Merge pull request #350 from alexarchambault/topic/spark-submit

Tweak spark submit

cache/src/main/scala/coursier/Cache.scala

@@ -53,7 +53,7 @@ object Cache {
     }
   }
 
-  private def localFile(url: String, cache: File, user: Option[String]): File = {
+  def localFile(url: String, cache: File, user: Option[String]): File = {
     val path =
       if (url.startsWith("file:///"))
         url.stripPrefix("file://")
@@ -155,7 +155,7 @@ object Cache {
     }
   }
 
-  private def withLockFor[T](cache: File, file: File)(f: => FileError \/ T): FileError \/ T = {
+  def withLockFor[T](cache: File, file: File)(f: => FileError \/ T): FileError \/ T = {
     val lockFile = new File(file.getParentFile, s"${file.getName}.lock")
 
     var out: FileOutputStream = null

cli/src/main/scala-2.11/coursier/cli/Bootstrap.scala

@@ -1,13 +1,14 @@
 package coursier
 package cli
 
-import java.io.{ FileInputStream, ByteArrayInputStream, ByteArrayOutputStream, File, IOException }
+import java.io.{ByteArrayInputStream, ByteArrayOutputStream, File, FileInputStream, IOException}
 import java.nio.file.Files
 import java.nio.file.attribute.PosixFilePermission
 import java.util.Properties
-import java.util.zip.{ ZipEntry, ZipOutputStream, ZipInputStream }
+import java.util.zip.{ZipEntry, ZipInputStream, ZipOutputStream}
 
 import caseapp._
+import coursier.cli.util.Zip
 
 case class Bootstrap(
   @Recurse
@@ -61,26 +62,6 @@ case class Bootstrap(
     sys.exit(1)
   }
 
-  def zipEntries(zipStream: ZipInputStream): Iterator[(ZipEntry, Array[Byte])] =
-    new Iterator[(ZipEntry, Array[Byte])] {
-      var nextEntry = Option.empty[ZipEntry]
-      def update() =
-        nextEntry = Option(zipStream.getNextEntry)
-
-      update()
-
-      def hasNext = nextEntry.nonEmpty
-      def next() = {
-        val ent = nextEntry.get
-        val data = Platform.readFullySync(zipStream)
-
-        update()
-
-        (ent, data)
-      }
-    }
-
-
   val isolatedDeps = options.isolated.isolatedDeps(
     options.common.defaultArtifactType,
     options.common.scalaVersion
@@ -141,7 +122,7 @@ case class Bootstrap(
   val bootstrapZip = new ZipInputStream(new ByteArrayInputStream(bootstrapJar))
   val outputZip = new ZipOutputStream(buffer)
 
-  for ((ent, data) <- zipEntries(bootstrapZip)) {
+  for ((ent, data) <- Zip.zipEntries(bootstrapZip)) {
     outputZip.putNextEntry(ent)
     outputZip.write(data)
     outputZip.closeEntry()

cli/src/main/scala-2.11/coursier/cli/Helper.scala

@@ -75,6 +75,7 @@ object Util {
 class Helper(
   common: CommonOptions,
   rawDependencies: Seq[String],
+  extraJars: Seq[File] = Nil,
   printResultStdout: Boolean = false,
   ignoreErrors: Boolean = false,
   isolated: IsolatedLoaderOptions = IsolatedLoaderOptions(),
@@ -584,7 +585,7 @@ class Helper(
   def contextLoader = Thread.currentThread().getContextClassLoader
 
   // TODO Would ClassLoader.getSystemClassLoader be better here?
-  val baseLoader: ClassLoader =
+  lazy val baseLoader: ClassLoader =
     Launch.mainClassLoader(contextLoader)
       .flatMap(cl => Option(cl.getParent))
       .getOrElse {
@@ -648,7 +649,7 @@ class Helper(
   }
 
   lazy val loader = new URLClassLoader(
-    filteredFiles.map(_.toURI.toURL).toArray,
+    (filteredFiles ++ extraJars).map(_.toURI.toURL).toArray,
     parentLoader
   )
 

cli/src/main/scala-2.11/coursier/cli/Launch.scala

@@ -1,6 +1,7 @@
 package coursier
 package cli
 
+import java.io.File
 import java.net.{ URL, URLClassLoader }
 
 import caseapp._
@@ -114,6 +115,7 @@ case class Launch(
   val helper = new Helper(
     options.common,
     remainingArgs ++ options.isolated.rawIsolated.map { case (_, dep) => dep },
+    extraJars = options.extraJars.map(new File(_)),
     isolated = options.isolated
   )
 
@@ -123,8 +125,19 @@ case class Launch(
     else
       options.mainClass
 
+  val extraJars = options.extraJars.filter(_.nonEmpty)
+
+  val loader =
+    if (extraJars.isEmpty)
+      helper.loader
+    else
+      new URLClassLoader(
+        extraJars.map(new File(_).toURI.toURL).toArray,
+        helper.loader
+      )
+
   Launch.run(
-    helper.loader,
+    loader,
     mainClass,
     userArgs,
     options.common.verbosityLevel

cli/src/main/scala-2.11/coursier/cli/Options.scala

@@ -188,6 +188,9 @@ case class LaunchOptions(
   @Short("M")
   @Short("main")
     mainClass: String,
+  @Short("J")
+  @Help("Extra JARs to be added to the classpath of the launched application. Directories accepted too.")
+    extraJars: List[String],
   @Recurse
     isolated: IsolatedLoaderOptions,
   @Recurse
@@ -226,6 +229,9 @@ case class SparkSubmitOptions(
   @Short("main")
   @Help("Main class to be launched (optional if in manifest)")
     mainClass: String,
+  @Short("J")
+  @Help("Extra JARs to be added in the classpath of the job")
+    extraJars: List[String],
   @Help("If master is yarn-cluster, write YARN app ID to a file. (The ID is deduced from the spark-submit output.)")
   @Value("file")
     yarnIdFile: String,

cli/src/main/scala-2.11/coursier/cli/SparkSubmit.scala

@@ -55,8 +55,23 @@ case class SparkSubmit(
     options: SparkSubmitOptions
 ) extends App with ExtraArgsApp {
 
-  val helper = new Helper(options.common, remainingArgs)
+  val rawExtraJars = options.extraJars.map(new File(_))
-  val jars = helper.fetch(sources = false, javadoc = false)
+
+  val extraDirs = rawExtraJars.filter(_.isDirectory)
+  if (extraDirs.nonEmpty) {
+    Console.err.println(s"Error: directories not allowed in extra job JARs.")
+    Console.err.println(extraDirs.map("  " + _).mkString("\n"))
+    sys.exit(1)
+  }
+
+  val helper: Helper = new Helper(
+    options.common,
+    remainingArgs,
+    extraJars = rawExtraJars
+  )
+  val jars =
+    helper.fetch(sources = false, javadoc = false) ++
+      options.extraJars.map(new File(_))
 
   val (scalaVersion, sparkVersion) =
     if (options.sparkVersion.isEmpty)
@@ -73,31 +88,15 @@ case class SparkSubmit(
       (options.common.scalaVersion, options.sparkVersion)
 
   val assemblyOrError =
-    if (options.sparkAssembly.isEmpty) {
+    if (options.sparkAssembly.isEmpty)
-
+      Assembly.spark(
-      // FIXME Also vaguely done in Helper and below
+        scalaVersion,
-
+        sparkVersion,
-      val (errors, modVers) = Parse.moduleVersionConfigs(
+        options.noDefaultAssemblyDependencies,
-        options.assemblyDependencies,
+        options.assemblyDependencies.flatMap(_.split(",")).filter(_.nonEmpty),
-        options.common.scalaVersion
+        options.common
       )
-
+    else {
-      val deps = modVers.map {
-        case (module, version, configOpt) =>
-          Dependency(
-            module,
-            version,
-            attributes = Attributes(options.common.defaultArtifactType, ""),
-            configuration = configOpt.getOrElse(options.common.defaultConfiguration),
-            exclusions = helper.excludes
-          )
-      }
-
-      if (errors.isEmpty)
-        Assembly.spark(scalaVersion, sparkVersion, options.noDefaultAssemblyDependencies, deps)
-      else
-        Left(s"Cannot parse assembly dependencies:\n${errors.map("  " + _).mkString("\n")}")
-    } else {
       val f = new File(options.sparkAssembly)
       if (f.isFile)
         Right((f, Nil))
@@ -170,7 +169,7 @@ case class SparkSubmit(
     scalaVersion,
     sparkVersion,
     options.noDefaultSubmitDependencies,
-    options.submitDependencies,
+    options.submitDependencies.flatMap(_.split(",")).filter(_.nonEmpty),
     options.common
   )
 

cli/src/main/scala-2.11/coursier/cli/spark/Assembly.scala

@@ -1,36 +1,213 @@
 package coursier.cli.spark
 
 import java.io.{File, FileInputStream, FileOutputStream}
-import java.util.zip.{ZipInputStream, ZipOutputStream}
+import java.math.BigInteger
+import java.nio.file.{Files, StandardCopyOption}
+import java.security.MessageDigest
+import java.util.jar.{Attributes, JarFile, JarOutputStream, Manifest}
+import java.util.regex.Pattern
+import java.util.zip.{ZipEntry, ZipInputStream, ZipOutputStream}
 
-import coursier.Dependency
+import coursier.Cache
+import coursier.cli.{CommonOptions, Helper}
+import coursier.cli.util.Zip
+
+import scala.collection.mutable
+import scalaz.\/-
 
 object Assembly {
 
   sealed abstract class Rule extends Product with Serializable
 
   object Rule {
-    case class Exclude(path: String) extends Rule
+    sealed abstract class PathRule extends Rule {
-    case class Append(path: String) extends Rule
+      def path: String
+    }
+
+    case class Exclude(path: String) extends PathRule
+    case class Append(path: String) extends PathRule
+
+    case class ExcludePattern(path: Pattern) extends Rule
+
+    object ExcludePattern {
+      def apply(s: String): ExcludePattern =
+        ExcludePattern(Pattern.compile(s))
+    }
   }
 
   def make(jars: Seq[File], output: File, rules: Seq[Rule]): Unit = {
 
-    val zos = new ZipOutputStream(new FileOutputStream(output))
+    val rulesMap = rules.collect { case r: Rule.PathRule => r.path -> r }.toMap
+    val excludePatterns = rules.collect { case Rule.ExcludePattern(p) => p }
 
-    for (jar <- jars) {
+    val manifest = new Manifest
-      new ZipInputStream(new FileInputStream(jar))
+    manifest.getMainAttributes.put(Attributes.Name.MANIFEST_VERSION, "1.0")
+
+    var fos: FileOutputStream = null
+    var zos: ZipOutputStream = null
+
+    try {
+      fos = new FileOutputStream(output)
+      zos = new JarOutputStream(fos, manifest)
+
+      val concatenedEntries = new mutable.HashMap[String, ::[(ZipEntry, Array[Byte])]]
+
+      var ignore = Set.empty[String]
+
+      for (jar <- jars) {
+        var fis: FileInputStream = null
+        var zis: ZipInputStream = null
+
+        try {
+          fis = new FileInputStream(jar)
+          zis = new ZipInputStream(fis)
+
+          for ((ent, content) <- Zip.zipEntries(zis))
+            rulesMap.get(ent.getName) match {
+              case Some(Rule.Exclude(_)) =>
+              // ignored
+
+              case Some(Rule.Append(path)) =>
+                concatenedEntries += path -> ::((ent, content), concatenedEntries.getOrElse(path, Nil))
+
+              case None =>
+                if (!excludePatterns.exists(_.matcher(ent.getName).matches()) && !ignore(ent.getName)) {
+                  ent.setCompressedSize(-1L)
+                  zos.putNextEntry(ent)
+                  zos.write(content)
+                  zos.closeEntry()
+
+                  ignore += ent.getName
+                }
+            }
+
+        } finally {
+          if (zis != null)
+            zis.close()
+          if (fis != null)
+            fis.close()
+        }
+      }
+
+      for ((_, entries) <- concatenedEntries) {
+        val (ent, _) = entries.head
+
+        ent.setCompressedSize(-1L)
+
+        if (entries.tail.nonEmpty)
+          ent.setSize(entries.map(_._2.length).sum)
+
+        zos.putNextEntry(ent)
+        // for ((_, b) <- entries.reverse)
+        //  zos.write(b)
+        zos.write(entries.reverse.toArray.flatMap(_._2))
+        zos.closeEntry()
+      }
+    } finally {
+      if (zos != null)
+        zos.close()
+      if (fos != null)
+        fos.close()
     }
-
-    ???
   }
 
+  val assemblyRules = Seq[Rule](
+    Rule.Append("META-INF/services/org.apache.hadoop.fs.FileSystem"),
+    Rule.Append("reference.conf"),
+    Rule.Exclude("log4j.properties"),
+    Rule.Exclude(JarFile.MANIFEST_NAME),
+    Rule.ExcludePattern("META-INF/.*\\.[sS][fF]"),
+    Rule.ExcludePattern("META-INF/.*\\.[dD][sS][aA]"),
+    Rule.ExcludePattern("META-INF/.*\\.[rR][sS][aA]")
+  )
+
+  def sparkAssemblyDependencies(
+    scalaVersion: String,
+    sparkVersion: String
+  ) = Seq(
+    s"org.apache.spark:spark-core_$scalaVersion:$sparkVersion",
+    s"org.apache.spark:spark-bagel_$scalaVersion:$sparkVersion",
+    s"org.apache.spark:spark-mllib_$scalaVersion:$sparkVersion",
+    s"org.apache.spark:spark-streaming_$scalaVersion:$sparkVersion",
+    s"org.apache.spark:spark-graphx_$scalaVersion:$sparkVersion",
+    s"org.apache.spark:spark-sql_$scalaVersion:$sparkVersion",
+    s"org.apache.spark:spark-repl_$scalaVersion:$sparkVersion",
+    s"org.apache.spark:spark-yarn_$scalaVersion:$sparkVersion"
+  )
+
   def spark(
     scalaVersion: String,
     sparkVersion: String,
     noDefault: Boolean,
-    extraDependencies: Seq[Dependency]
+    extraDependencies: Seq[String],
-  ): Either[String, (File, Seq[File])] =
+    options: CommonOptions
-    throw new Exception("Not implemented: automatic assembly generation")
+  ): Either[String, (File, Seq[File])] = {
+
+    val base = if (noDefault) Seq() else sparkAssemblyDependencies(scalaVersion, sparkVersion)
+    val helper = new Helper(options, extraDependencies ++ base)
+
+    val artifacts = helper.artifacts(sources = false, javadoc = false)
+    val jars = helper.fetch(sources = false, javadoc = false)
+
+    val checksums = artifacts.map { a =>
+      val f = a.checksumUrls.get("SHA-1") match {
+        case Some(url) =>
+          Cache.localFile(url, helper.cache, a.authentication.map(_.user))
+        case None =>
+          throw new Exception(s"SHA-1 file not found for ${a.url}")
+      }
+
+      val sumOpt = Cache.parseChecksum(
+        new String(Files.readAllBytes(f.toPath), "UTF-8")
+      )
+
+      sumOpt match {
+        case Some(sum) =>
+          val s = sum.toString(16)
+          "0" * (40 - s.length) + s
+        case None =>
+          throw new Exception(s"Cannot read SHA-1 sum from $f")
+      }
+    }
+
+
+    val md = MessageDigest.getInstance("SHA-1")
+
+    for (c <- checksums.sorted) {
+      val b = c.getBytes("UTF-8")
+      md.update(b, 0, b.length)
+    }
+
+    val digest = md.digest()
+    val calculatedSum = new BigInteger(1, digest)
+    val s = calculatedSum.toString(16)
+
+    val sum = "0" * (40 - s.length) + s
+
+    val destPath = Seq(
+      sys.props("user.home"),
+      ".coursier",
+      "spark-assemblies",
+      s"scala_${scalaVersion}_spark_$sparkVersion",
+      sum,
+      "spark-assembly.jar"
+    ).mkString("/")
+
+    val dest = new File(destPath)
+
+    def success = Right((dest, jars))
+
+    if (dest.exists())
+      success
+    else
+      Cache.withLockFor(helper.cache, dest) {
+        dest.getParentFile.mkdirs()
+        val tmpDest = new File(dest.getParentFile, s".${dest.getName}.part")
+        // FIXME Acquire lock on tmpDest
+        Assembly.make(jars, tmpDest, assemblyRules)
+        Files.move(tmpDest.toPath, dest.toPath, StandardCopyOption.ATOMIC_MOVE)
+        \/-((dest, jars))
+      }.leftMap(_.describe).toEither
+  }
 
 }

cli/src/main/scala-2.11/coursier/cli/util/Zip.scala

@@ -0,0 +1,28 @@
+package coursier.cli.util
+
+import java.util.zip.{ZipEntry, ZipInputStream}
+
+import coursier.Platform
+
+object Zip {
+
+  def zipEntries(zipStream: ZipInputStream): Iterator[(ZipEntry, Array[Byte])] =
+    new Iterator[(ZipEntry, Array[Byte])] {
+      var nextEntry = Option.empty[ZipEntry]
+      def update() =
+        nextEntry = Option(zipStream.getNextEntry)
+
+      update()
+
+      def hasNext = nextEntry.nonEmpty
+      def next() = {
+        val ent = nextEntry.get
+        val data = Platform.readFullySync(zipStream)
+
+        update()
+
+        (ent, data)
+      }
+    }
+
+}