From 6ec1e613a263ba1af19448f1873ed537e0515258 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Thu, 31 Jan 2013 11:40:40 -0500
Subject: [PATCH] Move AWS keys to a resources subdirectory within the
 phonehome package

Resources must be in a subdirectory called "resources" in the package
hierarchy to be picked up by the packaging system. Adding each resource
manually to the jars in build.xml does not cause the resource to be
added to the standalone GATK jar when we package the GATK, so it's best
to always use this convention.
---
 build.xml                                           |   3 ---
 .../sting/gatk/phonehome/GATKRunReport.java         |   4 ++--
 .../phonehome/{ => resources}/GATK_AWS_access.key   |   0
 .../phonehome/{ => resources}/GATK_AWS_secret.key   | Bin
 4 files changed, 2 insertions(+), 5 deletions(-)
 rename public/java/src/org/broadinstitute/sting/gatk/phonehome/{ => resources}/GATK_AWS_access.key (100%)
 rename public/java/src/org/broadinstitute/sting/gatk/phonehome/{ => resources}/GATK_AWS_secret.key (100%)

diff --git a/build.xml b/build.xml
index 1e88bb400..e92e41c10 100644
--- a/build.xml
+++ b/build.xml
@@ -708,9 +708,6 @@
                 <include name="**/sting/gatk/**/*.R"/>
                 <include name="**/sting/alignment/**/*.R"/>
             </fileset>
-            <fileset dir="${java.public.source.dir}">
-                <include name="**/phonehome/*.key"/>
-            </fileset>
             <fileset dir="${key.dir}">
                 <include name="**/*.key"/>
             </fileset>
diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
index 8ef24d373..12e87f613 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
@@ -350,7 +350,7 @@ public class GATKRunReport {
      * @return a non-null AWS access key for the GATK user
      */
     protected static String getAWSAccessKey() {
-        return getAWSKey("GATK_AWS_access.key");
+        return getAWSKey("resources/GATK_AWS_access.key");
     }
 
     /**
@@ -358,7 +358,7 @@ public class GATKRunReport {
      * @return a non-null AWS secret key for the GATK user
      */
     protected static String getAWSSecretKey() {
-        return getAWSKey("GATK_AWS_secret.key");
+        return getAWSKey("resources/GATK_AWS_secret.key");
     }
 
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATK_AWS_access.key b/public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/phonehome/GATK_AWS_access.key
rename to public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key
diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATK_AWS_secret.key b/public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/phonehome/GATK_AWS_secret.key
rename to public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key