From 5cd619ab0f6984400b2cfff0726415a6a8c7f201 Mon Sep 17 00:00:00 2001
From: asandrad22 <asandrad22x@gmail.com>
Date: Wed, 4 Nov 2015 20:28:59 +0000
Subject: [PATCH 1/4] Adding vagrant files to replicate server enviornments.
 Adding BuilderCompilerHandler.php. This file is what handles compiling
 request for arduino builder. Locations are currently hardcoded.

---
 BuilderCompilerHandler.php                    | 301 ++++++++++++++++++
 .../default/virtualbox/action_provision       |   1 +
 .../default/virtualbox/action_set_name        |   1 +
 .../machines/default/virtualbox/creator_uid   |   1 +
 .../.vagrant/machines/default/virtualbox/id   |   1 +
 .../machines/default/virtualbox/index_uuid    |   1 +
 .../machines/default/virtualbox/private_key   |  27 ++
 .../default/virtualbox/synced_folders         |   1 +
 vagrant/Vagrantfile                           |  71 +++++
 9 files changed, 405 insertions(+)
 create mode 100644 BuilderCompilerHandler.php
 create mode 100755 vagrant/.vagrant/machines/default/virtualbox/action_provision
 create mode 100755 vagrant/.vagrant/machines/default/virtualbox/action_set_name
 create mode 100755 vagrant/.vagrant/machines/default/virtualbox/creator_uid
 create mode 100755 vagrant/.vagrant/machines/default/virtualbox/id
 create mode 100755 vagrant/.vagrant/machines/default/virtualbox/index_uuid
 create mode 100755 vagrant/.vagrant/machines/default/virtualbox/private_key
 create mode 100755 vagrant/.vagrant/machines/default/virtualbox/synced_folders
 create mode 100755 vagrant/Vagrantfile

diff --git a/BuilderCompilerHandler.php b/BuilderCompilerHandler.php
new file mode 100644
index 0000000..a5a81bc
--- /dev/null
+++ b/BuilderCompilerHandler.php
@@ -0,0 +1,301 @@
+<?php
+
+
+namespace Codebender\CompilerBundle\Handler;
+
+// This file uses mktemp() to create a temporary directory where all the files
+// needed to process the compile request are stored.
+require_once "System.php";
+use System;
+use Codebender\CompilerBundle\Handler\MCUHandler;
+
+
+class BuilderCompilerHandler
+{
+
+	private $preproc;
+	private $postproc;
+	private $utility;
+
+	function __construct()
+	{
+		$this->preproc = new PreprocessingHandler();
+		$this->postproc = new PostprocessingHandler();
+		$this->utility = new UtilityHandler();
+	}
+
+	/**
+	\brief Processes a compile request.
+
+	\param string $request The body of the POST request.
+	\return A message to be JSON-encoded and sent back to the requestor.
+	 */
+	function main($request, $compiler_config)
+	{
+					
+		error_reporting(E_ALL & ~E_STRICT);
+
+		$this->set_values($compiler_config,
+			$CC, $CPP, $AS, $LD, $CLANG, $OBJCOPY, $SIZE, $CFLAGS, $CPPFLAGS, $ASFLAGS, $LDFLAGS, $LDFLAGS_TAIL,
+			$CLANG_FLAGS, $OBJCOPY_FLAGS, $SIZE_FLAGS, $OUTPUT, $ARDUINO_CORES_DIR, $ARDUINO_SKEL);
+
+		$start_time = microtime(true);
+		
+		
+		// Step 0: Reject the request if the input data is not valid.
+		//TODO: Replace $tmp variable name
+		$tmp = $this->requestValid($request);
+		if($tmp["success"] == false)
+			return $tmp;
+
+		$this->set_variables($request, $format, $libraries, $version, $mcu, $f_cpu, $core, $variant, $vid, $pid);
+
+		// Step 1: Extract the files included in the request.
+		$tmp = $this->extractFiles($request, $dir, $files);
+		if ($tmp["success"] == false)
+			return $tmp;
+		
+
+		$tmp = $this->doCompile($files, $dir, $format);
+		if ($tmp["success"] == false)
+			return $tmp;
+
+		if ($format == "syntax")
+			return array(
+				"success" => true,
+				"time" => microtime(true) - $start_time);
+
+		$build_path = '/tmp/codebender_object_files';
+		$tmp = $this->convertOutput($build_path, $format, $SIZE, "Blink Example.ino", $start_time);
+	    return $tmp;
+		
+
+	}
+	
+	
+    private function requestValid(&$request)
+	{
+		$request = $this->preproc->validate_input($request);
+		if (!$request)
+			return array(
+				"success" => false,
+				"step" => 0,
+				"message" => "Invalid input.");
+		else return array("success" => true);
+	}
+	
+	protected function extractFiles($request, &$dir, &$files)
+	{
+		// Create a temporary directory to place all the files needed to process
+		// the compile request. This directory is created in $TMPDIR or /tmp by
+		// default and is automatically removed upon execution completion.
+		$dir = "/tmp/compiler";
+		
+		mkdir($dir);
+
+		if (!$dir)
+			return array(
+				"success" => false,
+				"step" => 1,
+				"message" => "Failed to create temporary directory.");
+
+		$response = $this->utility->extract_files($dir, $request->files);
+		if ($response["success"] === false)
+			return $response;
+		$files = $response["files"];
+
+		if (!file_exists($dir."/libraries"))
+			mkdir($dir."/libraries/", 0777, true);
+		//TODO: check if it succeeded
+		$files["libs"] = array();
+		foreach($request->libraries as $library_name => $library_files)
+		{
+			//TODO: check if it succeeded
+			if (!file_exists($dir."/libraries".$library_name))
+				mkdir($dir."/libraries/".$library_name, 0777, true);
+			$tmp = $this->utility->extract_files($dir."/libraries/".$library_name, $library_files);
+			$files["libs"][] = $tmp["files"];
+		}
+
+		return array("success" => true);
+	}
+
+
+
+	protected function doCompile(&$files, $dir, $format)
+	{
+		$targets = '-hardware /home/vagrant/work/src/arduino.cc/builder/hardware -hardware /home/vagrant/arduino-nightly/hardware -hardware /home/vagrant/arduino-nightly/hardware/arduino/avr -hardware /home/vagrant/arduino-nightly/hardware/tools/avr  -libraries /home/vagrant/arduino-nightly/libraries -libraries /home/vagrant/arduino-nightly/hardware/arduino/avr/libraries -tools /usr/bin/ -tools /home/vagrant/arduino-nightly/hardware/tools/avr/ -tools /home/vagrant/arduino-nightly/tools-builder/';
+		$builder_compiler = '/home/vagrant/work/bin/builder';
+		$build_path = '/tmp/codebender_object_files';
+
+		$targets = escapeshellarg($targets);
+		$builder_compiler = escapeshellarg($builder_compiler);
+		$build_path = escapeshellarg($build_path);
+		foreach (array("c", "cpp", "S","ino") as $ext)
+		{
+			foreach ($files[$ext] as $file)
+			{
+			 	// From hereon, $file is shell escaped and thus should only be used in calls
+				// to exec().
+				$file = escapeshellarg($file);
+				exec("/home/vagrant/work/bin/builder -fqbn arduino:avr:uno -hardware /home/vagrant/work/src/arduino.cc/builder/hardware -hardware /home/vagrant/arduino-nightly/hardware -hardware /home/vagrant/arduino-nightly/hardware/arduino/avr -hardware /home/vagrant/arduino-nightly/hardware/tools/avr  -libraries /home/vagrant/arduino-nightly/libraries -libraries /home/vagrant/arduino-nightly/hardware/arduino/avr/libraries -tools /usr/bin/ -tools /home/vagrant/arduino-nightly/hardware/tools/avr/ -tools /home/vagrant/arduino-nightly/tools-builder/ -build-path $build_path $file.$ext 2>&1", $output, $ret_compile);
+				
+				
+				if (isset($ret_compile) && $ret_compile)
+				{
+					return array(
+						"success" => false,
+						"step" => 4,
+						"message" => $output,
+						"debug" => $avr_output);
+				}
+				unset($output);
+
+				$files["o"][] = array_shift($files[$ext]);
+			
+			}
+		}
+
+		return array("success" => true);
+	}
+
+    protected function convertOutput($dir, $format, $SIZE, $OUTPUT, $start_time)
+	{
+		if ($format == "elf")
+		{
+			$ret_objcopy = false;
+			//exec("$SIZE $SIZE_FLAGS --target=elf32-avr $dir/$OUTPUT.elf | awk 'FNR == 2 {print $1+$2}'", $size, $ret_size); // FIXME
+			$content = base64_encode(file_get_contents("$dir/$OUTPUT.elf"));
+		}
+		elseif ($format == "binary")
+		{
+			//exec("$OBJCOPY $OBJCOPY_FLAGS -O binary $dir/$OUTPUT.elf $dir/$OUTPUT.bin", $dummy, $ret_objcopy);
+			//exec("$SIZE $SIZE_FLAGS --target=binary $dir/$OUTPUT.bin | awk 'FNR == 2 {print $1+$2}'", $size, $ret_size); // FIXME
+			$content = base64_encode(file_get_contents("$dir/$OUTPUT.bin"));
+		}
+		elseif ($format == "hex")
+		{
+			//exec("$OBJCOPY $OBJCOPY_FLAGS -O ihex $dir/$OUTPUT.elf $dir/$OUTPUT.hex", $dummy, $ret_objcopy);
+			//exec("$SIZE $SIZE_FLAGS --target=ihex $dir/$OUTPUT.hex | awk 'FNR == 2 {print $1+$2}'", $size, $ret_size); // FIXME
+			$content = file_get_contents("$dir/$OUTPUT.hex");
+		}
+
+		// If everything went well, return the reply to the caller.
+		if ($ret_objcopy || $ret_size || $content === false)
+			return array(
+				"success" => false,
+				"step" => 8,
+				"message" => "There was a problem while generating the your binary file");
+		else
+			return array(
+				"success" => true,
+				"time" => microtime(true) - $start_time,
+				"size" => $size[0],
+				"output" => $content);
+
+	}
+
+	private function preprocessIno(&$files, $ARDUINO_CORES_DIR, $ARDUINO_SKEL, $version, $core)
+	{
+		foreach ($files["ino"] as $file)
+		{
+			//TODO: make it compatible with non-default hardware (variants & cores)
+			if (!isset($skel) && ($skel = file_get_contents("$ARDUINO_CORES_DIR/v$version/hardware/arduino/cores/$core/$ARDUINO_SKEL")) === false)
+				return array(
+					"success" => false,
+					"step" => 2,
+					"message" => "Failed to open Arduino skeleton file.");
+
+			$code = file_get_contents("$file.ino");
+			$new_code = $this->preproc->ino_to_cpp($skel, $code, "$file.ino");
+			$ret = file_put_contents("$file.cpp", $new_code);
+
+			if ($code === false || !$new_code || !$ret)
+				return array(
+					"success" => false,
+					"step" => 2,
+					"message" => "Failed to preprocess file '$file.ino'.");
+
+			$files["cpp"][] = array_shift($files["ino"]);
+		}
+
+		return array("success" => true);
+	}
+
+	public function preprocessHeaders(&$files, &$libraries, &$include_directories, $dir, $ARDUINO_CORES_DIR, $version, $core, $variant)
+	{
+		try
+		{
+			// Create command-line arguments for header search paths. Note that the
+			// current directory is added to eliminate the difference between <>
+			// and "" in include preprocessor directives.
+			//TODO: make it compatible with non-default hardware (variants & cores)
+			$include_directories = "-I$dir -I$ARDUINO_CORES_DIR/v$version/hardware/arduino/cores/$core -I$ARDUINO_CORES_DIR/v$version/hardware/arduino/variants/$variant";
+
+			//TODO: The code that rests on the main website looks for headers in all files, not just c, cpp and h. Might raise a security issue
+			$files["dir"] = array();
+			foreach($libraries as $library_name => $library_files)
+			{
+				$files["dir"][] = $dir."/libraries/".$library_name;
+			}
+
+			// Add the libraries' paths in the include paths in the command-line arguments
+			if (file_exists("$dir/utility"))
+				$include_directories .= " -I$dir/utility";
+			foreach ($files["dir"] as $directory)
+				$include_directories .= " -I$directory";
+		}
+		catch(\Exception $e)
+		{
+			return array("success" => false, "step" => 3, "message" => "Unknown Error:\n".$e->getMessage());
+		}
+
+		return array("success" => true);
+	}
+    private function set_values($compiler_config,
+	                            &$CC, &$CPP, &$AS, &$LD, &$CLANG, &$OBJCOPY, &$SIZE, &$CFLAGS, &$CPPFLAGS,
+	                            &$ASFLAGS, &$LDFLAGS, &$LDFLAGS_TAIL, &$CLANG_FLAGS, &$OBJCOPY_FLAGS, &$SIZE_FLAGS,
+	                            &$OUTPUT, &$ARDUINO_CORES_DIR, &$ARDUINO_SKEL)
+	{
+		// External binaries.
+		$CC = $compiler_config["cc"];
+		$CPP = $compiler_config["cpp"];
+		$AS = $compiler_config["as"];
+		$LD = $compiler_config["ld"];
+		$CLANG = $compiler_config["clang"];
+		$OBJCOPY = $compiler_config["objcopy"];
+		$SIZE = $compiler_config["size"];
+		// Standard command-line arguments used by the binaries.
+		$CFLAGS = $compiler_config["cflags"];
+		$CPPFLAGS = $compiler_config["cppflags"];
+		$ASFLAGS = $compiler_config["asflags"];
+		$LDFLAGS = $compiler_config["ldflags"];
+		$LDFLAGS_TAIL = $compiler_config["ldflags_tail"];
+		$CLANG_FLAGS = $compiler_config["clang_flags"];
+		$OBJCOPY_FLAGS = $compiler_config["objcopy_flags"];
+		$SIZE_FLAGS = $compiler_config["size_flags"];
+		// The default name of the output file.
+		$OUTPUT = $compiler_config["output"];
+		// Path to arduino-core-files repository.
+		$ARDUINO_CORES_DIR = $compiler_config["arduino_cores_dir"];
+		// The name of the Arduino skeleton file.
+		$ARDUINO_SKEL = $compiler_config["arduino_skel"];
+	}
+
+	private function set_variables($request, &$format, &$libraries, &$version, &$mcu, &$f_cpu, &$core, &$variant, &$vid, &$pid)
+	{
+		// Extract the request options for easier access.
+		$format = $request->format;
+		$libraries = $request->libraries;
+		$version = $request->version;
+		$mcu = $request->build->mcu;
+		$f_cpu = $request->build->f_cpu;
+		$core = $request->build->core;
+		$variant = $request->build->variant;
+
+		// Set the appropriate variables for vid and pid (Leonardo).
+		$vid = ($variant == "leonardo") ? $request->build->vid : "";
+		$pid = ($variant == "leonardo") ? $request->build->pid : "";
+	}
+	
+}
diff --git a/vagrant/.vagrant/machines/default/virtualbox/action_provision b/vagrant/.vagrant/machines/default/virtualbox/action_provision
new file mode 100755
index 0000000..95e57e1
--- /dev/null
+++ b/vagrant/.vagrant/machines/default/virtualbox/action_provision
@@ -0,0 +1 @@
+1.5:4f2169c0-47c5-4bce-9859-58fda0f7a877
\ No newline at end of file
diff --git a/vagrant/.vagrant/machines/default/virtualbox/action_set_name b/vagrant/.vagrant/machines/default/virtualbox/action_set_name
new file mode 100755
index 0000000..f995fa2
--- /dev/null
+++ b/vagrant/.vagrant/machines/default/virtualbox/action_set_name
@@ -0,0 +1 @@
+1445846899
\ No newline at end of file
diff --git a/vagrant/.vagrant/machines/default/virtualbox/creator_uid b/vagrant/.vagrant/machines/default/virtualbox/creator_uid
new file mode 100755
index 0000000..c227083
--- /dev/null
+++ b/vagrant/.vagrant/machines/default/virtualbox/creator_uid
@@ -0,0 +1 @@
+0
\ No newline at end of file
diff --git a/vagrant/.vagrant/machines/default/virtualbox/id b/vagrant/.vagrant/machines/default/virtualbox/id
new file mode 100755
index 0000000..c5cb3ad
--- /dev/null
+++ b/vagrant/.vagrant/machines/default/virtualbox/id
@@ -0,0 +1 @@
+4f2169c0-47c5-4bce-9859-58fda0f7a877
\ No newline at end of file
diff --git a/vagrant/.vagrant/machines/default/virtualbox/index_uuid b/vagrant/.vagrant/machines/default/virtualbox/index_uuid
new file mode 100755
index 0000000..78d5735
--- /dev/null
+++ b/vagrant/.vagrant/machines/default/virtualbox/index_uuid
@@ -0,0 +1 @@
+b2d9f07d2f6d42afbd0db6752774cf06
\ No newline at end of file
diff --git a/vagrant/.vagrant/machines/default/virtualbox/private_key b/vagrant/.vagrant/machines/default/virtualbox/private_key
new file mode 100755
index 0000000..ba45790
--- /dev/null
+++ b/vagrant/.vagrant/machines/default/virtualbox/private_key
@@ -0,0 +1,27 @@
+-----BEGIN RSA PRIVATE KEY-----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+-----END RSA PRIVATE KEY-----
diff --git a/vagrant/.vagrant/machines/default/virtualbox/synced_folders b/vagrant/.vagrant/machines/default/virtualbox/synced_folders
new file mode 100755
index 0000000..39695eb
--- /dev/null
+++ b/vagrant/.vagrant/machines/default/virtualbox/synced_folders
@@ -0,0 +1 @@
+{"virtualbox":{"/vagrant":{"guestpath":"/vagrant","hostpath":"C:/Users/Arturo/Documents/Computer-Engineer/vargant","disabled":false}}}
\ No newline at end of file
diff --git a/vagrant/Vagrantfile b/vagrant/Vagrantfile
new file mode 100755
index 0000000..c1653dc
--- /dev/null
+++ b/vagrant/Vagrantfile
@@ -0,0 +1,71 @@
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+# All Vagrant configuration is done below. The "2" in Vagrant.configure
+# configures the configuration version (we support older styles for
+# backwards compatibility). Please don't change it unless you know what
+# you're doing.
+Vagrant.configure(2) do |config|
+  # The most common configuration options are documented and commented below.
+  # For a complete reference, please see the online documentation at
+  # https://docs.vagrantup.com.
+
+  # Every Vagrant development environment requires a box. You can search for
+  # boxes at https://atlas.hashicorp.com/search.
+  config.vm.box = "ubuntu/trusty64"
+
+  # Disable automatic box update checking. If you disable this, then
+  # boxes will only be checked for updates when the user runs
+  # `vagrant box outdated`. This is not recommended.
+  # config.vm.box_check_update = true
+
+  # Create a forwarded port mapping which allows access to a specific port
+  # within the machine from a port on the host machine. In the example below,
+  # accessing "localhost:8080" will access port 80 on the guest machine.
+  config.vm.network "forwarded_port", guest: 80, host: 80
+
+  # Create a private network, which allows host-only access to the machine
+  # using a specific IP.
+  # config.vm.network "private_network", ip: "192.168.33.10"
+
+  # Create a public network, which generally matched to bridged network.
+  # Bridged networks make the machine appear as another physical device on
+  # your network.
+  # config.vm.network "public_network"
+
+  # Share an additional folder to the guest VM. The first argument is
+  # the path on the host to the actual folder. The second argument is
+  # the path on the guest to mount the folder. And the optional third
+  # argument is a set of non-required options.
+  #config.vm.synced_folder "./", "/home/vagrant"
+
+  # Provider-specific configuration so you can fine-tune various
+  # backing providers for Vagrant. These expose provider-specific options.
+  # Example for VirtualBox:
+  #
+  config.vm.provider "virtualbox" do |vb|
+  #   # Display the VirtualBox GUI when booting the machine
+    vb.gui = true
+  #
+  #   # Customize the amount of memory on the VM:
+     vb.memory = "2048"
+  end
+  #
+  # View the documentation for the provider you are using for more
+  # information on available options.
+
+  # Define a Vagrant Push strategy for pushing to Atlas. Other push strategies
+  # such as FTP and Heroku are also available. See the documentation at
+  # https://docs.vagrantup.com/v2/push/atlas.html for more information.
+  # config.push.define "atlas" do |push|
+  #   push.app = "YOUR_ATLAS_USERNAME/YOUR_APPLICATION_NAME"
+  # end
+
+  # Enable provisioning with a shell script. Additional provisioners such as
+  # Puppet, Chef, Ansible, Salt, and Docker are also available. Please see the
+  # documentation for more information about their specific syntax and use.
+   config.vm.provision "shell", inline: <<-SHELL
+     sudo apt-get update
+     sudo apt-get install -y apache2
+  SHELL
+end

From 46c6a61cb6945050c28b132a4d6879f5def2cb03 Mon Sep 17 00:00:00 2001
From: asandrad22 <asandrad22x@gmail.com>
Date: Fri, 27 Nov 2015 21:35:12 +0000
Subject: [PATCH 2/4] deleted vagrant folder moved BuilderCompilerHandler.php
 to modified files added modified-files so Codebender/compiler can support
 arduino-builder added setup.sh to set up server enviornment

---
 .gitignore                                    |   1 +
 BuilderCompilerHandler.php                    | 301 ------------------
 vagrant/Vagrantfile => Vagrantfile            |   4 +-
 .../Controller/DefaultController.php          | 180 +++++++++++
 .../Handler/BuilderCompilerHandler.php        | 262 +++++++++++++++
 .../Resources/config/routing.yml              |  27 ++
 .../Resources/config/services.yml             |  36 +++
 setup.sh                                      |  16 +
 .../default/virtualbox/action_provision       |   1 -
 .../default/virtualbox/action_set_name        |   1 -
 .../machines/default/virtualbox/creator_uid   |   1 -
 .../.vagrant/machines/default/virtualbox/id   |   1 -
 .../machines/default/virtualbox/index_uuid    |   1 -
 .../machines/default/virtualbox/private_key   |  27 --
 .../default/virtualbox/synced_folders         |   1 -
 15 files changed, 524 insertions(+), 336 deletions(-)
 create mode 100644 .gitignore
 delete mode 100644 BuilderCompilerHandler.php
 rename vagrant/Vagrantfile => Vagrantfile (95%)
 mode change 100755 => 100644
 create mode 100644 modified-files/CompilerBundle/Controller/DefaultController.php
 create mode 100644 modified-files/CompilerBundle/Handler/BuilderCompilerHandler.php
 create mode 100644 modified-files/CompilerBundle/Resources/config/routing.yml
 create mode 100644 modified-files/CompilerBundle/Resources/config/services.yml
 create mode 100644 setup.sh
 delete mode 100755 vagrant/.vagrant/machines/default/virtualbox/action_provision
 delete mode 100755 vagrant/.vagrant/machines/default/virtualbox/action_set_name
 delete mode 100755 vagrant/.vagrant/machines/default/virtualbox/creator_uid
 delete mode 100755 vagrant/.vagrant/machines/default/virtualbox/id
 delete mode 100755 vagrant/.vagrant/machines/default/virtualbox/index_uuid
 delete mode 100755 vagrant/.vagrant/machines/default/virtualbox/private_key
 delete mode 100755 vagrant/.vagrant/machines/default/virtualbox/synced_folders

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..997ca2f
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+.vagrant
\ No newline at end of file
diff --git a/BuilderCompilerHandler.php b/BuilderCompilerHandler.php
deleted file mode 100644
index a5a81bc..0000000
--- a/BuilderCompilerHandler.php
+++ /dev/null
@@ -1,301 +0,0 @@
-<?php
-
-
-namespace Codebender\CompilerBundle\Handler;
-
-// This file uses mktemp() to create a temporary directory where all the files
-// needed to process the compile request are stored.
-require_once "System.php";
-use System;
-use Codebender\CompilerBundle\Handler\MCUHandler;
-
-
-class BuilderCompilerHandler
-{
-
-	private $preproc;
-	private $postproc;
-	private $utility;
-
-	function __construct()
-	{
-		$this->preproc = new PreprocessingHandler();
-		$this->postproc = new PostprocessingHandler();
-		$this->utility = new UtilityHandler();
-	}
-
-	/**
-	\brief Processes a compile request.
-
-	\param string $request The body of the POST request.
-	\return A message to be JSON-encoded and sent back to the requestor.
-	 */
-	function main($request, $compiler_config)
-	{
-					
-		error_reporting(E_ALL & ~E_STRICT);
-
-		$this->set_values($compiler_config,
-			$CC, $CPP, $AS, $LD, $CLANG, $OBJCOPY, $SIZE, $CFLAGS, $CPPFLAGS, $ASFLAGS, $LDFLAGS, $LDFLAGS_TAIL,
-			$CLANG_FLAGS, $OBJCOPY_FLAGS, $SIZE_FLAGS, $OUTPUT, $ARDUINO_CORES_DIR, $ARDUINO_SKEL);
-
-		$start_time = microtime(true);
-		
-		
-		// Step 0: Reject the request if the input data is not valid.
-		//TODO: Replace $tmp variable name
-		$tmp = $this->requestValid($request);
-		if($tmp["success"] == false)
-			return $tmp;
-
-		$this->set_variables($request, $format, $libraries, $version, $mcu, $f_cpu, $core, $variant, $vid, $pid);
-
-		// Step 1: Extract the files included in the request.
-		$tmp = $this->extractFiles($request, $dir, $files);
-		if ($tmp["success"] == false)
-			return $tmp;
-		
-
-		$tmp = $this->doCompile($files, $dir, $format);
-		if ($tmp["success"] == false)
-			return $tmp;
-
-		if ($format == "syntax")
-			return array(
-				"success" => true,
-				"time" => microtime(true) - $start_time);
-
-		$build_path = '/tmp/codebender_object_files';
-		$tmp = $this->convertOutput($build_path, $format, $SIZE, "Blink Example.ino", $start_time);
-	    return $tmp;
-		
-
-	}
-	
-	
-    private function requestValid(&$request)
-	{
-		$request = $this->preproc->validate_input($request);
-		if (!$request)
-			return array(
-				"success" => false,
-				"step" => 0,
-				"message" => "Invalid input.");
-		else return array("success" => true);
-	}
-	
-	protected function extractFiles($request, &$dir, &$files)
-	{
-		// Create a temporary directory to place all the files needed to process
-		// the compile request. This directory is created in $TMPDIR or /tmp by
-		// default and is automatically removed upon execution completion.
-		$dir = "/tmp/compiler";
-		
-		mkdir($dir);
-
-		if (!$dir)
-			return array(
-				"success" => false,
-				"step" => 1,
-				"message" => "Failed to create temporary directory.");
-
-		$response = $this->utility->extract_files($dir, $request->files);
-		if ($response["success"] === false)
-			return $response;
-		$files = $response["files"];
-
-		if (!file_exists($dir."/libraries"))
-			mkdir($dir."/libraries/", 0777, true);
-		//TODO: check if it succeeded
-		$files["libs"] = array();
-		foreach($request->libraries as $library_name => $library_files)
-		{
-			//TODO: check if it succeeded
-			if (!file_exists($dir."/libraries".$library_name))
-				mkdir($dir."/libraries/".$library_name, 0777, true);
-			$tmp = $this->utility->extract_files($dir."/libraries/".$library_name, $library_files);
-			$files["libs"][] = $tmp["files"];
-		}
-
-		return array("success" => true);
-	}
-
-
-
-	protected function doCompile(&$files, $dir, $format)
-	{
-		$targets = '-hardware /home/vagrant/work/src/arduino.cc/builder/hardware -hardware /home/vagrant/arduino-nightly/hardware -hardware /home/vagrant/arduino-nightly/hardware/arduino/avr -hardware /home/vagrant/arduino-nightly/hardware/tools/avr  -libraries /home/vagrant/arduino-nightly/libraries -libraries /home/vagrant/arduino-nightly/hardware/arduino/avr/libraries -tools /usr/bin/ -tools /home/vagrant/arduino-nightly/hardware/tools/avr/ -tools /home/vagrant/arduino-nightly/tools-builder/';
-		$builder_compiler = '/home/vagrant/work/bin/builder';
-		$build_path = '/tmp/codebender_object_files';
-
-		$targets = escapeshellarg($targets);
-		$builder_compiler = escapeshellarg($builder_compiler);
-		$build_path = escapeshellarg($build_path);
-		foreach (array("c", "cpp", "S","ino") as $ext)
-		{
-			foreach ($files[$ext] as $file)
-			{
-			 	// From hereon, $file is shell escaped and thus should only be used in calls
-				// to exec().
-				$file = escapeshellarg($file);
-				exec("/home/vagrant/work/bin/builder -fqbn arduino:avr:uno -hardware /home/vagrant/work/src/arduino.cc/builder/hardware -hardware /home/vagrant/arduino-nightly/hardware -hardware /home/vagrant/arduino-nightly/hardware/arduino/avr -hardware /home/vagrant/arduino-nightly/hardware/tools/avr  -libraries /home/vagrant/arduino-nightly/libraries -libraries /home/vagrant/arduino-nightly/hardware/arduino/avr/libraries -tools /usr/bin/ -tools /home/vagrant/arduino-nightly/hardware/tools/avr/ -tools /home/vagrant/arduino-nightly/tools-builder/ -build-path $build_path $file.$ext 2>&1", $output, $ret_compile);
-				
-				
-				if (isset($ret_compile) && $ret_compile)
-				{
-					return array(
-						"success" => false,
-						"step" => 4,
-						"message" => $output,
-						"debug" => $avr_output);
-				}
-				unset($output);
-
-				$files["o"][] = array_shift($files[$ext]);
-			
-			}
-		}
-
-		return array("success" => true);
-	}
-
-    protected function convertOutput($dir, $format, $SIZE, $OUTPUT, $start_time)
-	{
-		if ($format == "elf")
-		{
-			$ret_objcopy = false;
-			//exec("$SIZE $SIZE_FLAGS --target=elf32-avr $dir/$OUTPUT.elf | awk 'FNR == 2 {print $1+$2}'", $size, $ret_size); // FIXME
-			$content = base64_encode(file_get_contents("$dir/$OUTPUT.elf"));
-		}
-		elseif ($format == "binary")
-		{
-			//exec("$OBJCOPY $OBJCOPY_FLAGS -O binary $dir/$OUTPUT.elf $dir/$OUTPUT.bin", $dummy, $ret_objcopy);
-			//exec("$SIZE $SIZE_FLAGS --target=binary $dir/$OUTPUT.bin | awk 'FNR == 2 {print $1+$2}'", $size, $ret_size); // FIXME
-			$content = base64_encode(file_get_contents("$dir/$OUTPUT.bin"));
-		}
-		elseif ($format == "hex")
-		{
-			//exec("$OBJCOPY $OBJCOPY_FLAGS -O ihex $dir/$OUTPUT.elf $dir/$OUTPUT.hex", $dummy, $ret_objcopy);
-			//exec("$SIZE $SIZE_FLAGS --target=ihex $dir/$OUTPUT.hex | awk 'FNR == 2 {print $1+$2}'", $size, $ret_size); // FIXME
-			$content = file_get_contents("$dir/$OUTPUT.hex");
-		}
-
-		// If everything went well, return the reply to the caller.
-		if ($ret_objcopy || $ret_size || $content === false)
-			return array(
-				"success" => false,
-				"step" => 8,
-				"message" => "There was a problem while generating the your binary file");
-		else
-			return array(
-				"success" => true,
-				"time" => microtime(true) - $start_time,
-				"size" => $size[0],
-				"output" => $content);
-
-	}
-
-	private function preprocessIno(&$files, $ARDUINO_CORES_DIR, $ARDUINO_SKEL, $version, $core)
-	{
-		foreach ($files["ino"] as $file)
-		{
-			//TODO: make it compatible with non-default hardware (variants & cores)
-			if (!isset($skel) && ($skel = file_get_contents("$ARDUINO_CORES_DIR/v$version/hardware/arduino/cores/$core/$ARDUINO_SKEL")) === false)
-				return array(
-					"success" => false,
-					"step" => 2,
-					"message" => "Failed to open Arduino skeleton file.");
-
-			$code = file_get_contents("$file.ino");
-			$new_code = $this->preproc->ino_to_cpp($skel, $code, "$file.ino");
-			$ret = file_put_contents("$file.cpp", $new_code);
-
-			if ($code === false || !$new_code || !$ret)
-				return array(
-					"success" => false,
-					"step" => 2,
-					"message" => "Failed to preprocess file '$file.ino'.");
-
-			$files["cpp"][] = array_shift($files["ino"]);
-		}
-
-		return array("success" => true);
-	}
-
-	public function preprocessHeaders(&$files, &$libraries, &$include_directories, $dir, $ARDUINO_CORES_DIR, $version, $core, $variant)
-	{
-		try
-		{
-			// Create command-line arguments for header search paths. Note that the
-			// current directory is added to eliminate the difference between <>
-			// and "" in include preprocessor directives.
-			//TODO: make it compatible with non-default hardware (variants & cores)
-			$include_directories = "-I$dir -I$ARDUINO_CORES_DIR/v$version/hardware/arduino/cores/$core -I$ARDUINO_CORES_DIR/v$version/hardware/arduino/variants/$variant";
-
-			//TODO: The code that rests on the main website looks for headers in all files, not just c, cpp and h. Might raise a security issue
-			$files["dir"] = array();
-			foreach($libraries as $library_name => $library_files)
-			{
-				$files["dir"][] = $dir."/libraries/".$library_name;
-			}
-
-			// Add the libraries' paths in the include paths in the command-line arguments
-			if (file_exists("$dir/utility"))
-				$include_directories .= " -I$dir/utility";
-			foreach ($files["dir"] as $directory)
-				$include_directories .= " -I$directory";
-		}
-		catch(\Exception $e)
-		{
-			return array("success" => false, "step" => 3, "message" => "Unknown Error:\n".$e->getMessage());
-		}
-
-		return array("success" => true);
-	}
-    private function set_values($compiler_config,
-	                            &$CC, &$CPP, &$AS, &$LD, &$CLANG, &$OBJCOPY, &$SIZE, &$CFLAGS, &$CPPFLAGS,
-	                            &$ASFLAGS, &$LDFLAGS, &$LDFLAGS_TAIL, &$CLANG_FLAGS, &$OBJCOPY_FLAGS, &$SIZE_FLAGS,
-	                            &$OUTPUT, &$ARDUINO_CORES_DIR, &$ARDUINO_SKEL)
-	{
-		// External binaries.
-		$CC = $compiler_config["cc"];
-		$CPP = $compiler_config["cpp"];
-		$AS = $compiler_config["as"];
-		$LD = $compiler_config["ld"];
-		$CLANG = $compiler_config["clang"];
-		$OBJCOPY = $compiler_config["objcopy"];
-		$SIZE = $compiler_config["size"];
-		// Standard command-line arguments used by the binaries.
-		$CFLAGS = $compiler_config["cflags"];
-		$CPPFLAGS = $compiler_config["cppflags"];
-		$ASFLAGS = $compiler_config["asflags"];
-		$LDFLAGS = $compiler_config["ldflags"];
-		$LDFLAGS_TAIL = $compiler_config["ldflags_tail"];
-		$CLANG_FLAGS = $compiler_config["clang_flags"];
-		$OBJCOPY_FLAGS = $compiler_config["objcopy_flags"];
-		$SIZE_FLAGS = $compiler_config["size_flags"];
-		// The default name of the output file.
-		$OUTPUT = $compiler_config["output"];
-		// Path to arduino-core-files repository.
-		$ARDUINO_CORES_DIR = $compiler_config["arduino_cores_dir"];
-		// The name of the Arduino skeleton file.
-		$ARDUINO_SKEL = $compiler_config["arduino_skel"];
-	}
-
-	private function set_variables($request, &$format, &$libraries, &$version, &$mcu, &$f_cpu, &$core, &$variant, &$vid, &$pid)
-	{
-		// Extract the request options for easier access.
-		$format = $request->format;
-		$libraries = $request->libraries;
-		$version = $request->version;
-		$mcu = $request->build->mcu;
-		$f_cpu = $request->build->f_cpu;
-		$core = $request->build->core;
-		$variant = $request->build->variant;
-
-		// Set the appropriate variables for vid and pid (Leonardo).
-		$vid = ($variant == "leonardo") ? $request->build->vid : "";
-		$pid = ($variant == "leonardo") ? $request->build->pid : "";
-	}
-	
-}
diff --git a/vagrant/Vagrantfile b/Vagrantfile
old mode 100755
new mode 100644
similarity index 95%
rename from vagrant/Vagrantfile
rename to Vagrantfile
index c1653dc..93a0c4f
--- a/vagrant/Vagrantfile
+++ b/Vagrantfile
@@ -45,7 +45,7 @@ Vagrant.configure(2) do |config|
   #
   config.vm.provider "virtualbox" do |vb|
   #   # Display the VirtualBox GUI when booting the machine
-    vb.gui = true
+  # vb.gui = true
   #
   #   # Customize the amount of memory on the VM:
      vb.memory = "2048"
@@ -66,6 +66,6 @@ Vagrant.configure(2) do |config|
   # documentation for more information about their specific syntax and use.
    config.vm.provision "shell", inline: <<-SHELL
      sudo apt-get update
-     sudo apt-get install -y apache2
+     #sudo apt-get install -y apache2
   SHELL
 end
diff --git a/modified-files/CompilerBundle/Controller/DefaultController.php b/modified-files/CompilerBundle/Controller/DefaultController.php
new file mode 100644
index 0000000..e30cda1
--- /dev/null
+++ b/modified-files/CompilerBundle/Controller/DefaultController.php
@@ -0,0 +1,180 @@
+<?php
+/**
+ * \file
+ * \brief Functions used by the compiler backend.
+ *
+ * \author Dimitrios Christidis
+ * \author Vasilis Georgitzikis
+ *
+ * \copyright (c) 2012-2013, The Codebender Development Team
+ * \copyright Licensed under the Simplified BSD License
+ */
+
+namespace Codebender\CompilerBundle\Controller;
+
+use Symfony\Bundle\FrameworkBundle\Controller\Controller;
+use Symfony\Component\HttpFoundation\Response;
+use Codebender\CompilerBundle\Handler\CompilerHandler;
+use Codebender\CompilerBundle\Handler\DeletionHandler;
+use Codebender\CompilerBundle\Handler\BuilderCompilerHandler;
+
+class DefaultController extends Controller
+{
+	public function statusAction()
+	{
+		return new Response(json_encode(array("success" => true, "status" => "OK")));
+	}
+
+	public function testAction($authorizationKey)
+	{
+		$params = $this->generateParameters();
+
+		if ($authorizationKey !== $params["authorizationKey"])
+		{
+			return new Response(json_encode(array("success" => false, "step" => 0, "message" => "Invalid authorization key.")));
+		}
+
+		set_time_limit(0); // make the script execution time unlimited (otherwise the request may time out)
+
+		// change the current Symfony root dir
+		chdir($this->get('kernel')->getRootDir()."/../");
+
+		//TODO: replace this with a less horrible way to handle phpunit
+		exec("phpunit -c app --stderr 2>&1", $output, $return_val);
+
+		return new Response(json_encode(array("success" => (bool) !$return_val, "message" => implode("\n", $output))));
+	}
+
+	public function indexAction($authorizationKey, $version)
+	{
+		$params = $this->generateParameters();
+
+		if ($authorizationKey !== $params["authorizationKey"])
+		{
+			return new Response(json_encode(array("success" => false, "step" => 0, "message" => "Invalid authorization key.")));
+		}
+
+		if ($version == "v1")
+		{
+			$request = $this->getRequest()->getContent();
+			
+			//Get the compiler service
+			/** @var CompilerHandler $compiler */
+			$compiler = $this->get('builder_compiler_handler');
+		
+			$reply = $compiler->main($request, $params);
+
+			return new Response(json_encode($reply));
+		}
+		else
+		{
+			return new Response(json_encode(array("success" => false, "step" => 0, "message" => "Invalid API version.")));
+		}
+	}
+
+	public function deleteAllObjectsAction($authorizationKey, $version)
+	{
+		if ($this->container->getParameter('authorizationKey') != $authorizationKey) {
+            return new Response(json_encode(
+                array('success' => false, 'step' => 0, 'message' => 'Invalid authorization key.')
+            ));
+        }
+
+		if ($version != 'v1') {
+            return new Response(json_encode(
+                array('success' => false, 'step' => 0, 'message' => 'Invalid API version.')
+            ));
+        }
+
+		//Get the compiler service
+		/** @var DeletionHandler $deleter */
+		$deleter = $this->get('deletion_handler');
+
+		$response = $deleter->deleteAllObjects();
+
+		if ($response['success'] !== true) {
+            return new Response(json_encode(
+                array('success' => false, 'step' => 0, 'message' => 'Failed to access object files directory.')
+            ));
+        }
+
+        return new Response(json_encode(
+            array_merge(
+                array(
+                    'success' => true,
+                    'message' => 'Object files deletion complete. Found ' . $response['fileCount'] . ' files.'
+                ),
+                $response['deletionStats'],
+                array("Files not deleted" => $response['notDeletedFiles'])
+            )));
+	}
+
+	public function deleteSpecificObjectsAction($authorizationKey, $version, $option, $cachedObjectToDelete)
+	{
+		if ($this->container->getParameter('authorizationKey') != $authorizationKey) {
+            return new Response(json_encode(
+                array('success' => false, 'step' => 0, 'message' => 'Invalid authorization key.')
+            ));
+        }
+
+		if ($version != 'v1') {
+            return new Response(json_encode(
+                array('success' => false, 'step' => 0, 'message' => 'Invalid API version.')
+            ));
+        }
+
+		//Get the compiler service
+		/** @var DeletionHandler $deleter */
+		$deleter = $this->get('deletion_handler');
+
+		$response = $deleter->deleteSpecificObjects($option, $cachedObjectToDelete);
+
+		if ($response['success'] !== true) {
+			return new Response(json_encode(
+                array('success' => false, 'step' => 0, 'message' => 'Failed to access object files directory.')
+            ));
+		}
+
+		if (!empty($response["notDeletedFiles"])) {
+			$message = 'Failed to delete one or more of the specified core object files.';
+            if ($option == 'library') {
+                $message = 'Failed to delete one or more of the specified library object files.';
+            }
+
+			return new Response(json_encode(
+                array_merge(array('success' => false, 'step' => 0, 'message' => $message), $response)
+            ));
+		}
+
+        $message = 'Core object files deleted successfully.';
+        if ($option == 'library'){
+            $message = 'Library deleted successfully.';
+        }
+
+		return new Response(json_encode(array_merge(array('success' => true, 'message' => $message), $response)));
+	}
+
+	/**
+	 * \brief Creates a list of the configuration parameters to be used in the compilation process.
+	 *
+	 * \return An array of the parameters.
+	 *
+	 * This function accesses the Symfony global configuration parameters, and creates an array that our handlers (which
+	 * don't have access to them) can use them.
+
+	 */
+	private function generateParameters()
+	{
+        $parameters = array("binutils", "python", "clang", "logdir", "temp_dir", "archive_dir", "autocompletion_dir", "autocompleter", "cflags", "cppflags", "asflags", "arflags", "ldflags", "ldflags_tail", "clang_flags", "objcopy_flags", "size_flags", "output", "arduino_cores_dir", "external_core_files", "authorizationKey");
+
+		$compiler_config = array();
+
+		foreach ($parameters as $parameter)
+		{
+			$compiler_config[$parameter] = $this->container->getParameter($parameter);
+		}
+
+		return $compiler_config;
+	}
+
+}
diff --git a/modified-files/CompilerBundle/Handler/BuilderCompilerHandler.php b/modified-files/CompilerBundle/Handler/BuilderCompilerHandler.php
new file mode 100644
index 0000000..ea8857f
--- /dev/null
+++ b/modified-files/CompilerBundle/Handler/BuilderCompilerHandler.php
@@ -0,0 +1,262 @@
+<?php
+
+
+namespace Codebender\CompilerBundle\Handler;
+
+// This file uses mktemp() to create a temporary directory where all the files
+// needed to process the compile request are stored.
+require_once "System.php";
+use System;
+use Codebender\CompilerBundle\Handler\MCUHandler;
+use Symfony\Bridge\Monolog\Logger;
+
+class BuilderCompilerHandler
+{
+	private $preproc;
+	private $postproc;
+	private $utility;
+	private $compiler_logger;
+	private $object_directory;
+	private $logger_id;
+
+	function __construct(PreprocessingHandler $preprocHandl, PostprocessingHandler $postprocHandl, UtilityHandler $utilHandl, Logger $logger, $objdir)
+	{
+		$this->preproc = $preprocHandl;
+		$this->postproc = $postprocHandl;
+		$this->utility = $utilHandl;
+		$this->compiler_logger = $logger;
+		$this->object_directory = $objdir;
+	}
+
+
+	function main($request, $compiler_config)
+	{
+					
+		error_reporting(E_ALL & ~E_STRICT);
+		
+				
+		$start_time = microtime(true);
+		
+		// Step 0: Reject the request if the input data is not valid.
+		$tmp = $this->requestValid($request);
+		if($tmp["success"] == false)
+			return $tmp;
+				
+		$this->setVariables($request, $format, $libraries, $version, $mcu, $f_cpu, $core, $variant, $vid, $pid, $compiler_config);
+		
+		$TEMP_DIR = $compiler_config["temp_dir"];
+		
+		// Step 1: Extract the files and filenames included in the request.
+		$filenames = array();
+	
+		foreach ($request["files"] as $file)
+		     array_push($filenames, $file["filename"]);
+		
+		
+		
+		$files = array();
+		$tmpVar = $this->extractFiles($request["files"], $TEMP_DIR, $compiler_dir, $files["sketch_files"], "files");
+		if ($tmp["success"] == false)
+			return $tmp;
+		
+		if (!array_key_exists("archive", $request) || ($request["archive"] !== false && $request["archive"] !== true))
+			$ARCHIVE_OPTION = false;
+		else
+			$ARCHIVE_OPTION = $request["archive"];
+
+		if ($ARCHIVE_OPTION === true)
+		{
+			$arch_ret = $this->createArchive($compiler_dir, $TEMP_DIR, $ARCHIVE_DIR, $ARCHIVE_PATH);
+			if ($arch_ret["success"] === false)
+				return $arch_ret;
+		}
+		
+			
+		$tmp = $this->doCompile($files["sketch_files"], $compiler_dir, $format, $version, $mcu, $f_cpu, $core, $variant, $pid, $vid);
+		if ($tmp["success"] == false)
+			return $tmp;
+			
+		
+	
+		if ($format == "syntax")
+			return array(
+				"success" => true,
+				"time" => microtime(true) - $start_time);
+
+		
+		$tmp = $this->convertOutput($compiler_dir, $format, $SIZE, $filenames , $start_time);
+	    return $tmp;
+	
+
+	}
+	
+	protected function convertOutput($dir, $format, $SIZE, $filenames, $start_time)
+	{
+		$OUTPUT = $filenames[0];  
+		// To Do, Handle multiple files than just one. 
+		
+		if ($format == "elf")
+		{
+			$ret_objcopy = false;
+			$content = base64_encode(file_get_contents("$dir/$OUTPUT.elf"));
+			$size = filesize("$dir/$OUTPUT.elf");
+		}
+		elseif ($format == "binary")
+		{
+			$content = base64_encode(file_get_contents("$dir/$OUTPUT.hex"));
+			$size = filesize("$dir/$OUTPUT.hex");
+		}
+		elseif ($format == "hex")
+		{
+			$content = file_get_contents("$dir/$OUTPUT.hex");
+			$size = filesize("$dir/$OUTPUT.hex");
+		}
+		elseif ($format == "object")
+		{
+			
+			$content = base64_encode(file_get_contents("$dir/sketch/$OUTPUT.cpp.o"));
+			$size = filesize("$dir/sketch/$OUTPUT.cpp.o");
+		}
+		
+		// If everything went well, return the reply to the caller.
+		if ($ret_objcopy || $content === false)
+			return array(
+				"success" => false,
+				"step" => 8,
+				"message" => "There was a problem while generating the your binary file for $dir/sketch/$OUTPUT.cpp.o");
+		else
+			return array(
+				"success" => true,
+				"time" => microtime(true) - $start_time,
+				"size" => $size,
+				"output" => $content);
+
+	}
+	private function requestValid(&$request)
+	{
+		$request = $this->preproc->validateInput($request);
+		if (!$request)
+			return array(
+				"success" => false,
+				"step" => 0,
+				"message" => "Invalid input.");
+		else return array("success" => true);
+	}
+	
+	private function extractFiles($request, $temp_dir, &$dir, &$files, $suffix, $lib_extraction = false)
+	{
+		// Create a temporary directory to place all the files needed to process
+		// the compile request. This directory is created in $TMPDIR or /tmp by
+		// default and is automatically removed upon execution completion.
+		
+		$cnt = 0;
+		
+		if (!$dir)
+			do
+			{
+				$dir = @System::mktemp(" -t $temp_dir/ -d compiler");
+				$cnt++;
+			} while (!$dir && $cnt <= 2);
+			
+		if (!$dir)
+			return array(
+				"success" => false,
+				"step" => 1,
+				"message" => "Failed to create temporary directory.");
+	
+		$response = $this->utility->extractFiles("$dir/$suffix", $request, $lib_extraction);
+		
+		if ($response["success"] === false)
+			return $response;
+		$files = $response["files"];
+
+		return array("success" => true);
+	}
+	
+	
+	protected function doCompile(&$files, $dir, $format, $version, $mcu, $f_cpu, $core, $variant, $pid, $vid)
+	{
+		$hardware = "-hardware /opt/codebender/arduino-core-files/v1.6.6/hardware -hardware /opt/codebender/arduino-core-files/v1.6.6/hardware/arduino";
+		$tools = "-tools /opt/arduino-builder/tools-builder -tools /opt/codebender/arduino-core-files/v1.6.6/hardware/tools/avr";
+		$libraries = "-libraries /opt/codebender/arduino-core-files/v1.6.6/libraries";
+		$build_path = "-build-path $dir";
+		
+		if(!file_exists($dir))
+			mkdir($dir);
+		
+		$prefs = "-prefs mcu=$mcu -prefs f_cpu=$f_cpu -prefs core=$core -prefs variant=$variant ";
+		
+		// If pid and vid build preferences were specified 
+		if($pid != "")
+		 	$prefs = $prefs."-prefs pid=$pid ";
+		
+		if($vid != "")
+			$prefs = $prefs."-prefs vid=$vid ";
+		
+		$hardware = stripslashes($hardware);
+		$tools = stripslashes($tools);
+		$libraries = stripslashes($libraries);
+		$build_path = stripslashes($build_path);
+		$prefs = stripslashes($prefs);
+		
+		foreach (array("c", "cpp", "S","ino") as $ext)
+		{
+			foreach ($files[$ext] as $file)
+			{
+			 	// From hereon, $file is shell escaped and thus should only be used in calls
+				// to exec().
+				$file = escapeshellarg($file);
+				
+				exec("/opt/arduino-builder/arduino-builder -fqbn arduino:avr:uno  $hardware  $tools  $libraries $prefs $build_path $file.$ext 2>&1", $output, $ret_compile);
+				
+
+				
+				if (isset($ret_compile) && $ret_compile)
+				{
+					return array(
+						"success" => false,
+						"step" => 4,
+						"message" => $output,
+						"debug" => $ret_compile);
+				}
+				unset($output);
+
+				$files["o"][] = array_shift($files[$ext]);
+			
+			}
+		}
+
+		return array("success" => true);
+	}
+	
+	
+	private function setVariables($request, &$format, &$libraries, &$version, &$mcu, &$f_cpu, &$core, &$variant, &$vid, &$pid, &$compiler_config)
+	{
+		// Extract the request options for easier access.
+		$format = $request["format"];
+		$libraries = $request["libraries"];
+		$version = $request["version"];
+		$mcu = $request["build"]["mcu"];
+		$f_cpu = $request["build"]["f_cpu"];
+		$core = $request["build"]["core"];
+		// Some cores do not specify any variants. In this case, set variant to be an empty string
+		if (!array_key_exists("variant", $request["build"]))
+			$variant = "";
+		else
+			$variant = $request["build"]["variant"];
+
+		if ($format == "autocomplete")
+		{
+			$compiler_config["autocmpfile"] = $request["position"]["file"];
+			$compiler_config["autocmprow"] = $request["position"]["row"];
+			$compiler_config["autocmpcol"] = $request["position"]["column"];
+			$compiler_config["autocmpmaxresults"] = 500;
+			$compiler_config["autocmpprefix"] = $request["prefix"];
+		}
+
+		// Set the appropriate variables for vid and pid (Leonardo).
+
+		$vid = (isset($request["build"]["vid"])) ? $request["build"]["vid"] : "null";
+		$pid = (isset($request["build"]["pid"])) ? $request["build"]["pid"] : "null";
+	}
+}
diff --git a/modified-files/CompilerBundle/Resources/config/routing.yml b/modified-files/CompilerBundle/Resources/config/routing.yml
new file mode 100644
index 0000000..bb0f875
--- /dev/null
+++ b/modified-files/CompilerBundle/Resources/config/routing.yml
@@ -0,0 +1,27 @@
+codebender_compiler_status_check:
+    pattern:  /status
+    defaults: { _controller: CodebenderCompilerBundle:Default:status }
+
+codebender_compiler_test:
+    pattern:  /{authorizationKey}/test/
+    defaults: { _controller: CodebenderCompilerBundle:Default:test }
+
+codebender_compiler_homepage:
+    pattern:  /{authorizationKey}/{version}
+    defaults: { _controller: CodebenderCompilerBundle:Default:index }
+
+codebender_compiler_delete_all:
+    pattern:  /{authorizationKey}/{version}/delete/all/
+    defaults: { _controller: CodebenderCompilerBundle:Default:deleteAllObjects }
+
+codebender_compiler_delete_specific:
+    pattern:  /{authorizationKey}/{version}/delete/{option}/{cachedObjectToDelete}
+    defaults: { _controller: CodebenderCompilerBundle:Default:deleteSpecificObjects }
+
+# redirecting the root
+root:
+    path: /
+    defaults:
+        _controller: FrameworkBundle:Redirect:urlRedirect
+        path: /status
+        permanent: true
diff --git a/modified-files/CompilerBundle/Resources/config/services.yml b/modified-files/CompilerBundle/Resources/config/services.yml
new file mode 100644
index 0000000..6a9ac30
--- /dev/null
+++ b/modified-files/CompilerBundle/Resources/config/services.yml
@@ -0,0 +1,36 @@
+parameters:
+#    codebender_compiler.example.class: Codebender\CompilerBundle\Example
+    buildercompiler_handler.class:	Codebender\CompilerBundle\Handler\BuilderCompilerHandler
+    compiler_handler.class:	Codebender\CompilerBundle\Handler\CompilerHandler
+    utility_handler.class:	Codebender\CompilerBundle\Handler\UtilityHandler
+    preprocessing_handler.class:	Codebender\CompilerBundle\Handler\PreprocessingHandler
+    postprocessing_handler.class:	Codebender\CompilerBundle\Handler\PostprocessingHandler
+    deletion_handler.class:	Codebender\CompilerBundle\Handler\DeletionHandler
+
+services:
+#    codebender_compiler.example:-
+#        class: %codebender_compiler.example.class%
+#        arguments: [@service_id, "plain_value", %parameter%]
+    buildercompiler_handler:
+        class:			"%buildercompiler_handler.class%"
+        arguments:		["@preprocessing_handler", "@postprocessing_handler", "@utility_handler", "@compiler_logger", "%temp_dir%/%objdir%"]
+    compiler_handler:
+        class:			"%compiler_handler.class%"
+        arguments:		["@preprocessing_handler", "@postprocessing_handler", "@utility_handler", "@compiler_logger", "%temp_dir%/%objdir%"]
+    utility_handler:
+        class:			"%utility_handler.class%"
+    preprocessing_handler:
+        class:			"%preprocessing_handler.class%"
+    postprocessing_handler:
+        class:			"%postprocessing_handler.class%"
+    deletion_handler:
+        class:			"%deletion_handler.class%"
+        arguments:		["%temp_dir%/%objdir%"]
+    compiler_logger:
+        class: Symfony\Bridge\Monolog\Logger
+        arguments: [cmplr_log]
+        calls:
+            - [pushHandler, [@compiler_log_handler]]
+    compiler_log_handler:
+        class: Monolog\Handler\StreamHandler
+        arguments: [%kernel.logs_dir%/compiler.log]
diff --git a/setup.sh b/setup.sh
new file mode 100644
index 0000000..b8a94fa
--- /dev/null
+++ b/setup.sh
@@ -0,0 +1,16 @@
+cd /home/vagrant
+sudo apt-get install git
+git clone https://github.com/codebendercc/compiler.git
+cp -r /vagrant/modified-files/CompilerBundle/ compiler/Symfony/src/Codebender/
+cd /home/vagrant/compiler/
+./scripts/install.sh
+cd /home/vagrant
+wget http://arduino.cc/download.php?f=/arduino-1.6.6-linux64.tar.xz -O arduino-1.6.6.tar.xz
+tar -xJf arduino-1.6.6.tar.xz
+sudo mkdir /opt/codebender/arduino-core-files
+sudo mkdir /opt/codebender/arduino-core-files/v1.6.6
+sudo cp -r arduino-1.6.6/hardware /opt/codebender/arduino-core-files/v1.6.6/
+sudo cp -r arduino-1.6.6/libraries /opt/codebender/arduino-core-files/v1.6.6/
+sudo mkdir /opt/arduino-builder
+sudo cp -r arduino-1.6.6/tools-builder /opt/arduino-builder/
+sudo cp -r arduino-1.6.6/arduino-builder /opt/arduino-builder/
\ No newline at end of file
diff --git a/vagrant/.vagrant/machines/default/virtualbox/action_provision b/vagrant/.vagrant/machines/default/virtualbox/action_provision
deleted file mode 100755
index 95e57e1..0000000
--- a/vagrant/.vagrant/machines/default/virtualbox/action_provision
+++ /dev/null
@@ -1 +0,0 @@
-1.5:4f2169c0-47c5-4bce-9859-58fda0f7a877
\ No newline at end of file
diff --git a/vagrant/.vagrant/machines/default/virtualbox/action_set_name b/vagrant/.vagrant/machines/default/virtualbox/action_set_name
deleted file mode 100755
index f995fa2..0000000
--- a/vagrant/.vagrant/machines/default/virtualbox/action_set_name
+++ /dev/null
@@ -1 +0,0 @@
-1445846899
\ No newline at end of file
diff --git a/vagrant/.vagrant/machines/default/virtualbox/creator_uid b/vagrant/.vagrant/machines/default/virtualbox/creator_uid
deleted file mode 100755
index c227083..0000000
--- a/vagrant/.vagrant/machines/default/virtualbox/creator_uid
+++ /dev/null
@@ -1 +0,0 @@
-0
\ No newline at end of file
diff --git a/vagrant/.vagrant/machines/default/virtualbox/id b/vagrant/.vagrant/machines/default/virtualbox/id
deleted file mode 100755
index c5cb3ad..0000000
--- a/vagrant/.vagrant/machines/default/virtualbox/id
+++ /dev/null
@@ -1 +0,0 @@
-4f2169c0-47c5-4bce-9859-58fda0f7a877
\ No newline at end of file
diff --git a/vagrant/.vagrant/machines/default/virtualbox/index_uuid b/vagrant/.vagrant/machines/default/virtualbox/index_uuid
deleted file mode 100755
index 78d5735..0000000
--- a/vagrant/.vagrant/machines/default/virtualbox/index_uuid
+++ /dev/null
@@ -1 +0,0 @@
-b2d9f07d2f6d42afbd0db6752774cf06
\ No newline at end of file
diff --git a/vagrant/.vagrant/machines/default/virtualbox/private_key b/vagrant/.vagrant/machines/default/virtualbox/private_key
deleted file mode 100755
index ba45790..0000000
--- a/vagrant/.vagrant/machines/default/virtualbox/private_key
+++ /dev/null
@@ -1,27 +0,0 @@
------BEGIN RSA PRIVATE KEY-----
-MIIEpAIBAAKCAQEAlqo2QzmjtMBEUMgCa0URlEnf0+PFYcX8G6xRQFtixOjfGX57
-4KhXkwLbO55vnytjGUjAbME7qvcUJqQlSaCYFjEpa66c4Li9Hx8fM0AZoLyeaT1s
-QH90FLvHlg61gysd5cXjmjAlgzHa/R/M++3deQlfgG8RxkkNPGv99dojlhDH2yXI
-TFXxVNeY5R0ohRIWxJBMCu01kXaM8t7uUavSomLm1UeLIHCuR33Bb4PJcI3aCgGM
-StySyxne+vvSAl0Y1QnyShmLrUyhE4QfyqceKwNSuP9aA7YgrqafbTq12tc6Bqf+
-RlLZjtUQVGpiMZia+joLSgVt91rxSZhHGhrE2wIDAQABAoIBAQCQfEE3bNJKp8ub
-8IMpXf5CyCmnaRpD7nscCr+MyVbJ4Uz6hOrFgoshR6742LLQ4OnTOIqYgSL4jKQ9
-flLn7eOL/K9tPfHiLCfp7Y2dN46cL+Z2pFno7JFkxMPdatO1K6crUAA6QIvo6enJ
-rzKEMxOeXFfCskFId4wC8smEeSKBaLObVum7EKAlYbAqyfUHhQmaRsosXMo22BiW
-U7QSaNpaYg5s/wNhDY6dSz696T5CoqhWTOdJcZaKccxKN6/cGhYM3/JzyHKk/tKp
-2I4zk0YLKHomd2lhcxJGBCdshxiXZUaqKh4pRQoLbLcAJ/e5JY8Vka9ud9yhXlIH
-MQ4MKhDRAoGBAMbBpKrAr2RR25k5+Gw6IGWRzC6MunmBeGlPoes0UcGNeVI3y8wg
-5I8z0cC7tllz0adAUhqurBQOAk4jvTpM4e9xyBiRzfIVR3nrmwrd0B1fvRKDYyJN
-Sh3+q6m6LETSClx2mEG/re62asj3sG5mEwB+7zbIKdfXAjOH+ewPejYjAoGBAMIO
-xOskpQjjMHCLbK+tCj/Uh5v3h0O4OqdfhfqUqnlHVnBlREAi7Yr0Gs+5kwjP6+mg
-1naS8ZNYWMvEvWN+paxx4mFT6yKqSnTqamhKvA5V+pW0BG/BzxPHSBr8wG8kczaA
-HqB+Ax06yhBN9wwtUtue3no6HURrhM3ZALcysPXpAoGAKnSMpwi3rlcp8EYIwZ18
-9BU7pynaXz//p4ciECrB1/VPV/ehKb5Q9CHeiSvPnLX3r6E2qIptKW+AoI5TylNH
-46zLUCw88JwJA4sHOD//R3b+3SiBkX8u+M9AfeXNtPmkyvFuPoUiMx52Gu2Fm19k
-abOzh2EkRv2fc8B06y63LT8CgYBgYoOOI3JRGr6Jd8aw7uqDT6VXYzds/EktrrVW
-A5c0i6k0RCgFDxQbCylx+UM9gkAzly5OUKfqPlxEQWCr1VCmeR4up0bHvfsjXPci
-+9Ox7yR6TKJTe9jFgxqeROGzklAjRrlvj4cucm/Ab2kARFa+PIdWAB1fSWP59glz
-9JqOWQKBgQCLptHSG681HMUIOgjibaAE/W2YVYSN7ePrpy7vMWB6UuETccFm13DE
-daN6+0swcW4HRPslCOKMPJ59zkPk6p+W93DRq2Stoob8IrKLbOItCoMGG89uQWEU
-0QtW8ctbPO2L/Gi348eEdGpWsq49ci9qbFN02jh3LV868fTjsPpvZA==
------END RSA PRIVATE KEY-----
diff --git a/vagrant/.vagrant/machines/default/virtualbox/synced_folders b/vagrant/.vagrant/machines/default/virtualbox/synced_folders
deleted file mode 100755
index 39695eb..0000000
--- a/vagrant/.vagrant/machines/default/virtualbox/synced_folders
+++ /dev/null
@@ -1 +0,0 @@
-{"virtualbox":{"/vagrant":{"guestpath":"/vagrant","hostpath":"C:/Users/Arturo/Documents/Computer-Engineer/vargant","disabled":false}}}
\ No newline at end of file

From d00c4bbd71c5b7bb0e18804fb9e621e34e84d5ec Mon Sep 17 00:00:00 2001
From: asandrad22 <asandrad22x@gmail.com>
Date: Fri, 27 Nov 2015 21:47:36 +0000
Subject: [PATCH 3/4] Edit README.md with instructions on how to setup API.

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index 533e169..9f2bd77 100644
--- a/README.md
+++ b/README.md
@@ -1 +1,5 @@
 # arduino-builder-service
+
+To setup arduino-builder-service Vagrant up the machine. Once in the machine
+/vagrant/setup.sh
+

From c2c96a26c1f1c30268ecb4099d61c9c2de99256e Mon Sep 17 00:00:00 2001
From: asandrad22 <asandrad22x@gmail.com>
Date: Fri, 4 Dec 2015 10:33:10 +0000
Subject: [PATCH 4/4] Modified to reflect setup for Arduino-Builder-Service

---
 README.md | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 9f2bd77..427c587 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,19 @@
 # arduino-builder-service
 
-To setup arduino-builder-service Vagrant up the machine. Once in the machine
-/vagrant/setup.sh
+Arduino Builder Service modifies codebender/compiler to compile skits with arduino-builder. As of now Arduino Builder Service compiles for version 166 for Arduino 1.6.6.
 
+## Setup Arduino Builder Service with Vagrant
+Install [Vagrant](https://www.vagrantup.com/downloads.html) on your machine.
+
+Next, copy the code into any directory. `git clone https://github.com/codebendercc/arduino-builder-service.git`
+Go into the directory with the code and `vagrant up`
+SSH into the virtual machine using
+```
+host: localhost
+port: 2222
+username: vagrant
+password: vagrant
+
+```
+Finally, set up the virtual machine by running `/vagrant/setup.sh`
+To test if it work run `curl https://localhost/status` should return {"success":true,"status":"OK"}.