From 2bda7f9b2faf29b2bdb24f81c1b94921b06c28d0 Mon Sep 17 00:00:00 2001
From: Louis Bergelson <louisb@broadinstitute.org>
Date: Tue, 21 Mar 2023 11:21:09 -0400
Subject: [PATCH] Incorporate build.gradle changes from gvs (#8249)

* Incorporate the necessary build and dependency changes to support GVS
* Adds Apache Orc as a dependency.
---
 build.gradle | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/build.gradle b/build.gradle
index 26d7e0a4fc3..cbc59ced5f6 100644
--- a/build.gradle
+++ b/build.gradle
@@ -64,6 +64,7 @@ final hadoopVersion = System.getProperty('hadoop.version', '3.3.1')
 final disqVersion = System.getProperty('disq.version','0.3.6')
 final genomicsdbVersion = System.getProperty('genomicsdb.version','1.4.4')
 final bigQueryVersion = System.getProperty('bigQuery.version', '2.9.0')
+final bigQueryStorageVersion = System.getProperty('bigQueryStorage.version', '2.9.1')
 final guavaVersion = System.getProperty('guava.version', '31.0.1-jre')
 final log4j2Version = System.getProperty('log4j2Version', '2.17.1')
 final testNGVersion = '7.0.0'
@@ -252,7 +253,7 @@ dependencies {
     implementation(googleCloudNioDependency)
 
     implementation 'com.google.cloud:google-cloud-bigquery:' + bigQueryVersion
-    implementation 'com.google.cloud:google-cloud-bigquerystorage:2.9.1'
+    implementation 'com.google.cloud:google-cloud-bigquerystorage:' + bigQueryStorageVersion
 
     implementation "gov.nist.math.jama:gov.nist.math.jama:1.1.1"
 
@@ -323,6 +324,7 @@ dependencies {
     implementation('org.apache.hadoop:hadoop-client:' + hadoopVersion) // should be a 'provided' dependency
     implementation('com.github.jsr203hadoop:jsr203hadoop:1.0.3')
 
+    implementation('org.apache.orc:orc:1.6.5')
     implementation('de.javakaffee:kryo-serializers:0.45') {
         exclude module: 'kryo' // use Spark's version
     }
@@ -348,7 +350,7 @@ dependencies {
 
     // Required for COSMIC Funcotator data source:
     implementation 'org.xerial:sqlite-jdbc:3.36.0.3'
-    
+
     // natural sort
     implementation('net.grey-panther:natural-comparator:1.1')
     implementation('com.fasterxml.jackson.module:jackson-module-scala_2.12:2.9.8')
@@ -615,6 +617,7 @@ task collectBundleIntoDir(type: Copy) {
 
 task bundle(type: Zip) {
     dependsOn collectBundleIntoDir
+    zip64 true
 
     archiveBaseName = project.name + "-" + project.version
     destinationDirectory = file("$buildDir")