[SPARK-8313] R Spark packages support #7139
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| # | ||
| # Licensed to the Apache Software Foundation (ASF) under one or more | ||
| # contributor license agreements. See the NOTICE file distributed with | ||
| # this work for additional information regarding copyright ownership. | ||
| # The ASF licenses this file to You under the Apache License, Version 2.0 | ||
| # (the "License"); you may not use this file except in compliance with | ||
| # the License. You may obtain a copy of the License at | ||
| # | ||
| # http://www.apache.org/licenses/LICENSE-2.0 | ||
| # | ||
| # Unless required by applicable law or agreed to in writing, software | ||
| # distributed under the License is distributed on an "AS IS" BASIS, | ||
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| # See the License for the specific language governing permissions and | ||
| # limitations under the License. | ||
| # | ||
| library(SparkR) | ||
| library(sparkPackageTest) | ||
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| sc <- sparkR.init() | ||
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| run1 <- myfunc(5L) | ||
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| run2 <- myfunc(-4L) | ||
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| sparkR.stop() | ||
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| if(run1 != 6) quit(save = "no", status = 1) | ||
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| if(run2 != -3) quit(save = "no", status = 1) |
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| /* | ||
| * Licensed to the Apache Software Foundation (ASF) under one or more | ||
| * contributor license agreements. See the NOTICE file distributed with | ||
| * this work for additional information regarding copyright ownership. | ||
| * The ASF licenses this file to You under the Apache License, Version 2.0 | ||
| * (the "License"); you may not use this file except in compliance with | ||
| * the License. You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
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| package org.apache.spark.deploy | ||
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| import java.io._ | ||
| import java.util.jar.JarFile | ||
| import java.util.logging.Level | ||
| import java.util.zip.{ZipEntry, ZipOutputStream} | ||
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| import scala.collection.JavaConversions._ | ||
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| import com.google.common.io.{ByteStreams, Files} | ||
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| import org.apache.spark.{SparkException, Logging} | ||
| import org.apache.spark.api.r.RUtils | ||
| import org.apache.spark.util.{RedirectThread, Utils} | ||
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| private[deploy] object RPackageUtils extends Logging { | ||
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| /** The key in the MANIFEST.mf that we look for, in case a jar contains R code. */ | ||
| private final val hasRPackage = "Spark-HasRPackage" | ||
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| /** Base of the shell command used in order to install R packages. */ | ||
| private final val baseInstallCmd = Seq("R", "CMD", "INSTALL", "-l") | ||
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| /** R source code should exist under R/pkg in a jar. */ | ||
| private final val RJarEntries = "R/pkg" | ||
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| /** Documentation on how the R source file layout should be in the jar. */ | ||
| private[deploy] final val RJarDoc = | ||
| s"""In order for Spark to build R packages that are parts of Spark Packages, there are a few | ||
| |requirements. The R source code must be shipped in a jar, with additional Java/Scala | ||
| |classes. The jar must be in the following format: | ||
| | 1- The Manifest (META-INF/MANIFEST.mf) must contain the key-value: $hasRPackage: true | ||
| | 2- The standard R package layout must be preserved under R/pkg/ inside the jar. More | ||
| | information on the standard R package layout can be found in: | ||
| | http://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf | ||
| | An example layout is given below. After running `jar tf $$JAR_FILE | sort`: | ||
| | | ||
| |META-INF/MANIFEST.MF | ||
| |R/ | ||
| |R/pkg/ | ||
| |R/pkg/DESCRIPTION | ||
| |R/pkg/NAMESPACE | ||
| |R/pkg/R/ | ||
| |R/pkg/R/myRcode.R | ||
| |org/ | ||
| |org/apache/ | ||
| |... | ||
| """.stripMargin.trim | ||
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| /** Internal method for logging. We log to a printStream in tests, for debugging purposes. */ | ||
| private def print( | ||
| msg: String, | ||
| printStream: PrintStream, | ||
| level: Level = Level.FINE, | ||
| e: Throwable = null): Unit = { | ||
| if (printStream != null) { | ||
| // scalastyle:off println | ||
| printStream.println(msg) | ||
| // scalastyle:on println | ||
| if (e != null) { | ||
| e.printStackTrace(printStream) | ||
| } | ||
| } else { | ||
| level match { | ||
| case Level.INFO => logInfo(msg) | ||
| case Level.WARNING => logWarning(msg) | ||
| case Level.SEVERE => logError(msg, e) | ||
| case _ => logDebug(msg) | ||
| } | ||
| } | ||
| } | ||
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| /** | ||
| * Checks the manifest of the Jar whether there is any R source code bundled with it. | ||
| * Exposed for testing. | ||
| */ | ||
| private[deploy] def checkManifestForR(jar: JarFile): Boolean = { | ||
| val manifest = jar.getManifest.getMainAttributes | ||
| manifest.getValue(hasRPackage) != null && manifest.getValue(hasRPackage).trim == "true" | ||
| } | ||
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| /** | ||
| * Runs the standard R package installation code to build the R package from source. | ||
| * Multiple runs don't cause problems. | ||
| */ | ||
| private def rPackageBuilder(dir: File, printStream: PrintStream, verbose: Boolean): Boolean = { | ||
| // this code should be always running on the driver. | ||
| val pathToSparkR = RUtils.localSparkRPackagePath.getOrElse( | ||
| throw new SparkException("SPARK_HOME not set. Can't locate SparkR package.")) | ||
| val pathToPkg = Seq(dir, "R", "pkg").mkString(File.separator) | ||
| val installCmd = baseInstallCmd ++ Seq(pathToSparkR, pathToPkg) | ||
| if (verbose) { | ||
| print(s"Building R package with the command: $installCmd", printStream) | ||
| } | ||
| try { | ||
| val builder = new ProcessBuilder(installCmd) | ||
| builder.redirectErrorStream(true) | ||
| val env = builder.environment() | ||
| env.clear() | ||
| val process = builder.start() | ||
| new RedirectThread(process.getInputStream, printStream, "redirect R packaging").start() | ||
| process.waitFor() == 0 | ||
| } catch { | ||
| case e: Throwable => | ||
| print("Failed to build R package.", printStream, Level.SEVERE, e) | ||
| false | ||
| } | ||
| } | ||
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| /** | ||
| * Extracts the files under /R in the jar to a temporary directory for building. | ||
| */ | ||
| private def extractRFolder(jar: JarFile, printStream: PrintStream, verbose: Boolean): File = { | ||
| val tempDir = Utils.createTempDir(null) | ||
| val jarEntries = jar.entries() | ||
| while (jarEntries.hasMoreElements) { | ||
| val entry = jarEntries.nextElement() | ||
| val entryRIndex = entry.getName.indexOf(RJarEntries) | ||
| if (entryRIndex > -1) { | ||
| val entryPath = entry.getName.substring(entryRIndex) | ||
| if (entry.isDirectory) { | ||
| val dir = new File(tempDir, entryPath) | ||
| if (verbose) { | ||
| print(s"Creating directory: $dir", printStream) | ||
| } | ||
| dir.mkdirs | ||
| } else { | ||
| val inStream = jar.getInputStream(entry) | ||
| val outPath = new File(tempDir, entryPath) | ||
| Files.createParentDirs(outPath) | ||
| val outStream = new FileOutputStream(outPath) | ||
| if (verbose) { | ||
| print(s"Extracting $entry to $outPath", printStream) | ||
| } | ||
| Utils.copyStream(inStream, outStream, closeStreams = true) | ||
| } | ||
| } | ||
| } | ||
| tempDir | ||
| } | ||
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| /** | ||
| * Extracts the files under /R in the jar to a temporary directory for building. | ||
| */ | ||
| private[deploy] def checkAndBuildRPackage( | ||
| jars: String, | ||
| printStream: PrintStream = null, | ||
| verbose: Boolean = false): Unit = { | ||
| jars.split(",").foreach { jarPath => | ||
| val file = new File(Utils.resolveURI(jarPath)) | ||
| if (file.exists()) { | ||
| val jar = new JarFile(file) | ||
| if (checkManifestForR(jar)) { | ||
| print(s"$file contains R source code. Now installing package.", printStream, Level.INFO) | ||
| val rSource = extractRFolder(jar, printStream, verbose) | ||
| try { | ||
| if (!rPackageBuilder(rSource, printStream, verbose)) { | ||
| print(s"ERROR: Failed to build R package in $file.", printStream) | ||
| print(RJarDoc, printStream) | ||
| } | ||
| } finally { | ||
| rSource.delete() // clean up | ||
| } | ||
| } else { | ||
| if (verbose) { | ||
| print(s"$file doesn't contain R source code, skipping...", printStream) | ||
| } | ||
| } | ||
| } else { | ||
| print(s"WARN: $file resolved as dependency, but not found.", printStream, Level.WARNING) | ||
| } | ||
| } | ||
| } | ||
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| private def listFilesRecursively(dir: File, excludePatterns: Seq[String]): Set[File] = { | ||
| if (!dir.exists()) { | ||
| Set.empty[File] | ||
| } else { | ||
| if (dir.isDirectory) { | ||
| val subDir = dir.listFiles(new FilenameFilter { | ||
| override def accept(dir: File, name: String): Boolean = { | ||
| !excludePatterns.map(name.contains).reduce(_ || _) // exclude files with given pattern | ||
| } | ||
| }) | ||
| subDir.flatMap(listFilesRecursively(_, excludePatterns)).toSet | ||
| } else { | ||
| Set(dir) | ||
| } | ||
| } | ||
| } | ||
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| /** Zips all the libraries found with SparkR in the R/lib directory for distribution with Yarn. */ | ||
| private[deploy] def zipRLibraries(dir: File, name: String): File = { | ||
|
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There was a problem hiding this comment. This method creates the zip |
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| val filesToBundle = listFilesRecursively(dir, Seq(".zip")) | ||
| // create a zip file from scratch, do not append to existing file. | ||
| val zipFile = new File(dir, name) | ||
| zipFile.delete() | ||
| val zipOutputStream = new ZipOutputStream(new FileOutputStream(zipFile, false)) | ||
| try { | ||
| filesToBundle.foreach { file => | ||
| // get the relative paths for proper naming in the zip file | ||
| val relPath = file.getAbsolutePath.replaceFirst(dir.getAbsolutePath, "") | ||
| val fis = new FileInputStream(file) | ||
| val zipEntry = new ZipEntry(relPath) | ||
| zipOutputStream.putNextEntry(zipEntry) | ||
| ByteStreams.copy(fis, zipOutputStream) | ||
| zipOutputStream.closeEntry() | ||
| fis.close() | ||
| } | ||
| } finally { | ||
| zipOutputStream.close() | ||
| } | ||
| zipFile | ||
| } | ||
| } | ||
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Just checking -- do we need this import ?
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for the
Process Builderbelow. It takes a Java Collection