[ADAM-1008] Modify jenkins-test script to support Java 8 build.

Resolves #1008. As per discussion with @shaneknapp, it is preferable to support builds across Java versions by manually setting JAVA_HOME in a shell script run inside of Jenkins. This is due to certain configuration limitations inside of Jenkins. Currently, we are doing this via a script tracked inside of Jenkins. I would rather roll all of that config into the ./scripts/jenkins-test script so that we have revision control, etc.
bigdatagenomics · Apr 28, 2016 · a9cc8f3 · a9cc8f3
1 parent 6b28217
commit a9cc8f3
Showing 1 changed file with 85 additions and 59 deletions.
diff --git a/scripts/jenkins-test b/scripts/jenkins-test
@@ -2,81 +2,107 @@
 
 set -e -x
 
+export JAVA_HOME=/usr/java/jdk1.8.0_60
+export PATH=${JAVA_HOME}/bin/:${PATH}
+
+if [ ${SCALAVER} == 2.11 ];
+then
+        echo "Rewriting POM.xml files for Scala 2.10."
+        ./scripts/move_to_scala_2.11.sh
+fi
+
+which mvn
+
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 PROJECT_ROOT="$DIR/.."
 
 VERSION="$(grep "<version>" "$PROJECT_ROOT/pom.xml"  | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g')"
 echo "Testing ADAM version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}"
-
 export MAVEN_OPTS="-Xmx1536m -XX:MaxPermSize=1g"
-mvn test -P distribution -Dnetworkconnected -Dhadoop.version="${HADOOP_VERSION}" -Dspark.version="${SPARK_VERSION}"
 
-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 "$ADAM_TMP_DIR"
+# first, build the sources and run the unit tests
+mvn clean package \
+    -Dhadoop.version=${HADOOP_VERSION} \
+    -Dspark.version=${SPARK_VERSION}
+
+# if those pass, build the distribution package and the integration tests
+mvn test \
+    -P distribution \
+    -Dnetworkconnected \
+    -Dhadoop.version="${HADOOP_VERSION}" \
+    -Dspark.version="${SPARK_VERSION}"
+
+if [ ${SCALAVER} == 2.10 ];
+then
 
-pushd "$PROJECT_ROOT"
-# Copy the jar into our temp space for testing
-cp -r . "$ADAM_TMP_DIR"
-popd
+    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"
 
-export SPARK_DRIVER_MEMORY=8g
+    pushd "$PROJECT_ROOT"
+    # Copy the jar into our temp space for testing
+    cp -r . "$ADAM_TMP_DIR"
+    popd
 
-pushd "$ADAM_TMP_DIR"
+    export SPARK_DRIVER_MEMORY=8g
 
+    pushd "$ADAM_TMP_DIR"
 
-if [[ $HADOOP_VERSION =~ ^1\.0 ]]; then
-    HADOOP=hadoop1
-elif [[ $HADOOP_VERSION =~ ^2\.6 ]]; then
-    HADOOP=hadoop2.6
-elif [[ $HADOOP_VERSION =~ ^2\.3 ]]; then
-    HADOOP=hadoop2.3
-else
-    echo "Unknown Hadoop version."
-    exit 1
-fi
 
-SPARK="spark-${SPARK_VERSION}"
-
-wget -q http://d3kbcqa49mib13.cloudfront.net/${SPARK}-bin-${HADOOP}.tgz
-tar xzvf ${SPARK}-bin-${HADOOP}.tgz
-export SPARK_HOME="${ADAM_TMP_DIR}/${SPARK}-bin-${HADOOP}"
-
-ADAM="./bin/adam-submit"
-
-echo "Fetching BAM file"
-BAM=mouse_chrM.bam
-READS="$BAM".reads.adam
-SORTED_READS="$BAM".reads.sorted.adam
-FRAGMENTS="$BAM".fragments.adam
-rm -rf "$BAM"
-wget -q https://s3.amazonaws.com/bdgenomics-test/"$BAM"
-echo "Converting BAM to ADAM read format"
-rm -rf "$READS"
-"$ADAM" transform "$BAM" "$READS"
-echo "Converting BAM to ADAM read format with sorting"
-rm -rf "$SORTED_READS"
-"$ADAM" transform -sort_reads "$READS" "$SORTED_READS"
-echo "Converting read file to fragments"
-rm -rf "$FRAGMENTS"
-"$ADAM" reads2fragments "$READS" "$FRAGMENTS"
-echo "Printing reads and fragments"
-"$ADAM" print "$READS" 1>/dev/null 2>/dev/null
-"$ADAM" print "$FRAGMENTS" 1>/dev/null 2>/dev/null
-echo "Printing read statistics"
-"$ADAM" flagstat -print_metrics "$READS"
-rm -rf "$ADAM_TMP_DIR"
-popd
-
-pushd "$PROJECT_ROOT"
-./scripts/format-source
-if test -n "$(git status --porcelain)"
-then
+    if [[ $HADOOP_VERSION =~ ^1\.0 ]]; then
+        HADOOP=hadoop1
+    elif [[ $HADOOP_VERSION =~ ^2\.6 ]]; then
+        HADOOP=hadoop2.6
+    elif [[ $HADOOP_VERSION =~ ^2\.3 ]]; then
+        HADOOP=hadoop2.3
+    else
+        echo "Unknown Hadoop version."
+        exit 1
+    fi
+
+    SPARK="spark-${SPARK_VERSION}"
+
+    wget -q http://d3kbcqa49mib13.cloudfront.net/${SPARK}-bin-${HADOOP}.tgz
+    tar xzvf ${SPARK}-bin-${HADOOP}.tgz
+    export SPARK_HOME="${ADAM_TMP_DIR}/${SPARK}-bin-${HADOOP}"
+
+    ADAM="./bin/adam-submit"
+
+    echo "Fetching BAM file"
+    BAM=mouse_chrM.bam
+    READS="$BAM".reads.adam
+    SORTED_READS="$BAM".reads.sorted.adam
+    FRAGMENTS="$BAM".fragments.adam
+    rm -rf "$BAM"
+    wget -q https://s3.amazonaws.com/bdgenomics-test/"$BAM"
+    echo "Converting BAM to ADAM read format"
+    rm -rf "$READS"
+    "$ADAM" transform "$BAM" "$READS"
+    echo "Converting BAM to ADAM read format with sorting"
+    rm -rf "$SORTED_READS"
+    "$ADAM" transform -sort_reads "$READS" "$SORTED_READS"
+    echo "Converting read file to fragments"
+    rm -rf "$FRAGMENTS"
+    "$ADAM" reads2fragments "$READS" "$FRAGMENTS"
+    echo "Printing reads and fragments"
+    "$ADAM" print "$READS" 1>/dev/null 2>/dev/null
+    "$ADAM" print "$FRAGMENTS" 1>/dev/null 2>/dev/null
+    echo "Printing read statistics"
+    "$ADAM" flagstat -print_metrics "$READS"
+    rm -rf "$ADAM_TMP_DIR"
+    popd
+
+    pushd "$PROJECT_ROOT"
+    ./scripts/format-source
+    if test -n "$(git status --porcelain)"
+    then
         echo "Please run './scripts/format-source'"
         exit 1
+    fi
+    popd
+
 fi
-popd
 
 echo
 echo "All the tests passed"