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rm -rf ${ADAM_MVN_TMP_DIR}
+ rm -rf /tmp/adamTestMvnrsrQsaT

find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${ADAM_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \
    {} \;
+ find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/adamTestMvnrsrQsaT:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

if test -n "$(git status --porcelain)"
then
    echo "Applying move_to_xyz script marred a pom.xml file."
    echo "Exiting..."
    exit 1
fi
git status --porcelain
++ git status --porcelain
+ test -n ''

# run integration tests
# prebuilt spark distributions are scala 2.11 for spark 2.x
if [[ ( ${SPARK_VERSION} == 2.3.3 && ${SCALAVER} == 2.11 ) ]];
then

    # make a temp directory
    ADAM_TMP_DIR=$(mktemp -d -t adamTestXXXXXXX)

    # Just to be paranoid.. use a directory internal to the ADAM_TMP_DIR
    ADAM_TMP_DIR=$ADAM_TMP_DIR/deleteMePleaseThisIsNoLongerNeeded
    mkdir $ADAM_TMP_DIR

    # set the TMPDIR envar, which is used by python to choose where to make temp directories
    export TMPDIR=${ADAM_TMP_DIR}

    pushd $PROJECT_ROOT

    # Copy the jar into our temp space for testing
    cp -r . $ADAM_TMP_DIR
    popd

    pushd $ADAM_TMP_DIR

    # what hadoop version are we on? format string for downloading spark assembly
    if [[ $HADOOP_VERSION =~ ^2\.6 ]]; then
        HADOOP=hadoop2.6
    elif [[ $HADOOP_VERSION =~ ^2\.7 ]]; then
        HADOOP=hadoop2.7
    else
        echo "Unknown Hadoop version."
        exit 1
    fi

    # set spark artifact string for downloading assembly
    SPARK=spark-${SPARK_VERSION}
    
    # download prepackaged spark assembly
    curl \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-${HADOOP}.tgz" \
        -o ${SPARK}-bin-${HADOOP}.tgz

    tar xzvf ${SPARK}-bin-${HADOOP}.tgz
    export SPARK_HOME=${ADAM_TMP_DIR}/${SPARK}-bin-${HADOOP}
    
    # set the path to the adam submit script
    ADAM=./bin/adam-submit

    # test running adam-shell
    ./bin/adam-shell -i scripts/jenkins-test-adam-shell.scala
    
    # add pyspark to the python path
    PY4J_ZIP="$(ls -1 "${SPARK_HOME}/python/lib" | grep py4j)"
    export PYTHONPATH=${SPARK_HOME}/python:${SPARK_HOME}/python/lib/${PY4J_ZIP}:${PYTHONPATH}

    # put adam jar on the pyspark path
    ASSEMBLY_DIR="${ADAM_TMP_DIR}/adam-assembly/target"
    ASSEMBLY_JAR="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam[0-9A-Za-z\_\.-]*\.jar$" | grep -v javadoc | grep -v sources || true)"
    export PYSPARK_SUBMIT_ARGS="--jars ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} --driver-class-path ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} pyspark-shell"

    # create a conda environment for python build, if necessary
    pythons=( 2.7 3.6 )

    for python in ${pythons[*]}
    do
    	uuid=$(uuidgen)
        conda create -y -q -n adam-build-${uuid} python=${python}
        source activate adam-build-${uuid}

        # prepare adam python
        pushd adam-python
        make prepare
        popd
    	
    	# we only support SparkR on Spark 2.x
        if [ ${SPARK_VERSION} == 2.3.3 ];
    	then
    	    
    	    # make a directory to install SparkR into, and set the R user libs path
    	    export R_LIBS_USER=${SPARK_HOME}/local_R_libs
    	    mkdir -p ${R_LIBS_USER}
    	    R CMD INSTALL \
    	      -l ${R_LIBS_USER} \
    	      ${SPARK_HOME}/R/lib/SparkR/
    	    
    	    export SPARKR_SUBMIT_ARGS="--jars ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} --driver-class-path ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} sparkr-shell"
    	    
                # we can run the python build, now that we have a spark executable
    	    # -DskipTests appears to skip the python/r tests?
    	    mvn -U \
    		-P python,r,distribution \
    		package \
    		-Dsuites=select.no.suites\* \
    		-Dhadoop.version=${HADOOP_VERSION} \
    		-Dspark.version=${SPARK_VERSION}

    	    # make sure that the distribution package contains an egg
    	    # if no assembly jar is found, this will exit with code 1 and fail the build
    	    tar tzvf adam-distribution/target/adam-distribution*-bin.tar.gz | \
    		grep bdgenomics.adam | \
    		grep egg
    	fi
    	
    	# run pyadam test
    	./bin/pyadam < scripts/jenkins-test-pyadam.py
    	
    	# deactivate and remove the conda env
    	source deactivate
    	conda remove -y -n adam-build-${uuid} --all

    	# copy python targets back
    	cp -r adam-python/target ${PROJECT_ROOT}/adam-python/

    	# clean after each python version
      pushd adam-python
      make clean
    	make clean_sdist
      popd

    done
	
    # define filenames
    BAM=mouse_chrM.bam
    READS=${BAM}.reads.adam
    SORTED_READS=${BAM}.reads.sorted.adam
    FRAGMENTS=${BAM}.fragments.adam
    
    # fetch our input dataset
    echo "Fetching BAM file"
    rm -rf ${BAM}
    wget -q https://s3.amazonaws.com/bdgenomics-test/${BAM}

    # once fetched, convert BAM to ADAM
    echo "Converting BAM to ADAM read format"
    rm -rf ${READS}
    ${ADAM} transformAlignments ${BAM} ${READS}

    # then, sort the BAM
    echo "Converting BAM to ADAM read format with sorting"
    rm -rf ${SORTED_READS}
    ${ADAM} transformAlignments -sort_reads ${READS} ${SORTED_READS}

    # convert the reads to fragments to re-pair the reads
    echo "Converting read file to fragments"
    rm -rf ${FRAGMENTS}
    ${ADAM} transformFragments -load_as_reads ${READS} ${FRAGMENTS}

    # test that printing works
    echo "Printing reads and fragments"
    ${ADAM} print ${READS} 1>/dev/null 2>/dev/null
    ${ADAM} print ${FRAGMENTS} 1>/dev/null 2>/dev/null

    # run flagstat to verify that flagstat runs OK
    echo "Printing read statistics"
    ${ADAM} flagstat -print_metrics ${READS}
    rm -rf ${ADAM_TMP_DIR}
    popd
    
    # test that the source is formatted correctly
    # we had modified the poms to add a temp dir, so back out that modification first
    pushd ${PROJECT_ROOT}
    ./scripts/format-source
    if test -n "$(git status --porcelain)"
    then
        echo "Please run './scripts/format-source'"
        exit 1
    fi
    popd    
fi
+ [[ 2.3.2 == 2.3.3 ]]

echo
+ echo

echo "All the tests passed"
+ echo 'All the tests passed'
All the tests passed
echo
+ echo

Recording test results
Publishing Scoverage XML and HTML report...
Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/e03b0308ee79f9443c7c2c339b07f84964da5e49
Finished: SUCCESS