From 61b89e236ab13b073a3572e983b6c730efd5331e Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Tue, 20 Sep 2011 00:14:35 -0400
Subject: [PATCH] To work around potential problem with invalid javax.mail
 1.4.1 in ivy cache, added explicit javax.mail 1.4.4 along with build.xml code
 to remove 1.4.1.

---
 build.xml | 8 ++++++++
 ivy.xml   | 6 ++----
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/build.xml b/build.xml
index e5ad9daf0..1f26e7b7a 100644
--- a/build.xml
+++ b/build.xml
@@ -163,6 +163,14 @@
       <!-- Remove old versions of ivy jars AFTER the ivy:retrieve has been class loaded. -->
       <delete file="${ivy.jar.dir}/ivy-2.0.0.jar"/>
       <delete file="${ivy.jar.dir}/ivy-2.2.0-rc1.jar"/>
+      <!--
+         An old versions of the ivy-1.4.1.xml does not contain /ivy-module/configuration/conf/@name="compile".
+         Easier to upgrade to 1.4.4 than try to deal with xmlproperty and conditional deletion in ant.
+         Just in case we remove explicit 1.4.4 and go back to 1.4.1, try to clean out the file for now.
+        -->
+      <delete file="${ivy.home}/cache/javax.mail/mail/ivy-1.4.1.xml"/>
+      <delete file="${ivy.home}/cache/javax.mail/mail/ivydata-1.4.1.properties"/>
+      <delete file="${ivy.home}/cache/javax.mail/mail/jars/mail-1.4.1.jar"/>
     </target>
 
     <target name="init.buildall">
diff --git a/ivy.xml b/ivy.xml
index 115f4062a..f90b9a010 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -15,10 +15,8 @@
     <!-- Tribble -->
     <dependency org="org.broad" name="tribble" rev="latest.integration"/>
 
-    <dependency org="log4j" name="log4j" rev="1.2.15">
-      <!-- Don't include javax.mail here in default, only used in scala->default by commons-email -->
-      <exclude org="javax.mail" />
-    </dependency>
+    <dependency org="log4j" name="log4j" rev="1.2.15"/>
+    <dependency org="javax.mail" name="mail" rev="1.4.4"/>
     <dependency org="colt" name="colt" rev="1.2.0"/>
     <dependency org="jboss" name="javassist" rev="3.7.ga"/>
     <dependency org="org.simpleframework" name="simple-xml" rev="2.0.4"/>