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 1/2] 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

From a779840fac6fd9d17eff65ec10fd935796a87a3c Mon Sep 17 00:00:00 2001
From: Alyssa Morrow <akmorrow@berkeley.edu>
Date: Mon, 1 Jul 2019 16:49:28 -0700
Subject: [PATCH 2/2] mango docker now runs with nodejs 8.X and Spark 2.4.3

---
 mango/Makefile           |  2 +-
 mango/build/Dockerfile   | 19 ++++++++-----------
 mango/runtime/Dockerfile | 27 ++++++++++++++-------------
 mango/test.py            |  2 +-
 4 files changed, 24 insertions(+), 26 deletions(-)

diff --git a/mango/Makefile b/mango/Makefile
index 07a06b7..4811f4e 100644
--- a/mango/Makefile
+++ b/mango/Makefile
@@ -7,7 +7,7 @@ build_tool = runtime-container.DONE
 build_number ?= none
 git_commit ?= $(shell git log --pretty=oneline -n 1 -- ../mango | cut -f1 -d " ")
 name = quay.io/ucsc_cgl/mango
-tag = 0.0.1--${git_commit}
+tag = 0.0.3--${git_commit}
 
 
 # Steps
diff --git a/mango/build/Dockerfile b/mango/build/Dockerfile
index f5e35b1..2125f79 100644
--- a/mango/build/Dockerfile
+++ b/mango/build/Dockerfile
@@ -13,21 +13,18 @@ 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
+# install curl to get nodejs script
+RUN apt-get update && apt-get install -y curl
+
+# get nodejs v6.X
+RUN curl -sL https://deb.nodesource.com/setup_8.x | bash -
+
+RUN apt-get install -y nodejs
 
 # build mango
 WORKDIR /home/mango
+RUN git checkout c85b5d2178dbf7ec84cee20c56c57493524d510e # 0.0.3-SNAPSHOT
 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 59c34b9..5694e48 100644
--- a/mango/runtime/Dockerfile
+++ b/mango/runtime/Dockerfile
@@ -15,7 +15,6 @@ 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"
@@ -26,16 +25,22 @@ ENV PYTHONPATH ${SPARK_HOME}/python:${SPARK_HOME}/python/lib/py4j-0.10.4-src.zip
 #environment variables PYSPARK_PYTHON and PYSPARK_DRIVER_PYTHON
 ENV PYSPARK_PYTHON /usr/bin/python3
 
-# Install make and pip/python dependencies
 RUN apt-get update && apt-get install -y \
-  git \
-  make \
-  python3.5 \
-  python3-pip \
-  npm \
-  nodejs \
-  python-tk
+   git \
+   make \
+   python3.5 \
+   python3-pip \
+   python-tk \
+   curl
+
+# get nodejs v8.X
+RUN apt-cache policy nodejs
+RUN curl -sL https://deb.nodesource.com/setup_8.x | bash -
+RUN apt-cache policy nodejs
+
 
+# Install make and pip/python dependencies
+RUN apt-get install -y nodejs
 
 # alias python to python3.6
 RUN alias pip=pip3
@@ -47,13 +52,9 @@ RUN echo '#!/bin/bash\npython3 "$@"' > /usr/bin/python && \
 RUN echo '#!/bin/bash\npip3 "$@"' > /usr/bin/pip && \
     chmod +x /usr/bin/pip
 
-RUN pip
-RUN ln -s /usr/bin/nodejs /usr/bin/node
-
 # set permissions for running npm. Required for mango-viz
 RUN npm config set bdgenomics.mango.pileup:unsafe-perm
 
-
 # prepare mango-viz and mango-python
 WORKDIR /opt/cgl-docker-lib/mango/mango-python
 RUN make prepare && make develop
diff --git a/mango/test.py b/mango/test.py
index eeadaea..ef7972d 100644
--- a/mango/test.py
+++ b/mango/test.py
@@ -10,7 +10,7 @@ class TestMango(unittest.TestCase):
     def test_docker_call_browser(self):
         out, err = check_docker_output(tool='quay.io/ucsc_cgl/mango')
         self.assertTrue('Using spark-submit=' in out)
-        self.assertTrue('Argument "reference" is required' in out)
+        self.assertTrue('Argument "genome" is required' in out)
 
     def test_docker_call_notebook(self):
         out, err = check_docker_output(tool='--entrypoint=/opt/cgl-docker-lib/mango/bin/mango-notebook quay.io/ucsc_cgl/mango')