[Plugin] fix: reimplement command line parsing (because we can and also...

[Plugin] fix: reimplement command line parsing (because we can and also because apache exec is buggy).

libraries/build.sbt

@@ -259,7 +259,7 @@ lazy val math = OsgiProject(dir, "org.apache.commons.math", exports = Seq("org.a
   (libraryDependencies += "org.apache.commons" % "commons-math3" % mathVersion, version := mathVersion) settings(settings: _*)
 
 lazy val exec = OsgiProject(dir, "org.apache.commons.exec") settings
-  (libraryDependencies += "org.apache.commons" % "commons-exec" % "1.1", version := "1.1") settings(settings: _*)
+  (libraryDependencies += "org.apache.commons" % "commons-exec" % "1.3", version := "1.3") settings(settings: _*)
 
 lazy val log4j = OsgiProject(dir, "org.apache.log4j") settings
   (libraryDependencies += "log4j" % "log4j" % "1.2.17", version := "1.2.17") settings(settings: _*)

openmole/plugins/org.openmole.plugin.task.care/src/main/scala/org/openmole/plugin/task/care/CARETask.scala

@@ -171,14 +171,14 @@ object CARETask extends Logger {
 
       reExecute.setExecutable(true)
 
-      val commandline = commandLine(command.map(s"./${reExecute.getName} " + _), userWorkDirectory).from(preparedContext)
+      val cl = commandLine(command.map(s"./${reExecute.getName} " + _), userWorkDirectory).from(preparedContext)
 
       def prootNoSeccomp = if (preference(CARETask.disableSeccomp)) Vector(("PROOT_NO_SECCOMP", "1")) else Vector()
 
       val allEnvironmentVariables = environmentVariables.map { case (varName, variable) ⇒ (varName, variable.from(context)) } ++ prootNoSeccomp
-      val executionResult = execute(commandline, extractedArchive, allEnvironmentVariables, stdOut.isDefined, stdErr.isDefined)
+      val executionResult = execute(cl.toArray, extractedArchive, allEnvironmentVariables, stdOut.isDefined, stdErr.isDefined)
 
-      if (errorOnReturnValue && returnValue.isEmpty && executionResult.returnCode != 0) throw error(commandline.toVector, executionResult)
+      if (errorOnReturnValue && returnValue.isEmpty && executionResult.returnCode != 0) throw error(cl, executionResult)
 
       def rootDirectory = extractedArchive / rootfs
 

openmole/plugins/org.openmole.plugin.task.r/src/main/scala/org/openmole/plugin/task/r/RTask.scala

@@ -17,7 +17,7 @@ import org.openmole.core.dsl._
 
 object RTask {
 
-  def installLibraries(libraries: Seq[String]) = s"""R -e "install.packages(c(${libraries.map(lib ⇒ s"'$lib'").mkString(",")}), dependencies = T)""""
+  def installLibraries(libraries: Seq[String]) = s"""R -e 'install.packages(c(${libraries.map(lib ⇒ '"' + s"$lib" + '"').mkString(",")}), dependencies = T)'"""
   def rImage(version: OptionalArgument[String]) = DockerImage("r-base", version.getOrElse("latest"))
 
   def apply(
@@ -28,7 +28,7 @@ object RTask {
   )(implicit name: sourcecode.Name, newFile: NewFile, workspace: Workspace, preference: Preference, fileService: FileService) =
     UDockerTask(
       rImage(version),
-      s"R --slave -f ${script.getName}" + arguments.map(a ⇒ " --args ${a}").getOrElse(""),
+      s"R --slave -f ${script.getName}" + arguments.map(a ⇒ s" --args ${a}").getOrElse(""),
       installCommands = Vector(installLibraries(libraries))
     ) set (
         resources += script,

openmole/plugins/org.openmole.plugin.task.systemexec/src/main/scala/org/openmole/plugin/task/systemexec/package.scala

@@ -18,9 +18,9 @@
 package org.openmole.plugin.task
 
 import java.io.{ File, IOException, PrintStream }
+import java.text.ParseException
 
 import monocle.Lens
-import org.apache.commons.exec.CommandLine
 import org.openmole.core.context._
 import org.openmole.core.exception._
 import org.openmole.core.expansion.FromContext
@@ -176,14 +176,14 @@ package object systemexec extends external.ExternalPackage with SystemExecPackag
 
   case class ExecutionResult(returnCode: Int, output: Option[String], errorOutput: Option[String])
 
-  def commandLine(cmd: String) = CommandLine.parse(cmd).toStrings
+  def commandLine(cmd: String) = parse(cmd)
 
   def commandLine(
     cmd:     FromContext[String],
     workDir: String
   ) = FromContext { p ⇒
     import p._
-    CommandLine.parse(cmd.from(context + Variable(External.PWD, workDir))).toStrings
+    parse(cmd.from(context + Variable(External.PWD, workDir)))
   }
 
   def execute(
@@ -269,11 +269,63 @@ package object systemexec extends external.ExternalPackage with SystemExecPackag
     cmds match {
       case Nil ⇒ acc
       case cmd :: t ⇒
-        val commandline = commandLine(cmd, workDirectory.getAbsolutePath).from(context)
-        val result = execute(commandline, workDirectory, environmentVariables, returnOutput = stdOut.isDefined, returnError = stdErr.isDefined, errorOnReturnValue = false)
-        if (errorOnReturnValue && !returnValue.isDefined && result.returnCode != 0) throw error(commandline.toVector, result)
+        val cl = commandLine(cmd, workDirectory.getAbsolutePath).from(context)
+        val result = execute(cl.toArray, workDirectory, environmentVariables, returnOutput = stdOut.isDefined, returnError = stdErr.isDefined, errorOnReturnValue = false)
+        if (errorOnReturnValue && !returnValue.isDefined && result.returnCode != 0) throw error(cl, result)
         else executeAll(workDirectory, environmentVariables, errorOnReturnValue, returnValue, stdOut, stdErr, t, ExecutionResult.append(acc, result))(p)
     }
   }
 
+  def parse(line: String) = {
+    var inDoubleQuote = false
+    var inSingleQuote = false
+    var blocked = false
+    var afterSpace = false
+
+    val arguments = collection.mutable.ListBuffer[String]()
+    val currentArguments = new StringBuilder
+
+    def addArgument() = {
+      arguments += currentArguments.toString()
+      currentArguments.clear()
+    }
+
+    for (character ← line) {
+      (inDoubleQuote, inSingleQuote, blocked, character, afterSpace) match {
+        case (_, _, true, c, _) ⇒
+          currentArguments.append(c)
+          blocked = false
+
+        case (_, _, false, '\\', _) ⇒ blocked = true
+        case (false, false, false, ' ', _) ⇒
+          if (!currentArguments.isEmpty) addArgument()
+
+        case (false, false, false, '"', _) ⇒
+          inDoubleQuote = true
+        // currentArguments.append(character)
+        case (true, false, false, '"', false) ⇒
+          inDoubleQuote = false
+        //currentArguments.append(character)
+
+        case (false, false, false, ''', _) ⇒
+          inSingleQuote = true
+        //currentArguments.append(character)
+        case (false, true, false, ''', false) ⇒
+          inSingleQuote = false
+        //currentArguments.append(character)
+
+        case (false, false, false, c, _) ⇒ currentArguments.append(c)
+        case (true, false, false, c, _)  ⇒ currentArguments.append(c)
+        case (false, true, false, c, _)  ⇒ currentArguments.append(c)
+        case _                           ⇒ throw new RuntimeException(s"Error while parsing command line: $line")
+      }
+
+      afterSpace = character == ' '
+    }
+
+    if (!currentArguments.isEmpty) addArgument()
+
+    arguments.toVector
+  }
+
 }

openmole/plugins/org.openmole.plugin.task.systemexec/src/test/scala/org/openmole/plugin/task/systemexec/ParserSpec.scala

+package org.openmole.plugin.task.systemexec
+
+import org.scalatest._
+
+class ParserSpec extends FlatSpec with Matchers {
+
+  "Command line arguments" should "be parsed propely" in {
+    val l1 = """R -e "install.packages(c(\"lib\"), dependencies = T)""""
+    parse(l1).size should equal(3)
+
+    val l2 = s"/tmp/udocker create --name=eiav80eaiuE imageId"
+    parse(l2).size should equal(4)
+
+    val l3 = """/home/reuillon/.openmole/simplet/.tmp/3d48df46-a2b5-46f3-bcf8-e0a99bb0f2de/execution9ee99d7e-52e4-4ff4-bd6a-6942b7104eec/udocker/udocker run --workdir="/"  -v "/home/reuillon/.openmole/simplet/.tmp/3d48df46-a2b5-46f3-bcf8-e0a99bb0f2de/execution9ee99d7e-52e4-4ff4-bd6a-6942b7104eec/externalTask035caba5-a447-4267-8f5d-a67e5fdc80b6/inputs/data.csv":"/data.csv" -v "/home/reuillon/.openmole/simplet/.tmp/3d48df46-a2b5-46f3-bcf8-e0a99bb0f2de/execution9ee99d7e-52e4-4ff4-bd6a-6942b7104eec/externalTask035caba5-a447-4267-8f5d-a67e5fdc80b6/inputs/test.R":"/test.R" jfdoimamfhkdkbekapobfgofgdebbjni R -e "install.packages(c('spdep'), dependencies = T)""""
+    parse(l3).size should equal(11)
+  }
+
+}

openmole/plugins/org.openmole.plugin.task.udocker/src/main/scala/org/openmole/plugin/task/udocker/UDockerTask.scala

@@ -316,11 +316,15 @@ object UDockerTask {
 
       def newContainer(imageId: String)() = newFile.withTmpDir { tmpDirectory ⇒
         val name = containerName(UUID.randomUUID().toString)
-        val commandline = commandLine(s"${uDockerFile.getAbsolutePath} create --name=$name $imageId")
-        execute(commandline, tmpDirectory, udockerVariables(), returnOutput = true, returnError = true)
+
+        val cl = commandLine(s"${uDockerFile.getAbsolutePath} create --name=$name $imageId")
+        execute(cl.toArray, tmpDirectory, udockerVariables(), returnOutput = true, returnError = true)
 
         if (!uDocker.installCommands.isEmpty) {
           val runInstall = uDocker.installCommands.map(ic ⇒ runCommand(uDocker)(uDockerFile, volumes.toVector, name, ic))
+
+          println(runInstall.map(_.from(preparedContext)))
+
           executeAll(
             tmpDirectory,
             udockerVariables(),

openmole/project/Libraries.scala

@@ -58,7 +58,7 @@ object Libraries {
   lazy val scalatexSite = "org.openmole.library" %% "com-lihaoyi-scalatex-site" % "0.3.7"
   lazy val math = "org.openmole.library" %% "org-apache-commons-math" % "3.6.1"
   lazy val collections = "org.openmole.library" %% "org-apache-commons-collections" % "4.1"
-  lazy val exec = "org.openmole.library" %% "org-apache-commons-exec" % "1.1"
+  lazy val exec = "org.openmole.library" %% "org-apache-commons-exec" % "1.3"
   lazy val log4j = "org.openmole.library" %% "org-apache-log4j" % "1.2.17"
   lazy val logging = "org.openmole.library" %% "org-apache-commons-logging" % "1.2"
   lazy val lang3 = "org.openmole.library" %% "org-apache-commons-lang3" % "3.4"