BUG: Refs #212. Work towards exporting batchmake scripts.

This commit breaks out much functionality into KWBatchmakeComponent.php and
also further into a library (KWUtils.php).  Included are tests for both of
these, along with testing data.  The functionality provided would allow
for creating a tmp work directory in the batchmake module, copying in
the needed .bms and .bmm files, compiling the batchmake script, creating
the condor DAG and scripts from the .bms file, and submitting the DAG to
condor.

Author: Michael Grauer

library/KWUtils.php

@@ -0,0 +1,279 @@
+<?php
+/*=========================================================================
+Program:   MIDAS Server
+Language:  PHP/HTML/Java/Javascript/SQL
+Date:      $Date$
+Version:   $Revision$
+
+Copyright (c) Kitware Inc. 28 Corporate Drive. All rights reserved.
+Clifton Park, NY, 12065, USA.
+
+See Copyright.txt for details.
+This software is distributed WITHOUT ANY WARRANTY; without even
+the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+PURPOSE.  See the above copyright notices for more information.
+=========================================================================*/
+?>
+<?php
+/**
+ * globally useful utility functions.
+ */
+class KWUtils
+{
+  
+  CONST DEFAULT_MKDIR_MODE = 0775;  
+    
+  /**
+   * @method mkDir
+   * @TODO what to do with errors in a way that is consistent with error reporting
+   * Will create the directory $dir and set the filemode so that the newly
+   * created dir is writable by the current user.
+   * @return true on success, false otherwise
+   */
+  public static function mkDir($dir, $mode = self::DEFAULT_MKDIR_MODE)
+    {
+    if(!file_exists($dir) && !mkdir($dir, $mode, true))
+      {
+      return false;
+      }
+    // change file mode
+    // even though we are swallowing the error messages, we return false
+    // if the operation can't be completed
+    if(!is_writeable($dir) || @!chmod($dir, $mode))
+      {
+      return false;
+      }
+    return true; 
+    }
+    
+  /** 
+   * @method createSubDirectories recursively create subdirectories starting at
+   * baseDirectory, sequentially creating each of the directories in the
+   * subDirectories array, according to the passed in mode.
+   * @param $baseDirectory the first directory to create
+   * @param $subDirectories an array of directories that will be created in a 
+   * recursive fashion, each one appending to the last as a deeper subdirectory
+   * of baseDirectory
+   * @param the mode to create the new directories
+   */  
+  public static function createSubDirectories($baseDirectory, $subDirectories, $mode = self::DEFAULT_MKDIR_MODE)
+    {
+    if(!file_exists($baseDirectory) )
+      {
+      throw new Zend_Exception($baseDirectory . ' does not exist');
+      }
+    $relpath = ''; 
+    foreach($subDirectories as $directory)
+      {
+      $relpath .= $directory . "/"; 
+      
+      if(!KwUtils::mkDir($baseDirectory . $relpath, $mode))
+        { 
+        throw new Zend_Exception($baseDirectory . $relpath . ' could not be created');
+        }
+      }
+    return $baseDirectory . $relpath;
+    }
+
+  /** 
+   * @method isWindows()
+   * @return True if the current platform is windows
+   */
+  public static function isWindows()
+    {
+    return (strtolower(substr(PHP_OS, 0, 3)) == "win"); 
+    }
+    
+    
+  /**
+   * @method escapeCommand
+   * will escape a command respecting the format of the current platform
+   * @param $command, the command to be escaped
+   * @return the $command, $escaped for the current platform
+   * @TODO, how to test this?
+   */
+  public static function escapeCommand($command )
+    {
+    // if windows platform, add extra double-quote
+    // See http://www.mail-archive.com/internals@lists.php.net/msg29874.html
+    if(KWUtils::isWindows() )
+      {
+      $command = '"'.$command.'"';
+      }
+    
+    return $command; 
+    }  
+    
+  /**  
+   * @method appendStringIfNot will append the string $ext to
+   * $subject if it is not already a suffix of $subject
+   * @param $subject, the string to be appended to
+   * @param $ext, the extension to check for and append
+   * @return $subject, will end with the suffix $ext
+   */
+  public static function appendStringIfNot($subject, $ext)
+    {
+    if(!(substr($subject, strlen($subject) - strlen($ext)) === $ext)  )
+      {
+      $subject .= $ext; 
+      }
+    return $subject; 
+    }
+
+  /**
+   * @method exec
+   * will execute a command, respecting the format of the current platform.
+   * @param $command to be executed, with all arguments, and formatted correctly
+   * @param $output, a reference to put the output of the command
+   * @param $chdir, the dir to change to for execution, if any
+   * @param $return_val, a reference to put the return value of the command
+   *  the temporary work dir 
+   */
+  public static function exec($command, &$output = null, $chdir = "", &$return_val = null)
+    {
+    if(!empty($chdir) && is_dir($chdir))
+      { 
+      if(!chdir($chdir))
+        {
+        throw new Zend_Exception("Failed to change directory: [".$chdir."]");
+        }
+      }
+    // on Linux need to add redirection to handle stderr
+    $redirect_error = KWUtils::isLinux() ? " 2>&1" : ""; 
+    exec(KWUtils::escapeCommand($command) . $redirect_error, $output, $return_val);
+    }    
+    
+    
+  /** 
+   * @method isLinux()
+   * @return True if the current platform is Linux
+   */
+  public static function isLinux()
+    {
+    return (strtolower(substr(PHP_OS, 0, 5)) == "linux"); 
+    }  
+    
+    
+    
+  /**
+   * @method prepareExecCommand
+   * will prepare an executable application and params for command line 
+   * execution, including escaping and quoting arguments.
+   * @param $app_name, the application to be executed
+   * @param $params, an array of arguments to the application
+   * @return the full command line command, escaped and quoted, will throw a 
+   * Zend_Exception if the app is not in the path and not executable
+   */
+  public static function prepareExecCommand($app_name, $params = array())
+    {
+    // Check if application is executable, if not, see if you can find it
+    // in the path
+    if(!KWUtils::isExecutable($app_name, false)) 
+      {
+      $app_name = KWUtils::findApp($app_name, true);
+      }
+      
+    // escape parameters
+    $escapedParams = array();
+    foreach($params as $param)
+      {
+      $escapedParams[] = escapeshellarg($param);
+      }
+     
+    // glue together app_name and params using spaces
+    return escapeshellarg($app_name)." ".implode(" ", $escapedParams);
+    }    
+    
+    
+  /** 
+   * @method isExecutable will return true if the app can be found and is
+   * executable, can optionally look in the path.
+   * @param string $app_name, the app to check
+   * @param boolean $check_in_path, if true, will search in path for app
+   * @return True if app_name is found and executable, False otherwise
+   */
+  public static function isExecutable($app_name, $check_in_path = false)
+    {
+    if(!is_executable($app_name ))
+      {
+      if($check_in_path)
+        {
+        try 
+          {
+          if(KWUtils::findApp($app_name, true))
+            {
+            return true;
+            }
+          }
+        catch(Zend_Exception $ze)
+          {
+          return false;
+          }
+        }
+      return false;
+      }
+    return true; 
+    }    
+    
+  /**
+   * @method findApp will return the absolute path of an application 
+   * @param $app_name, the name of the application
+   * @param $check_execution_flag, whether to include in the check that the
+   * application is executable
+   * @return the path to the application, throws a Zend_Exception if the app
+   * can't be found, or if $check_execution_flag  is set and the app is not
+   * executable.
+   */
+  public static function findApp($app_name, $check_execution_flag )
+    {
+    $PHP_PATH_SEPARATOR = ":"; 
+    // split path
+    $path_list = explode($PHP_PATH_SEPARATOR, getenv("PATH")); 
+    
+    // loop through paths 
+    foreach($path_list as $path)
+      {
+      $status = false;
+      $path_to_app = KWUtils::appendStringIfNot($path, DIRECTORY_SEPARATOR).$app_name;
+      if($check_execution_flag)
+        {
+        if(is_executable($path_to_app))
+          {
+          $status = true; 
+          break; 
+          } 
+        }
+      else
+        {
+        if(file_exists($path_to_app))
+          {
+          $status = true;
+          break; 
+          }
+        }
+      }
+    if(!$status)
+      {
+      throw new Zend_Exception("Failed to locate the application: [".$app_name."] [check_execution_flag:".$check_execution_flag."]");
+      }
+    return $path_to_app; 
+    }  
+    
+    
+
+
+  /** 
+   * @method formatAppName
+   * Format the application name according to the platform.
+   */
+  public static function formatAppName($app_name)
+    {
+    if(substr(PHP_OS, 0, 3) == "WIN")
+      { 
+      $app_name = KWUtils::appendStringIfNot($app_name, ".exe"); 
+      }
+    return $app_name; 
+    }    
+    
+    
+}

modules/batchmake/Notification.php

@@ -21,10 +21,16 @@ class Batchmake_Notification extends MIDAS_Notification
   public function init()
     {
     $this->addCallBack('CALLBACK_CORE_GET_DASHBOARD', 'getDashboard');
+    $this->addCallBack('CALLBACK_CORE_GET_LEFT_LINKS', 'getLeftLink');
     }//end init
 
-
-  /** generate Dashboard information */
+    
+  /**
+   *@method getDashboard
+   * will generate information about this module to display on the Dashboard
+   *@return array with key being a string describing if the configuration of
+   * the module is correct or not, and value being a 1/0 for the same info.
+   */
   public function getDashboard()
     {    
     $return = array();
@@ -38,5 +44,21 @@ public function getDashboard()
       }
     return $return;
     } 
+
+    
+  /**
+   *@method getLeftLink
+   * will generate a link for this module to be displayed in the main view.
+   *@return ['batchmake' => [ link to batchmake module, module icon image path]]
+   */
+  public function getLeftLink()
+    {
+    $fc = Zend_Controller_Front::getInstance();
+    $moduleWebroot = $fc->getBaseUrl() . MIDAS_BATCHMAKE_MODULE;
+    return array(ucfirst(MIDAS_BATCHMAKE_MODULE) => array($moduleWebroot,  $moduleWebRoot . '/public/images/cmake.png'));
+    }
+        
   } //end class
+    
+    
 ?>

modules/batchmake/constant/module.php

@@ -16,7 +16,7 @@
 define("MIDAS_BATCHMAKE_CHECK_IF_CHMODABLE", 0x10);
 define("MIDAS_BATCHMAKE_CHECK_IF_CHMODABLE_RW", 0x16); // 0x10 + 0x6
 
-define("MIDAS_BATCHMAKE_DEFAULT_MKDIR_MODE", 0775);
+
 
 // Condor executables
 define("MIDAS_BATCHMAKE_CONDOR_STATUS", "condor_status");
@@ -26,7 +26,10 @@
 
 // Batchmake executable
 define("MIDAS_BATCHMAKE_EXE", "BatchMake");
-  
+// Batchmake temporary execution dir
+define("MIDAS_BATCHMAKE_SSP_DIR", "SSP");
+
+
 // Extension automatically appended to dagman 
 // description file when 'condor_dag_submit' generates it
 define("MIDAS_BATCHMAKE_CONDOR_DAGMAN_EXT", ".condor.sub");
@@ -88,7 +91,10 @@
 define("MIDAS_BATCHMAKE_NOT_FOUND_ON_CURRENT_SYSTEM_STRING", 'Not found on the current system');
 define("MIDAS_BATCHMAKE_FILE_OR_DIRECTORY_DOESNT_EXIST_STRING", "File or directory doesn't exist:");
 
-
+define("MIDAS_BATCHMAKE_NO_SCRIPT_SPECIFIED", "No script specified");
+define("MIDAS_BATCHMAKE_NO_SCRIPT_FOUND", "No script found at: ");
+define("MIDAS_BATCHMAKE_CREATE_TMP_DIR_FAILED", "Failed to create temporary directory: ");
+define("MIDAS_BATCHMAKE_SYMLINK_FAILED", "Failed to create symbolic link: ");
 
 
 // property keys

modules/batchmake/controllers/ConfigController.php

@@ -136,7 +136,9 @@ public function testconfigAction()
       }
 
     $config_status =  $this->ModuleComponent->KWBatchmake->testconfig($configPropertiesParamVals);
-    echo JsonComponent::encode($config_status);
+    $jsonout = JsonComponent::encode($config_status);
+    echo $jsonout;
+//    echo JsonComponent::encode($config_status);
     }//end testconfigAction