From a7d1904c63e7729b3904b09510639531024b4d73 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Wed, 9 Jul 2014 23:12:56 +0800
Subject: [PATCH] Appending to md5db in the gatkdir, with additional logging.

---
 public/external-example/pom.xml               |  8 ++++++++
 public/gatk-root/pom.xml                      | 20 +++++++++++++++++++
 .../broadinstitute/gatk/utils/BaseTest.java   |  3 +++
 .../org/broadinstitute/gatk/utils/MD5DB.java  | 20 +++++++++++++++----
 4 files changed, 47 insertions(+), 4 deletions(-)

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 @@
                             <includes>
                                 <include>**/*UnitTest.class</include>
                             </includes>
+                            <systemPropertyVariables>
+                                <gatkdir>${gatk.basedir}</gatkdir>
+                                <testType>unit</testType>
+                            </systemPropertyVariables>
                         </configuration>
                     </execution>
                 </executions>
@@ -236,6 +240,10 @@
                             <includes>
                                 <include>**/*IntegrationTest.class</include>
                             </includes>
+                            <systemPropertyVariables>
+                                <gatkdir>${gatk.basedir}</gatkdir>
+                                <testType>integrationtest</testType>
+                            </systemPropertyVariables>
                         </configuration>
                     </execution>
                 </executions>
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 @@
                                 <includes>
                                     <include>**/*UnitTest.class</include>
                                 </includes>
+                                <systemPropertyVariables>
+                                    <gatkdir>${gatk.basedir}</gatkdir>
+                                    <testType>unit</testType>
+                                </systemPropertyVariables>
                             </configuration>
                         </execution>
                     </executions>
@@ -474,6 +478,10 @@
                                 <includes>
                                     <include>**/*IntegrationTest.class</include>
                                 </includes>
+                                <systemPropertyVariables>
+                                    <gatkdir>${gatk.basedir}</gatkdir>
+                                    <testType>integration</testType>
+                                </systemPropertyVariables>
                             </configuration>
                         </execution>
                         <execution>
@@ -491,6 +499,10 @@
                                 <includes>
                                     <include>**/*QueueTest.class</include>
                                 </includes>
+                                <systemPropertyVariables>
+                                    <gatkdir>${gatk.basedir}</gatkdir>
+                                    <testType>queue</testType>
+                                </systemPropertyVariables>
                             </configuration>
                         </execution>
                         <execution>
@@ -507,6 +519,10 @@
                                 <includes>
                                     <include>**/*LargeScaleTest.class</include>
                                 </includes>
+                                <systemPropertyVariables>
+                                    <gatkdir>${gatk.basedir}</gatkdir>
+                                    <testType>largescale</testType>
+                                </systemPropertyVariables>
                             </configuration>
                         </execution>
                         <execution>
@@ -523,6 +539,10 @@
                                 <includes>
                                     <include>**/*KnowledgeBaseTest.class</include>
                                 </includes>
+                                <systemPropertyVariables>
+                                    <gatkdir>${gatk.basedir}</gatkdir>
+                                    <testType>knowledgebasetests</testType>
+                                </systemPropertyVariables>
                             </configuration>
                         </execution>
                     </executions>
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() {