ if (!exists) {
+ logger.warn("Creating md5 mismatch db at " + MD5MismatchesFile);
+ } else {
+ logger.warn("Updating md5 mismatch db at " + MD5MismatchesFile);
+ }
+ logger.warn("GATK directory: " + BaseTest.gatkDirectory);
+ logger.warn("Base directory: " + BaseTest.baseDirectory);
+ logger.warn("Test type: " + BaseTest.testType);
+
try {
- md5MismatchStream = new PrintStream(new FileOutputStream(MD5MismatchesFile));
- md5MismatchStream.printf("%s\t%s\t%s%n", "expected", "observed", "test");
+ md5MismatchStream = new PrintStream(new FileOutputStream(MD5MismatchesFile, true));
} catch ( FileNotFoundException e ) {
throw new ReviewedGATKException("Failed to open md5 mismatch file", e);
}
+ if (!exists) {
+ md5MismatchStream.printf("%s\t%s\t%s%n", "expected", "observed", "test");
+ }
}
public void close() {