From b3aa6f0e6aeb8d6fe697e5994020fb97463a1376 Mon Sep 17 00:00:00 2001
From: akmorrow13 <akmorrow@berkeley.edu>
Date: Mon, 1 Jul 2019 21:03:36 +0000
Subject: [PATCH] update Spark version to 2.4.3

---
 mango/build/Dockerfile            | 15 +++++++++++++--
 mango/runtime/Dockerfile          |  4 ++++
 spark-and-maven/build/download.sh |  2 +-
 3 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/mango/build/Dockerfile b/mango/build/Dockerfile
index 9c2aeca..f5e35b1 100644
--- a/mango/build/Dockerfile
+++ b/mango/build/Dockerfile
@@ -13,10 +13,21 @@ WORKDIR /home
 RUN git clone https://github.com/bigdatagenomics/mango.git
 ENV MAVEN_OPTS "-Xmx2g"
 
+RUN apt-get update && apt-get install -y \
+  unzip \
+  npm \
+  nodejs
+
 # build mango
 WORKDIR /home/mango
-
-RUN /opt/apache-maven-3.3.9/bin/mvn package -DskipTests
+RUN /opt/apache-maven-3.3.9/bin/mvn clean package -DskipTests
+RUN ls /home/mango/mango-cli/src/main/webapp/resources
+
+# where is node_modules?
+RUN mkdir /home/mango/mango-assembly/target/test
+WORKDIR /home/mango/mango-assembly/target
+RUN unzip mango-assembly-0.0.3-SNAPSHOT.jar -d /home/mango/mango-assembly/target/test
+RUN ls test/resources/node_modules/pileup
 
 # remove git libraries to avoid permission errors when copying
 RUN rm -rf /home/mango/.git
diff --git a/mango/runtime/Dockerfile b/mango/runtime/Dockerfile
index 5d616e4..59c34b9 100644
--- a/mango/runtime/Dockerfile
+++ b/mango/runtime/Dockerfile
@@ -6,6 +6,8 @@ MAINTAINER Alyssa Morrow, akmorrow@berkeley.edu
 RUN mkdir /opt/cgl-docker-lib
 COPY mango /opt/cgl-docker-lib/mango
 
+WORKDIR /opt/cgl-docker-lib/mango
+
 # copy spark
 COPY apache-spark /opt/cgl-docker-lib/apache-spark
 
@@ -13,6 +15,8 @@ ENV SPARK_HOME /opt/cgl-docker-lib/apache-spark
 
 # put mango jar on the pyspark path for packaging
 ENV ASSEMBLY_DIR /opt/cgl-docker-lib/mango/mango-assembly/target
+RUN ls /opt/cgl-docker-lib/mango/mango-cli/src/main/webapp/resources
+
 ENV ASSEMBLY_JAR "$(ls -1 "$ASSEMBLY_DIR" | grep "^mango-assembly[0-9A-Za-z\_\.-]*\.jar$" | grep -v javadoc | grep -v sources || true)"
 ENV PYSPARK_SUBMIT_ARGS "--jars ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} --driver-class-path ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} pyspark-shell"
 
diff --git a/spark-and-maven/build/download.sh b/spark-and-maven/build/download.sh
index ea61773..0d9fc96 100755
--- a/spark-and-maven/build/download.sh
+++ b/spark-and-maven/build/download.sh
@@ -7,7 +7,7 @@ mirror=$(python -c "from urllib2 import urlopen; import json; print json.load( u
 
 # pull down spark
 mkdir /opt/apache-spark
-curl ${mirror}spark/spark-2.3.2/spark-2.3.2-bin-hadoop2.7.tgz \
+curl ${mirror}spark/spark-2.4.3/spark-2.4.3-bin-hadoop2.7.tgz \
   | tar --strip-components=1 -xzC /opt/apache-spark
 
 # we rely on apache maven > 3.1.1 to build ADAM, so we can't use the