Read whole text files from a compression in Spark

Solution 1:

One possible solution is to read data with binaryFiles and extract content manually.

Scala:

import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream
import org.apache.spark.input.PortableDataStream
import scala.util.Try
import java.nio.charset._

def extractFiles(ps: PortableDataStream, n: Int = 1024) = Try {
  val tar = new TarArchiveInputStream(new GzipCompressorInputStream(ps.open))
  Stream.continually(Option(tar.getNextTarEntry))
    // Read until next exntry is null
    .takeWhile(_.isDefined)
    // flatten
    .flatMap(x => x)
    // Drop directories
    .filter(!_.isDirectory)
    .map(e => {
      Stream.continually {
        // Read n bytes
        val buffer = Array.fill[Byte](n)(-1)
        val i = tar.read(buffer, 0, n)
        (i, buffer.take(i))}
      // Take as long as we've read something
      .takeWhile(_._1 > 0)
      .map(_._2)
      .flatten
      .toArray})
    .toArray
}

def decode(charset: Charset = StandardCharsets.UTF_8)(bytes: Array[Byte]) = 
  new String(bytes, StandardCharsets.UTF_8)

sc.binaryFiles("somePath").flatMapValues(x => 
  extractFiles(x).toOption).mapValues(_.map(decode()))

libraryDependencies += "org.apache.commons" % "commons-compress" % "1.11"

Full usage example with Java: https://bitbucket.org/zero323/spark-multifile-targz-extract/src

Python:

import tarfile
from io import BytesIO

def extractFiles(bytes):
    tar = tarfile.open(fileobj=BytesIO(bytes), mode="r:gz")
    return [tar.extractfile(x).read() for x in tar if x.isfile()]

(sc.binaryFiles("somePath")
    .mapValues(extractFiles)
    .mapValues(lambda xs: [x.decode("utf-8") for x in xs]))