From e4a539ca3ea2b8f7f4b9bdef243e7498347bb4bf Mon Sep 17 00:00:00 2001
From: Frank Austin Nothaft <fnothaft@alumni.stanford.edu>
Date: Wed, 24 Aug 2016 08:32:19 -0700
Subject: [PATCH] [ADAM-1093] Move to support Spark 2.0.0.

Relies on https://github.com/bigdatagenomics/utils/pull/78. Resolves #1093:

* Clean up logging in VariantContextRDD
* Add move_to_spark_2.sh script and CI hooks
---
 .../bdgenomics/adam/rdd/variation/VariantContextRDD.scala | 2 +-
 pom.xml                                                   | 2 +-
 scripts/jenkins-test                                      | 7 +++++++
 scripts/move_to_spark_2.sh                                | 8 ++++++++
 4 files changed, 17 insertions(+), 2 deletions(-)
 create mode 100755 scripts/move_to_spark_2.sh

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variation/VariantContextRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variation/VariantContextRDD.scala
index a525891846..11c29da4f3 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variation/VariantContextRDD.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variation/VariantContextRDD.scala
@@ -18,7 +18,6 @@
 package org.bdgenomics.adam.rdd.variation
 
 import org.apache.hadoop.io.LongWritable
-import org.apache.spark.Logging
 import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.converters.VariantContextConverter
 import org.bdgenomics.adam.models.{
@@ -28,6 +27,7 @@ import org.bdgenomics.adam.models.{
 }
 import org.bdgenomics.adam.rdd.MultisampleGenomicRDD
 import org.bdgenomics.formats.avro.Sample
+import org.bdgenomics.utils.misc.Logging
 import org.bdgenomics.utils.cli.SaveArgs
 import org.seqdoop.hadoop_bam._
 
diff --git a/pom.xml b/pom.xml
index 6306bbe26f..028db07497 100644
--- a/pom.xml
+++ b/pom.xml
@@ -28,7 +28,7 @@
     <hadoop-bam.version>7.6.0</hadoop-bam.version>
     <slf4j.version>1.7.21</slf4j.version>
     <bdg-formats.version>0.9.0</bdg-formats.version>
-    <bdg-utils.version>0.2.7</bdg-utils.version>
+    <bdg-utils.version>0.2.8-SNAPSHOT</bdg-utils.version>
     <htsjdk.version>2.5.0</htsjdk.version>
   </properties>
 
diff --git a/scripts/jenkins-test b/scripts/jenkins-test
index edff72a826..008a4867da 100755
--- a/scripts/jenkins-test
+++ b/scripts/jenkins-test
@@ -28,6 +28,13 @@ then
     exit 1
 fi
 
+# are we testing for spark 2.0.0? if so, we need to rewrite our poms first
+if [ ${SPARK_VERSION} == 2.0.0 ];
+then
+        echo "Rewriting POM.xml files for Scala 2.10."
+        ./scripts/move_to_spark_2.sh
+fi
+
 # are we testing for scala 2.11? if so, we need to rewrite our poms to 2.11 first
 if [ ${SCALAVER} == 2.11 ];
 then
diff --git a/scripts/move_to_spark_2.sh b/scripts/move_to_spark_2.sh
new file mode 100755
index 0000000000..5b829e49cc
--- /dev/null
+++ b/scripts/move_to_spark_2.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+set +x
+
+find . -name "pom.xml" -exec sed -e "/utils-/ s/_2.10/-spark2_2.10/g" \
+    -e "/adam-/ s/_2.10/-spark2_2.10/g" \
+    -e "/spark.version/ s/1.6.1/2.0.0/g" \
+    -i .spark2.bak '{}' \;