added new portabledatastream to code so that it can be serialized cor…

…rectly

core/src/main/scala/org/apache/spark/SparkContext.scala

@@ -40,7 +40,7 @@ import org.apache.mesos.MesosNativeLibrary
 import org.apache.spark.annotation.{DeveloperApi, Experimental}
 import org.apache.spark.broadcast.Broadcast
 import org.apache.spark.deploy.{LocalSparkCluster, SparkHadoopUtil}
-import org.apache.spark.input.{StreamInputFormat, StreamFileInputFormat, WholeTextFileInputFormat, ByteInputFormat, FixedLengthBinaryInputFormat}
+import org.apache.spark.input.{StreamInputFormat, PortableDataStream, WholeTextFileInputFormat, ByteInputFormat, FixedLengthBinaryInputFormat}
 import org.apache.spark.partial.{ApproximateEvaluator, PartialResult}
 import org.apache.spark.rdd._
 import org.apache.spark.scheduler._
@@ -533,7 +533,7 @@ class SparkContext(config: SparkConf) extends Logging {
   }
 
   /**
-   * Get an RDD for a Hadoop-readable dataset as DataInputStreams for each file
+   * Get an RDD for a Hadoop-readable dataset as PortableDataStream for each file
    * (useful for binary data)
    *
    *
@@ -544,15 +544,15 @@ class SparkContext(config: SparkConf) extends Logging {
    */
   @DeveloperApi
   def dataStreamFiles(path: String, minPartitions: Int = defaultMinPartitions):
-  RDD[(String, DataInputStream)] = {
+  RDD[(String, PortableDataStream)] = {
     val job = new NewHadoopJob(hadoopConfiguration)
     NewFileInputFormat.addInputPath(job, new Path(path))
     val updateConf = job.getConfiguration
     new BinaryFileRDD(
       this,
       classOf[StreamInputFormat],
       classOf[String],
-      classOf[DataInputStream],
+      classOf[PortableDataStream],
       updateConf,
       minPartitions).setName(path)
   }

core/src/main/scala/org/apache/spark/api/java/JavaSparkContext.scala

@@ -23,7 +23,7 @@ import java.util.{Map => JMap}
 import java.io.DataInputStream
 
 import org.apache.hadoop.io.{BytesWritable, LongWritable}
-import org.apache.spark.input.FixedLengthBinaryInputFormat
+import org.apache.spark.input.{PortableDataStream, FixedLengthBinaryInputFormat}
 
 import scala.collection.JavaConversions
 import scala.collection.JavaConversions._
@@ -257,7 +257,7 @@ class JavaSparkContext(val sc: SparkContext) extends JavaSparkContextVarargsWork
    * @param minPartitions A suggestion value of the minimal splitting number for input data.
    */
   def dataStreamFiles(path: String, minPartitions: Int = defaultMinPartitions):
-  JavaPairRDD[String,DataInputStream] = new JavaPairRDD(sc.dataStreamFiles(path,minPartitions))
+  JavaPairRDD[String,PortableDataStream] = new JavaPairRDD(sc.dataStreamFiles(path,minPartitions))
 
   /**
    * Read a directory of files as DataInputStream from HDFS,

core/src/main/scala/org/apache/spark/input/RawFileInput.scala

@@ -51,40 +51,66 @@ abstract class StreamFileInputFormat[T]
   }
 
   def createRecordReader(split: InputSplit, taContext: TaskAttemptContext):
-    RecordReader[String,T]
+  RecordReader[String,T]
 
 }
 
+/**
+ * A class that allows DataStreams to be serialized and moved around by not creating them
+ * until they need to be read
+ * @param split
+ * @param context
+ * @param index
+ */
+class PortableDataStream(split: CombineFileSplit, context: TaskAttemptContext, index: Integer)
+  extends Serializable {
+  private var path = ""
+  private var fileIn: FSDataInputStream = null.asInstanceOf[FSDataInputStream]
+  private var isOpen = false
+
+  def open(): FSDataInputStream= {
+    val pathp = split.getPath(index)
+    path = pathp.toString
+    val fs = pathp.getFileSystem(context.getConfiguration)
+    fileIn = fs.open(pathp)
+    isOpen=true
+    fileIn
+  }
+
+  def close() = {
+    if (isOpen) {
+      try {
+        fileIn.close()
+        isOpen=false
+      } catch {
+        case ioe: java.io.IOException => // do nothing
+      }
+    }
+  }
+  def getPath(): String = path
+}
+
 /**
  * An abstract class of [[org.apache.hadoop.mapreduce.RecordReader RecordReader]]
  * to reading files out as streams
  */
 abstract class StreamBasedRecordReader[T](
-                                      split: CombineFileSplit,
-                                      context: TaskAttemptContext,
-                                      index: Integer)
+                                           split: CombineFileSplit,
+                                           context: TaskAttemptContext,
+                                           index: Integer)
   extends RecordReader[String, T] {
 
-  private val path = split.getPath(index)
-  private val fs = path.getFileSystem(context.getConfiguration)
+
 
   // True means the current file has been processed, then skip it.
   private var processed = false
 
-  private val key = path.toString
+  private var key = ""
   private var value: T = null.asInstanceOf[T]
-  // the file to be read when nextkeyvalue is called
-  private lazy val fileIn: FSDataInputStream = fs.open(path)
+
 
   override def initialize(split: InputSplit, context: TaskAttemptContext) = {}
-  override def close() = {
-    // make sure the file is closed
-    try {
-      fileIn.close()
-    } catch {
-      case ioe: java.io.IOException => // do nothing
-    }
-  }
+  override def close() = {}
 
   override def getProgress = if (processed) 1.0f else 0.0f
 
@@ -93,10 +119,13 @@ abstract class StreamBasedRecordReader[T](
   override def getCurrentValue = value
 
 
+
   override def nextKeyValue = {
     if (!processed) {
-
+      val fileIn = new PortableDataStream(split,context,index)
+      key = fileIn.getPath
       value = parseStream(fileIn)
+      fileIn.close() // if it has not been open yet, close does nothing
       processed = true
       true
     } else {
@@ -109,29 +138,29 @@ abstract class StreamBasedRecordReader[T](
    * @param inStream the stream to be read in
    * @return the data formatted as
    */
-  def parseStream(inStream: DataInputStream): T
+  def parseStream(inStream: PortableDataStream): T
 }
 
 /**
  * Reads the record in directly as a stream for other objects to manipulate and handle
  */
 private[spark] class StreamRecordReader(
-                        split: CombineFileSplit,
-                        context: TaskAttemptContext,
-                        index: Integer)
-  extends StreamBasedRecordReader[DataInputStream](split,context,index) {
+                                         split: CombineFileSplit,
+                                         context: TaskAttemptContext,
+                                         index: Integer)
+  extends StreamBasedRecordReader[PortableDataStream](split,context,index) {
 
-  def parseStream(inStream: DataInputStream): DataInputStream = inStream
+  def parseStream(inStream: PortableDataStream): PortableDataStream = inStream
 }
 
 /**
  * A class for extracting the information from the file using the
  * BinaryRecordReader (as Byte array)
  */
-private[spark] class StreamInputFormat extends StreamFileInputFormat[DataInputStream] {
+private[spark] class StreamInputFormat extends StreamFileInputFormat[PortableDataStream] {
   override def createRecordReader(split: InputSplit, taContext: TaskAttemptContext)=
   {
-    new CombineFileRecordReader[String,DataInputStream](
+    new CombineFileRecordReader[String,PortableDataStream](
       split.asInstanceOf[CombineFileSplit],taContext,classOf[StreamRecordReader]
     )
   }
@@ -143,12 +172,13 @@ private[spark] class StreamInputFormat extends StreamFileInputFormat[DataInputSt
  * the file as a byte array
  */
 abstract class BinaryRecordReader[T](
-                                 split: CombineFileSplit,
-                                 context: TaskAttemptContext,
-                                 index: Integer)
+                                      split: CombineFileSplit,
+                                      context: TaskAttemptContext,
+                                      index: Integer)
   extends StreamBasedRecordReader[T](split,context,index) {
 
-  def parseStream(inStream: DataInputStream): T = {
+  def parseStream(inpStream: PortableDataStream): T = {
+    val inStream = inpStream.open()
     val innerBuffer = ByteStreams.toByteArray(inStream)
     Closeables.close(inStream, false)
     parseByteArray(innerBuffer)
@@ -157,13 +187,14 @@ abstract class BinaryRecordReader[T](
 }
 
 
+
 private[spark] class ByteRecordReader(
-                          split: CombineFileSplit,
-                          context: TaskAttemptContext,
-                          index: Integer)
+                                       split: CombineFileSplit,
+                                       context: TaskAttemptContext,
+                                       index: Integer)
   extends BinaryRecordReader[Array[Byte]](split,context,index) {
 
-  def parseByteArray(inArray: Array[Byte]) = inArray
+  override def parseByteArray(inArray: Array[Byte]) = inArray
 }
 
 /**

core/src/test/scala/org/apache/spark/FileSuite.scala

@@ -226,9 +226,8 @@ class FileSuite extends FunSuite with LocalSparkContext {
 
   test("binary file input as byte array") {
     sc = new SparkContext("local", "test")
-    val outputDir = new File(tempDir).getAbsolutePath
-    val outFile = new File(outputDir, "record-bytestream-00000.bin")
-    val outFileName = outFile.toPath().toString()
+    val outFile = new File(tempDir, "record-bytestream-00000.bin")
+    val outFileName = outFile.getAbsolutePath()
 
     // create file
     val testOutput = Array[Byte](1,2,3,4,5,6)
@@ -252,10 +251,8 @@ class FileSuite extends FunSuite with LocalSparkContext {
     // a fixed length of 6 bytes
 
     sc = new SparkContext("local", "test")
-
-    val outputDir = new File(tempDir).getAbsolutePath
-    val outFile = new File(outputDir, "record-bytestream-00000.bin")
-    val outFileName = outFile.toPath().toString()
+    val outFile = new File(tempDir, "record-bytestream-00000.bin")
+    val outFileName = outFile.getAbsolutePath()
 
     // create file
     val testOutput = Array[Byte](1,2,3,4,5,6)

pom.xml

@@ -90,6 +90,7 @@
     <module>bagel</module>
     <module>graphx</module>
     <module>mllib</module>
+    <module>imglib</module>
     <module>tools</module>
     <module>streaming</module>
     <module>sql/catalyst</module>
@@ -743,6 +744,10 @@
         <artifactId>jackson-mapper-asl</artifactId>
         <version>1.8.8</version>
       </dependency>
+      <dependency>
+        <groupId>io.scif</groupId>
+        <artifactId>pom-scifio</artifactId>
+      </dependency>
     </dependencies>
   </dependencyManagement>