[SPARK-1681] Include datanucleus jars in Spark Hive distribution

This copies the datanucleus jars over from `lib_managed` into `dist/lib`, if any. The `CLASSPATH` must also be updated to reflect this change.

Author: Andrew Or <andrewor14@gmail.com>

Closes #610 from andrewor14/hive-distribution and squashes the following commits:

a4bc96f [Andrew Or] Rename search path in jar error check
fa205e1 [Andrew Or] Merge branch 'master' of github.com:apache/spark into hive-distribution
7855f58 [Andrew Or] Have jar command respect JAVA_HOME + check for jar errors both cases
c16bbfd [Andrew Or] Merge branch 'master' of github.com:apache/spark into hive-distribution
32f6826 [Andrew Or] Leave the double colons
940a1bb [Andrew Or] Add back 2>/dev/null
58357cc [Andrew Or] Include datanucleus jars in Spark distribution built with Hive support

bin/compute-classpath.sh

@@ -32,8 +32,8 @@ CLASSPATH="$SPARK_CLASSPATH:$SPARK_SUBMIT_CLASSPATH:$FWDIR/conf"
 
 ASSEMBLY_DIR="$FWDIR/assembly/target/scala-$SCALA_VERSION"
 
-if [ -n "${JAVA_HOME}" ]; then
-  JAR_CMD="${JAVA_HOME}/bin/jar"
+if [ -n "$JAVA_HOME" ]; then
+  JAR_CMD="$JAVA_HOME/bin/jar"
 else
   JAR_CMD="jar"
 fi
@@ -52,40 +52,48 @@ if [ -f "$ASSEMBLY_DIR"/spark-assembly*hadoop*-deps.jar ]; then
   CLASSPATH="$CLASSPATH:$FWDIR/sql/hive/target/scala-$SCALA_VERSION/classes"
   CLASSPATH="$CLASSPATH:$FWDIR/yarn/stable/target/scala-$SCALA_VERSION/classes"
 
-  DEPS_ASSEMBLY_JAR=`ls "$ASSEMBLY_DIR"/spark-assembly*hadoop*-deps.jar`
-  CLASSPATH="$CLASSPATH:$DEPS_ASSEMBLY_JAR"
+  ASSEMBLY_JAR=$(ls "$ASSEMBLY_DIR"/spark-assembly*hadoop*-deps.jar 2>/dev/null)
 else
   # Else use spark-assembly jar from either RELEASE or assembly directory
   if [ -f "$FWDIR/RELEASE" ]; then
-    ASSEMBLY_JAR=`ls "$FWDIR"/lib/spark-assembly*hadoop*.jar`
+    ASSEMBLY_JAR=$(ls "$FWDIR"/lib/spark-assembly*hadoop*.jar 2>/dev/null)
   else
-    ASSEMBLY_JAR=`ls "$ASSEMBLY_DIR"/spark-assembly*hadoop*.jar`
+    ASSEMBLY_JAR=$(ls "$ASSEMBLY_DIR"/spark-assembly*hadoop*.jar 2>/dev/null)
   fi
-  jar_error_check=$($JAR_CMD -tf $ASSEMBLY_JAR org/apache/spark/SparkContext 2>&1)
-  if [[ "$jar_error_check" =~ "invalid CEN header" ]]; then
-    echo "Loading Spark jar with '$JAR_CMD' failed. "
-    echo "This is likely because Spark was compiled with Java 7 and run "
-    echo "with Java 6. (see SPARK-1703). Please use Java 7 to run Spark "
-    echo "or build Spark with Java 6."
-    exit 1
-  fi
-  CLASSPATH="$CLASSPATH:$ASSEMBLY_JAR"
 fi
 
+# Verify that versions of java used to build the jars and run Spark are compatible
+jar_error_check=$("$JAR_CMD" -tf "$ASSEMBLY_JAR" nonexistent/class/path 2>&1)
+if [[ "$jar_error_check" =~ "invalid CEN header" ]]; then
+  echo "Loading Spark jar with '$JAR_CMD' failed. "
+  echo "This is likely because Spark was compiled with Java 7 and run "
+  echo "with Java 6. (see SPARK-1703). Please use Java 7 to run Spark "
+  echo "or build Spark with Java 6."
+  exit 1
+fi
+
+CLASSPATH="$CLASSPATH:$ASSEMBLY_JAR"
+
 # When Hive support is needed, Datanucleus jars must be included on the classpath.
-# Datanucleus jars do not work if only included in the  uber jar as plugin.xml metadata is lost.
+# Datanucleus jars do not work if only included in the uber jar as plugin.xml metadata is lost.
 # Both sbt and maven will populate "lib_managed/jars/" with the datanucleus jars when Spark is
 # built with Hive, so first check if the datanucleus jars exist, and then ensure the current Spark
 # assembly is built for Hive, before actually populating the CLASSPATH with the jars.
 # Note that this check order is faster (by up to half a second) in the case where Hive is not used.
-num_datanucleus_jars=$(ls "$FWDIR"/lib_managed/jars/ 2>/dev/null | grep "datanucleus-.*\\.jar" | wc -l)
-if [ $num_datanucleus_jars -gt 0 ]; then
-  AN_ASSEMBLY_JAR=${ASSEMBLY_JAR:-$DEPS_ASSEMBLY_JAR}
-  num_hive_files=$(jar tvf "$AN_ASSEMBLY_JAR" org/apache/hadoop/hive/ql/exec 2>/dev/null | wc -l)
-  if [ $num_hive_files -gt 0 ]; then
+if [ -f "$FWDIR/RELEASE" ]; then
+  datanucleus_dir="$FWDIR"/lib
+else
+  datanucleus_dir="$FWDIR"/lib_managed/jars
+fi
+
+datanucleus_jars=$(find "$datanucleus_dir" 2>/dev/null | grep "datanucleus-.*\\.jar")
+datanucleus_jars=$(echo "$datanucleus_jars" | tr "\n" : | sed s/:$//g)
+
+if [ -n "$datanucleus_jars" ]; then
+  hive_files=$("$JAR_CMD" -tf "$ASSEMBLY_JAR" org/apache/hadoop/hive/ql/exec 2>/dev/null)
+  if [ -n "$hive_files" ]; then
     echo "Spark assembly has been built with Hive, including Datanucleus jars on classpath" 1>&2
-    DATANUCLEUSJARS=$(echo "$FWDIR/lib_managed/jars"/datanucleus-*.jar | tr " " :)
-    CLASSPATH=$CLASSPATH:$DATANUCLEUSJARS
+    CLASSPATH="$CLASSPATH:$datanucleus_jars"
   fi
 fi
 
@@ -105,10 +113,10 @@ fi
 # Add hadoop conf dir if given -- otherwise FileSystem.*, etc fail !
 # Note, this assumes that there is either a HADOOP_CONF_DIR or YARN_CONF_DIR which hosts
 # the configurtion files.
-if [ "x" != "x$HADOOP_CONF_DIR" ]; then
+if [ -n "$HADOOP_CONF_DIR" ]; then
   CLASSPATH="$CLASSPATH:$HADOOP_CONF_DIR"
 fi
-if [ "x" != "x$YARN_CONF_DIR" ]; then
+if [ -n "$YARN_CONF_DIR" ]; then
   CLASSPATH="$CLASSPATH:$YARN_CONF_DIR"
 fi
 

make-distribution.sh

@@ -51,13 +51,13 @@ if [ $? != 0 ]; then
     exit -1;
 fi
 
-if [ -z "${JAVA_HOME}" ]; then
+if [ -z "$JAVA_HOME" ]; then
   echo "Error: JAVA_HOME is not set, cannot proceed."
   exit -1
 fi
 
-JAVA_CMD=$JAVA_HOME/bin/java
-JAVA_VERSION=$($JAVA_CMD -version 2>&1)
+JAVA_CMD="$JAVA_HOME"/bin/java
+JAVA_VERSION=$("$JAVA_CMD" -version 2>&1)
 if ! [[ "$JAVA_VERSION" =~ "1.6" ]]; then
   echo "Error: JAVA_HOME must point to a JDK 6 installation (see SPARK-1703)."
   echo "Output from 'java -version' was:"
@@ -162,6 +162,10 @@ echo "Spark $VERSION built for Hadoop $SPARK_HADOOP_VERSION" > "$DISTDIR/RELEASE
 cp $FWDIR/assembly/target/scala*/*assembly*hadoop*.jar "$DISTDIR/lib/"
 cp $FWDIR/examples/target/scala*/spark-examples*.jar "$DISTDIR/lib/"
 
+if [ "$SPARK_HIVE" == "true" ]; then
+  cp $FWDIR/lib_managed/jars/datanucleus*.jar "$DISTDIR/lib/"
+fi
+
 # Copy other things
 mkdir "$DISTDIR"/conf
 cp "$FWDIR"/conf/*.template "$DISTDIR"/conf
@@ -170,7 +174,6 @@ cp -r "$FWDIR/bin" "$DISTDIR"
 cp -r "$FWDIR/python" "$DISTDIR"
 cp -r "$FWDIR/sbin" "$DISTDIR"
 
-
 # Download and copy in tachyon, if requested
 if [ "$SPARK_TACHYON" == "true" ]; then
   TACHYON_VERSION="0.4.1"