tripal/tripal_gbrowse/tripal_gbrowse.module

<?php
// $Id$

/**
 * @file
 * This file contains all the functions which provide functionality to this module.
 * This module was developed by Chad N.A. Krilow and Lacey-Anne Sanderson, 
 * University of Saskatchewan. 
 *
 * The GBrowse manamgenet module allows you to sync data in a chado/Tripal instance with
 * multiple GBrowse/mysql instances as well as manage and create such GBrowse instances
 */

include('tripal_gbrowse.align_features.inc');

//-----------------------------------------------------------------------------
//  SECTION: Main Outline Menu for GBrowse Management 
//-----------------------------------------------------------------------------


/**
 * Tripal-GBrowse-Menu
 *
 * Implemets hook_menu(): Adds menu items for the tripal_gbrowse module menu. This section
 * gives the outline for the main menu of the Tripal-GBrowse module
 *
 * @return
 *   An array of menu items that is visible within the Drupal Menu, returned as soon
 *   as the program is ran
 */
function tripal_gbrowse_menu() {
  
  $items = array();
  
  $items[ 'admin/tripal/tripal_gbrowse' ]= array(
    'title' => t('GBrowse Management'),
    'description' => ('GBrowse management allows a user to create a database, register
     a GBrowse instance and to load/delete feature libraries'),
    'page callback' => 'tripal_gbrowse_administration_description_page',
    'access arguments' => array('administer site configuration'),
    'type' => MENU_NORMAL_ITEM
  ); 

  $items['admin/tripal/tripal_gbrowse/configuration'] = array(
    'title' => t('Configuration'),
    'description' => t('Configuration for this module'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_gbrowse_administration_form'),
    'access arguments' => array('administer site configuration'),
    'type' => MENU_NORMAL_ITEM
  );

  $items['admin/tripal/tripal_gbrowse/register_gbrowse'] = array(
    'title' => t('Register GBrowse Instance'),
    'description' => t('Interface to enter gbrowse details and save to the database'), 
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_gbrowse_register_gbrowse_form'), 
    'access arguments' => array('administer site configuration'),
    'weight' => 20,
    'type' => MENU_NORMAL_ITEM
  );
  
  $items['admin/tripal/tripal_gbrowse/unregister_gbrowse']=array(
    'title' => t('Un-Register GBrowse Instance'),
    'description' => t('Interface to remove gbrowse details from the database'), 
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_gbrowse_unregister_gbrowse_instances_form'), 
    'access arguments' => array('administer site configuration'),
    'type' => MENU_NORMAL_ITEM
  );
  
  $items['admin/tripal/tripal_gbrowse/load_library_features'] = array(
    'title' => t('Load Library Features'),
    'description' => t('Load features associated with a specified library into a GBrowse instance.'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_gbrowse_load_library_features_form'),
    'access arguments' => array('administer site configuration'),
    'type' => MENU_NORMAL_ITEM
  );
  
  $items['admin/tripal/tripal_gbrowse/load_analysis_features'] = array(
    'title' => t('Load Analysis Features'),
    'description' => t('Load features associated with a specified analyses into a GBrowse instance.'),
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_gbrowse_load_analyses_form'),
    'access arguments' => array('administer site configuration'),
    'type' => MENU_NORMAL_ITEM
  );
  
  $items['admin/tripal/tripal_gbrowse/delete_library_features']=array(
    'title' => t('Delete Library Features'),
    'description' => t('Interface to delete features of a given library from a GBrowse Instance'), 
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_gbrowse_delete_library_features_from_gbrowse_form'), 
    'access arguments' => array('administer site configuration'),
    'type' => MENU_NORMAL_ITEM
  );
  
  $items['admin/tripal/tripal_gbrowse/delete_analysis_features']=array(
    'title' => t('Delete Analysis Features'),
    'description' => t('Interface to delete features of a given analysis from a GBrowse Instance'), 
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_gbrowse_delete_analysis_features_from_gbrowse_form'), 
    'access arguments' => array('administer site configuration'),
    'type' => MENU_NORMAL_ITEM
  );
  
  $items['admin/tripal/tripal_gbrowse/add_tracks']=array(
      'title' => t('Add Tracks'),
      'description' => t('Interface for Adding tracks to a GBrowse Instance'), 
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_gbrowse_add_tracks_form'), 
      'access arguments' => array('administer site configuration'),
      'type' => MENU_NORMAL_ITEM
  );
  
  $items['admin/tripal/tripal_gbrowse/delete_tracks']=array(
      'title' => t('Delete Tracks'),
      'description' => t('Interface for Deleting tracks from a GBrowse Instance'), 
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_gbrowse_delete_tracks_form'), 
      'access arguments' => array('administer site configuration'),
      'type' => MENU_NORMAL_ITEM
  );
  
  $items['admin/tripal/tripal_gbrowse/align_features']=array(
      'title' => t('Align Features'),
      'description' => t('Align a group of features (either library or analysis) against another grouping of features.'), 
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_gbrowse_align_features_form'), 
      'access arguments' => array('administer site configuration'),
      'type' => MENU_NORMAL_ITEM
  );  

  return $items;
}


/**
 * Implements hook_theme(): Register themeing functions for this module
 *
 * Contains the seperate tripal_gbrowse_X.tpl.php files, so as they can be included in the
 * theme for the designed module
 *
 * @return
 *   An array of themeing functions to register
 *
 */
function tripal_gbrowse_theme() {
	
	return array(
    // Block Templates------------------------------
    'tripal_gbrowse_database_details' => array (
      'arguments' => array('node'=> null),
      'template' => 'tripal_gbrowse_database_details',
    ),
    'tripal_gbrowse_details' => array (
      'arguments' => array('node'=> null),
      'template' => 'tripal_gbrowse_details',
    ),
    'tripal_gbrowse_gbrowse_instance' => array (
      'arguments' => array('node'=> null),
      'template' => 'tripal_gbrowse_gbrowse_instance',
    ),
    'tripal_gbrowse_teaser' => array (
      'arguments' => array('node'=> null),
      'template' => 'tripal_gbrowse_teaser',
    ),
    'tripal_gbrowse_loaded_sources' => array (
      'arguments' => array('node'=> null),
      'template' => 'tripal_gbrowse_loaded_sources',
    ),
	);
}


/**
 * Purpose: Implement Blocks relating to Tripal GBrowse content
 *
 * @param $op
 *   What kind of information to retrieve about the block or blocks. 
 *   Possible values include list, configure, save, view.
 * @param $delta
 *   Which block to return (not applicable if $op is 'list').
 * @param $edit
 *   If $op is 'save', the submitted form data from the configuration form.
 *
 * @return
 *   One of the following depending on $op: An array of block descriptions (list), the configuration 
 *   form (configure), nothing (save), an array defining subject and content for the block indexed 
 *   by $delta (view)
 *
 */
function tripal_gbrowse_block ($op = 'list', $delta = 0, $edit=array()) {
  switch($op) {
    case 'list':
      $blocks['database_details']['info'] = t('Tripal GBrowse Database Details');
      $blocks['database_details']['cache'] = BLOCK_NO_CACHE;

      $blocks['details']['info'] = t('Tripal GBrowse Details');
      $blocks['details']['cache'] = BLOCK_NO_CACHE;
         
      $blocks['gbrowse_instance']['info'] = t('Tripal GBrowse Instance');
      $blocks['gbrowse_instance']['cache'] = BLOCK_NO_CACHE;
         
      $blocks['teaser']['info'] = t('Tripal GBrowse Teaser');
      $blocks['teaser']['cache'] = BLOCK_NO_CACHE;
      
      $blocks['teaser']['info'] = t('Tripal GBrowse Sources');
      $blocks['teaser']['cache'] = BLOCK_NO_CACHE;
      
      return $blocks;

 		case 'view':
 			if(user_access('access tripal_gbrowse content') and arg(0) == 'node' and is_numeric(arg(1))) {
      	$nid = arg(1);
      	$node = node_load($nid);
 
        $block = array();
        switch($delta){
					case 'database_details':
						$block['subject'] = t('Tripal GBrowse Database Details');
						$block['content'] = theme('tripal_gbrowse_database_details',$node);
						break;
						
					case 'details':
						$block['subject'] = t('Tripal GBrowse Details');
						$block['content'] = theme('tripal_gbrowse_details',$node);
						break;
						
					case 'gbrowse_instance':
						$block['subject'] = t('Tripal GBrowse Instance');
						$block['content'] = theme('tripal_gbrowse_gbrowse_instance',$node);
						break;
						
					case 'teaser':
						$block['subject'] = t('Tripal GBrowse Teaser');
						$block['content'] = theme('tripal_gbrowse_teaser',$node);
						break;
						
					case 'teaser':
						$block['subject'] = t('Tripal GBrowse Sources');
						$block['content'] = theme('tripal_gbrowse_loaded_sources',$node);
						break;	
							
        }
				return $block;
			}
	}
}


/**
 * Implements hook_views_api()
 * Purpose: Essentially this hook tells drupal that there is views support
 *  for this module which then includes tripal_db.views.inc where all the
 *  views integration code is
 */ 
function tripal_gbrowse_views_api() {
   return array(
      'api' => 2.0,
   );
}


/**
 * This section uses HTML to output the descriptions of the module, through the Tripal Management
 * Administation window.Any installation instructions are given as well as included features
 * as well as a overview of the purpose Module.
 *
 * @return
 *   Returns '$text'The HTML description of the Module, its instructions, features, and any other 
 *   important aspects. This is returned when the Administration page is selected.
 */
function tripal_gbrowse_administration_description_page() {

  $text = ' ';

  $text .= '</p><h3>GBrowse Feature Administrative Tools Quick Links:</h3>';
  
  $text .= "<ul>";
  
  $text .= "<li>".l("Configuration", "admin/tripal/tripal_gbrowse/configuration"). "</li>";
	$text .= "<li>".l('Register GBrowse Instance', 'node/add/tripal-gbrowse')."</li>";
  $text .= "<li>".l("Load Library Features", "admin/tripal/tripal_gbrowse/load_library_features"). "</li>";
  $text .= "<li>".l("Delete Library Features", "admin/tripal/tripal_gbrowse/delete_library_features"). "</li>";
  $text .= "<li>".l("Load Analysis Features", "admin/tripal/tripal_gbrowse/load_analysis_features"). "</li>";
  $text .= "<li>".l("Delete Analysis Features", "admin/tripal/tripal_gbrowse/delete_analysis_features"). "</li>";
  $text .= "<li>".l("Add Tracks","admin/tripal/tripal_gbrowse/add_tracks"). "</li>";
  $text .= "<li>".l("Delete Tracks","admin/tripal/tripal_gbrowse/delete_tracks"). "</li>";

   
   $text .= "</ul>";
 
  $text .= '<h3>Module Description:</h3>';
  $text .= '<p>This module provides an interface to register already existing GBrowse instances with Drupal/Tripal and/or create new '
            .'GBrowse Instances. Furthermore, it allows basic management of these GBrowse instances including un-registering and/or '
            .'deleting and loading of features in Tripal/Chado into a MySQL GBrowse instance. As such, it provides interoperability '
            .'and syncronization between a Tripal/Chado installation and GBrowse</p>';

  $text .= '<h3>Setup Instructions:</h3>';
  $text .= '<ol>';
  $text .= '<li><b>Ensure the PHP-MySQL extension is installed:</b> Installation instructions are dependant upon your operating system.</li>';
  $text .= '<li><b>Move Template Configuration File:</b> Move the template.conf file included with this module into the GBrowse configuration file directory.</li>';
    $text .= '<li><b>Set GBrowse Instance Defaults :</b> Set default repository for Configuration files, also set the default GBrowse web link address.</li>'
						.'<a href="tripal_gbrowse/configuration">Administration -> Tripal Management -> GBrowse Management -> Configuration</a>.</li>';
  
  $text .= '<li><b>Register Existing GBrowse Instances</b>: Register any existing GBrowse instances through the form provided at '
            .'<a href="tripal_gbrowse/register_gbrowse">Administration -> Tripal Management -> GBrowse Management -> Register GBrowse Instance</a>.</li>';
  $text .= '<li><b>Load desired Feature Libraries into GBrowse Instances</b>: Additional feature libraries should be loaded through the form provided at '.l('Administration -> Tripal Management -> GBrowse Management -> Load Features','admin/tripal/tripal_gbrowse/load_features').'</li>';
  $text .= '<ol>';
  
  $text .= '<h3>Features of this Module:</h3>';
    $text .= '<ul>';
      $text .= '<li><b>Register GBrowse Instance:</b> In order to load features into a GBrowse instance you need to first register it with Tripal/Drupal. Any existing '
                .'GBrowse instance that utilizes a MySQL database can be registered with the module. Furthermore, you can create new GBrowse Instances '
                .'through this module by selecting that option in the register GBrowse Instance form. This'
                .'newly created GBrowse instance uses a MySQL database with is created and '
                .'a user name and password is setup and a default configuration file is created. Finally, the database is initialized and the first sequence '
                .'set is loaded into the GBrowse instance.</li>';
    
      $text .= '<li><b>Un-Register/Delete GBrowse Instance:</b> Un-registering a GBrowse instance alone will remove the GBrowse instance from the Drupal site.'
                .'When removing the entire instance, the database and the configuration file will be deleted. This cannot be undone!</li>';
    	
    	$text .='<li><b>Intergrated GBrowse Node/Page:</b> Allows users to easily access GBrowse instances that have been created.' 
    						.'This module provides details for a registered GBrowse Instance, including an I-Frame, providing instance access to the GBrowse display,' 
    						.'as well,the module provides a link to a GBrowse instance in a new window.</li>';
    
      $text .= '<li><b>Load Library Features:</b> Simply by selecting a Tripal Library and a GBrowse Instance, '
              .'the features associated with the selected Library are loaded into the selected GBrowse Instance. Libraries can also be updated by selecting that option. This removes all of the pre-existing'
              .'features associated with that library, then reloades them. Both loading and updating utilize the Perl script "bp_seqfeature_load.pl" which should be installed when you install GBrowse.</li>';
    
    	$text .= '<li><b>Load Analysis Features:</b> Simply by selecting a Tripal Analysis and a GBrowse Instance, '
              .'the analyses associated with the selected Library are loaded into the selected GBrowse Instance. Analyses can also be updated by selecting that option. This removes all of the pre-existing'
              .'features associated with that analysis, then reloades them. Both loading and updating utilize the Perl script "bp_seqfeature_load.pl" which should be installed when you install GBrowse.</li>';
    
      $text .= '<li><b>Delete Feature (Libraries) Libraries:</b> A user can select a desired Tripal Library and a specific GBrowse instance and all of the features associated with that library in the selected isntance are removed.'
              .' This section uses the Perl "script bp_seqfeature_delete.pl" to delete the specified features.</li>';
      $text .= '<li><b>Delete (Libraries) Analysis :</b> A user can select a desired Tripal Analysis  and a specific GBrowse instance and all of the features associated with that analysis in the selected isntance are removed.'
              .' This section uses the Perl "script bp_seqfeature_delete.pl" to delete the specified features.</li>';
              
      $text .= '<li><b>Add Tracks:</b> Allows a user to add tracks to a given GBrowse instance. This allows them to define exactly how they want their features to be displayed, as well as, to separate their features into their own GBrowse track.</li>';
      
      $text .= '<li><b>Delete Tracks:</b> Allows a user to delete default tracks or user created  tracks for a given GBrowse instance.</li>';
              
  $text .= '</ul>';
  
  return $text;
}


/**
 *  Implements hook_job_describe_args()
 *
 *  This function modifies the Job Arguments page and represents the job arguments with
 *  meaningfull descriptive names, sends a link to the library and shows if the database  
 *  was cleared or not.
 *
 *  @param $call_back
 *    The name of the function being called by tripal_jobs
 *
 *  @param $args
 *    The arguments that are passed, given if the selected proccess is 
 *				1-'tripal_gbrowse_delete_library_features_from_gbrowse'
 *				2-'tripal_gbrowse_load_library_features_into_gbrowse'*				
 *				3-'tripal_gbrowse_delete_analysis_features_from_gbrowse'
 *				3-'tripal_gbrowse_load_analysis_features_into_gbrowse'
 *    If 1- then the arguments are based on deleting a library feature from GBrowse.
 *    If 2- then the arguments are based on loading library features into GBrowse.
 *    If 3- then the arguments are based on deleting a analysis feature from GBrowse.
 *    If 4- then the arguments are based on loading analysis features into GBrowse.
 *
 * @return
 *     Job arguments:Database name, user Name, Password, Library ID, If GBrowse database was cleared, 
 *    to be displayed in Job Details page. 
 */
function tripal_gbrowse_job_describe_args($call_back, $args){

  switch ($call_back){
  
    case 'tripal_gbrowse_delete_library_features_from_gbrowse':
        
        $new_args['GBrowse Database Name']=$args[0];
        
        $new_args['User Name']=$args[1];
        
        $new_args['Password']=$args[2];
        $result = db_fetch_object(db_query("SELECT nid FROM chado_library WHERE library_id=%d",$args[3]));
        
        $node = node_load($result->nid);
        
        $new_args['Library']= l($node->title, 'node/'.$result->nid);
        
          if(empty($args[4])){
            $new_args['Clear GBrowse Database']= 'No';
          }else{
            $new_args['Clear GBrowse Database']= 'Yes';
          }
      
        break;
  
    case 'tripal_gbrowse_load_library_features_into_gbrowse':
        
        $new_args['GBrowse Database Name']=$args[0];
        
        $new_args['User Name']=$args[1];
        
        $new_args['Password']=$args[2];
        
        $result = db_fetch_object(db_query("SELECT nid FROM chado_library WHERE library_id=%d",$args[3]));
        
        $node = node_load($result->nid);
        
        $new_args['Library']= l($node->title, 'node/'.$result->nid);
        
          if(empty($args[4])){
            $new_args['Clear GBrowse Database']= 'No';
          }else{
            $new_args['Clear GBrowse Database']= 'Yes';
          }
      
        break;
        
  case 'tripal_gbrowse_delete_analysis_features_from_gbrowse':
        
        $new_args['GBrowse Database Name']=$args[0];
        
        $new_args['User Name']=$args[1];
        
        $new_args['Password']=$args[2];
        $result = db_fetch_object(db_query("SELECT nid FROM chado_analysis WHERE analysis_id=%d",$args[3]));
        
        $node = node_load($result->nid);
        
        $new_args['Analysis']= l($node->title, 'node/'.$result->nid);
        
          if(empty($args[4])){
            $new_args['Clear GBrowse Database']= 'No';
          }else{
            $new_args['Clear GBrowse Database']= 'Yes';
          }
      
        break;
  
  case 'tripal_gbrowse_load_analysis_features_into_gbrowse':
        
        $new_args['GBrowse Database Name']=$args[0];
        
        $new_args['User Name']=$args[1];
        
        $new_args['Password']=$args[2];
        
        $result = db_fetch_object(db_query("SELECT nid FROM chado_analysis WHERE analysis_id=%d",$args[3]));
        
        $node = node_load($result->nid);
        
        $new_args['Analysis']= l($node->title, 'node/'.$result->nid);
        
          if(empty($args[4])){
            $new_args['Clear GBrowse Database']= 'No';
          }else{
            $new_args['Clear GBrowse Database']= 'Yes';
          }
      
        break;
  
  }

  return $new_args;

}


//-----------------------------------------------------------------------------
//  SECTION: Database API
//-----------------------------------------------------------------------------


/**
 * The purpose of this function is to retrieve the previousley loaded libraries from database.
 *
 * @param $gbrowse
 *   A GBrowse instance that contains the information of the current instance	
 *
 * @return 
 * 	An array of libraries that have been loaded into the database
 */
function tripal_gbrowse_getloaded_sources($gbrowse){

  $loaded_libraries = array();
	
	$link = mysql_connect('localhost', $gbrowse->database_user, $gbrowse->user_password);
	
	if (!$link) {
		drupal_set_message('Could not connect to database: ' . mysql_error(), 'error');
	}
 
	//Sending query to the database
	$resource = mysql_query('use ' .$gbrowse->database_name);
	
	if (empty($resource)) {
		drupal_set_message ('Database is empty or Non-existent','error');
	}
	
	$resource = mysql_query('select * from typelist');
	
	if (empty($resource)) {
		drupal_set_message ('Missing table typelist in database. Check sequence backbone has been loaded (Execute: tripal jobs) ','error');
	}  else {
	
		$library_array = array();
		
		while($record = mysql_fetch_object($resource)){
				preg_match('/^[^:]+:(.+)/', $record->tag, $matches);	
				$library_array[$matches[1]]= $matches[1];
		}
	}
	mysql_close($link);

	return $library_array;

}


/**
 * The purpose of this function is to firstly create a file for backup purposes. Secondly, this
 * function uses a 'mysqldump' the contents of the selected database to a backup file. It then
 * access the database, drops the old database, creates a new one with the modified infromation,
 * then uploads the previously backed up infromation into the newly created database.
 * 
 *
 *  @param $node
 *    A node object containing the data and infromation of the GBrowse instance
 *
 *  @param $old_database
 *    The name of the originally created database, which will be replaced if the user
 *	  changes the name of the database that they have created
 *
 *  @return FALSE
 *    If error in creating database, or creating database, else nothing is returned
 */
function tripal_gbrowse_database_modification($node,$old_database){
		
  global $user;
		
	$user_name = $node->database_user;
		
	$user_password = $node->user_password;
		
	//creating a file in the /tmp directory for back-up purposes
	$back_upfile = '/tmp/' .$old_database .'_'.time().'.sql';
	
	//Using the 'mysqldump' command to dump the database for backup purposses
	$command = 'mysqldump -u' .$user_name .' -p' .$user_password .' ' .$old_database .' > ' .$back_upfile;
		
	exec($command);
		
	//To create a database use the mysql_query() function to execute an SQL query
	$link = mysql_connect('localhost', $user_name,$user_password);
			
	//Link operation verification
	if (!$link) {      
		drupal_set_message('Could not connect: ' . mysql_error(), 'error');
		return false;
	}

	//Dropping original database name and information
	$sql = 'DROP DATABASE ' . $old_database;
			
	if(mysql_query($sql, $link)){
		drupal_set_message( "Database Dropped Successfully\n");
	}else{
		drupal_set_message( 'Error Dropping Database: ' . mysql_error(), 'error');
		return false;
	}

	$sql = 'CREATE DATABASE ' . $node->database_name;

	if (mysql_query($sql, $link)) {
		drupal_set_message( "Database Created Successfully\n");
	} 
	else {
		drupal_set_message( 'Error Creating Database: ' . mysql_error() . "\n");  
		return false;
	}

	mysql_query( "GRANT SELECT ON " .$node->database_name.".* TO 'www-data'@'localhost'",$link);
	
	$command = 'mysql -u' .$user_name .' -p' .$user_password .' ' .$node->database_name .' < ' .$back_upfile;
	
	exec($command);
	
	mysql_close($link);
	
}


//-----------------------------------------------------------------------------
//  SECTION: Node Capability
//-----------------------------------------------------------------------------


/**
* Implementation of hook_tripal_gbrowse_node_info()
*
* This node_info, is a simple node that describes the functionallity of the module. It specifies
* that the title(gbrowse Name) and body(Description) set to true so that they information can be
* entered
*
*/
function tripal_gbrowse_node_info() {
  return array(
    'tripal_gbrowse' => array(
      'name' => t('GBrowse Instance'),
      'module' => 'tripal_gbrowse',
      'description' => t('A module for interfacing the GMOD database with Drupal, providing:
      Registration,Alteration and Deletion of GBrowse Instances,Configuration Files and Databases
      and the option to load/delete Sequence & Analysis Libraries'),
    	'has_title' => TRUE,
    	'title_label' =>t('gbrowse Name'),
    	'had_body' => FALSE,
    )
  );
}


/**
* Implementation of tripal_gbrowse_form().
*
*  This form takes the gbrowse Title infromation and the gbrowse description from the user. It 
*  then puts the infromation into the Chado_gbrowse database table.
*
*  @parm &$node
*    The node that is created when the database is initialized
*
*  @parm $form_state
*    The state of the form, that has the user entered information that is neccessary for, setting
*    up the database of the gbrowse
*
*  @return $form
*    The information that was enterd allong with   
*
*/
function tripal_gbrowse_form(&$node, $form_state) {
  
  $type = node_get_types('type', $node);

  //Creating Fieldset for multiple fields in form
  $form['register_gbrowse'] = array(
    '#type' => 'fieldset',
    '#title' => t('Data Base Specific Fields'),
  );
  
   //field for the name of the database
   $form['register_gbrowse']['database_name'] = array(
    '#type' => 'textfield',
    '#title' => t('GBrowse Database Name'),
    '#size' => 30,
    '#maxlength' => 64,
    '#description' => t('Desired Database Name Field'),
    '#default_value' => isset($node->gbrowse->database_name) ? $node->gbrowse->database_name : '',
    '#required' => TRUE,
  );
  
   //User of database 
   $form['register_gbrowse']['database_user'] = array(
    '#type' => 'textfield',
    '#title' => t('GBrowse User'),
    '#size' => 30,
    '#maxlength' => 64,
    '#description' => t('GBrowse MySQL User Field'),
    '#default_value' => isset($node->gbrowse->database_user) ? $node->gbrowse->database_user : '',
    '#required' => TRUE,
  );
  
   //Specified password for access to database 
   $form['register_gbrowse']['user_password'] = array(
    '#type' => 'password',
    '#title' => t('Password'),
    '#size' => 30,
    '#maxlength' => 64,
    '#description' => t('User Password Field'),
    '#default_value' => isset($node->gbrowse->user_password) ? $node->gbrowse->user_password : '',
    '#required' => TRUE,
  );
  
   //Creating Fieldset for multiple fields in form
   $form['gbrowse_details'] = array(
     '#type' => 'fieldset',
     '#title'=>'GBrowse Specifications' ,
   );
  
   //Human-readable name for the gbrowse instance 
   $form['gbrowse_details']['title'] = array(
    '#type' => 'textfield',
    '#title' => t('GBrowse Name'),
    '#size' => 30,
    '#maxlength' => 256,
    '#description' => t('GBrowse Instance'),
    '#default_value' => isset($node->gbrowse->gbrowse_name) ? $node->gbrowse->gbrowse_name : '',
    '#required' => TRUE,
  );
  
   //$_SERVER: takes the current url and sets to variable
   $default_value = variable_get('tripal_gbrowse_gbrowse_address_stub', '');
    
   //Link to the gbrowse instance
   $form['gbrowse_details']['gbrowse_link'] = array(
    '#type' => 'textfield',
    '#title' => t('GBrowse Link'),
    '#size' => 30,
    '#maxlength' => 256,
    '#description'=>t('Enter Full HTML address Including Host 
    (ex:http://knowpulse2.usask.ca/) of the new GBrowse instance. By default this is '.$default_value.'[configuration file name] where the configuration file name is the same as that entered below except without .conf'),
    '#default_value' => isset($node->gbrowse->gbrowse_link) ? $node->gbrowse->gbrowse_link : $default_value,
    '#required' => TRUE,
  );

  //Fully qualified location to the gbrowse configuration file 
   $form['gbrowse_details']['config_file'] = array(
    '#type' => 'textfield',
    '#title' => t('Configuration File'),
    '#size' => 30,
    '#maxlength' => 256,
    '#description' => t('Enter Fully Qualified File Name including Path (ex: file.conf) '),
    '#default_value' => isset($node->gbrowse->config_file) ? $node->gbrowse->config_file : variable_get('tripal_gbrowse_configuration_file_path', ''),
    '#required' => TRUE,
  );
  
  $result = tripal_core_chado_select ( 'library', array('library_id','name'), array() );

  foreach ($result as $value) {
  
    $newArray[$value->library_id]=$value->name;        //options for the select list
	
	}
	
	if (!$node->gbrowse->gbrowse_id) {
	
	 		// Creating Fieldset for multiple fields in form
  		$form['create_instance'] = array(
    		'#type' => 'fieldset',
    		'#title' => t('Create New GBrowse Instance'),
  		);
	
		if(empty($newArray)){
		
			drupal_set_message('There are currently no libraries to load.','error');
		
			$form['create_instance']['check_box'] = array(
				'#type' => 'item',
				'#value'=>'A GBrowse instance can not be created without a valid loadable backbone. 
				To make a valid loadable backbone available, please load features grouped in a library using 
				any of the feature loaders available.'
			);
		
		
		}else { 
		
			//A box if checked creates GBrowse Instances if they do not exist
			$form['create_instance']['check_box'] = array(
				'#type' => 'checkbox',
				'#title' => t('Create Instance'),
				'#description' => t('Create GBrowse Instane Unless Previous Existance'),
			);
		
				//Library ID
				$form['create_instance']['library_id'] = array(
					'#type' => 'select',
					'#title' => t('Sequence BackBone'),
					'#options' => $newArray,
					'#description' => t('Sequence Features Locations'),
				);
		}
	
	}
	
  return $form;
  
}

function tripal_gbrowse_validate ($node, $form) {

  if (!preg_match('/\.conf$/',$node->config_file)) {
    form_set_error('config_file','Configuration file must end in .conf');
  }
  
  if (!preg_match('/^http:\/\//',$node->gbrowse_link)) {
    form_set_error('gbrowse_link','GBrowse Link must be an absolute path (include http://)');
  }
}

/**
 *  Implements tripal_gbrowse_help()
 *
 *  This function simply states, in HTML tags, the creator of the the module and the contact	
 *  for the programmer
 *
 *  @parm $path
 *    The absolute path of the module and help information
 *
 *  @parm $arg
 *    The argument
 */
function tripal_gbrowse_help($path, $arg) {
  switch ($path) {
    
    case 'admin/help#tripal_gbrowse':
      
      return '<p>'. t('Module created by:Chad Krilow (e-mail:cnk046@mail.usask.ca)') .'</p>';
			
			break;
  }
}


/**
 * Implements hook_perm()
 *
 *  This function sets the permission for the user to access the information in the database.
 *  This includes creating, inserting, deleting and updating of information in the database
 *
 */
function tripal_gbrowse_perm(){

  return array('create tripal_gbrowse', 'edit own tripal_gbrowse', 'access database-related details' ,'access tripal_gbrowse content');

}


/**
 * Implements tripal_gbrowse_access()
 *
 *  This function sets the access permission for operations on the database.
 *  
 *
 *  @parm $op
 *    The operation that is to be performed
 *
 *  @parm $node
 *    The specific node that is to have the operation performed  
 *
 *  @parm $account
 *    The account of the user that is performing the operations  
 *
 *  @return
 *    True if a operation was performed
 *
 */
function tripal_gbrowse_access($op, $node, $account) {

  if($op == 'create') {
    // Only users with permission to do so may create this node type.
    if(!user_access('create tripal_gbrowse', $account)){
       return FALSE;
    }  
  }

  // Users who create a node may edit or delete it later, assuming they have the
  // necessary permissions.
  if($op == 'update' || $op == 'delete') {   
    if(!user_access('edit own tripal_gbrowse',$account)){
       return FALSE;
    } 
    if(user_access('edit own tripal_gbrowse',$account) && 
       $account->uid != $node->uid){
      return FALSE;
    }
  }
  return NULL;
}


/**
* Implementation of tripal_gbrowse_insert()
*
* This function inserts user entered information pertaining to the GBrowse instance into the
* 'tripal_gbrowse_instances' talble of the database, requiring that a 'Check Box' has been selected.
*
*  @parm $node
*    Then node which contains the information stored within the node-ID
*
*
*
*/
function tripal_gbrowse_insert($node) {
		
  $values = array(
    'database_name'=> $node->database_name,
    'database_user'=> $node->database_user,
    'user_password'=> $node->user_password,
    'gbrowse_name'=> $node->title,
    'gbrowse_link'=> $node->gbrowse_link,
    'config_file'=> $node->config_file,
    'library_id'=>$node->library_id,
    'nid'=>$node->nid,
    'vid'=>$node->vid,
   );
  
  //used to write to a database table described by Drupal Schema (not workable for chado)
  drupal_write_record('tripal_gbrowse_instances', $values);
  
  if($node->check_box==1){
  	tripal_gbrowse_create_gbrowse_instance($values);
	}else{
		drupal_set_message("Create instance check box not selected, unable initialize instance");
	}
	
}


/**
* Implementation of tripal_gbrowse_delete().
*
* This function takes a node and if the variable 'tripal_gbrowse_delete_all' has been defined,
* the GBrowse instance pertaining to the node passed into the function is deleted. Following,
* given the node-ID, the instance will be deleted from the 'tripal_gbrowse_instances' table.
*
*
*  @parm $node
*    Then node which contains the information stored within the node-ID
*
*/
function tripal_gbrowse_delete($node){
  
 	if(variable_get('tripal_gbrowse_delete_all', '')){ 
 		tripal_gbrowse_delete_gbrowse_instance($node->gbrowse);
 	}
 	
 	//deleteing in drupal chado_gbrowse table
  db_query('DELETE FROM {tripal_gbrowse_instances} WHERE nid = %d', $node->nid);
	
}


/*
*
* Implements hook_update
*
* The purpose of the function is to allow the module to take action when an edited node is being 
* updated in the database. It also updates any name changes to the configuration file that was
* created upon registering a GBrowse instance. This is done by moving the contents of the original 
* configuration file to the newly named file.As well, the database will be changed, if the name
* is altered by a registered user.If this is the case, the function 'tripal_gbrowse_database_modification'
* is called and the node and the old database infromation is passed, so as it may be altered and updated
* accordingley.
*
* @param $node 
*   The node being updated
*
*/
function tripal_gbrowse_update($node){
	
	//select from table before doing this, cause i wont be able to see the old details afterwards	
	$old_data = db_fetch_object(
  db_query('SELECT database_name,config_file FROM {tripal_gbrowse_instances} WHERE nid=%d AND vid=%d',
	$node->nid, $node->vid));
	
	$old_config_file=$old_data->config_file;
	
	$old_database_name=$old_data->database_name;
		
	$match= array(
		  'nid',
		  'vid',
	);
	
	$values =  array(
    'database_name'  => $node->database_name,
    'database_user'  => $node->database_user,
    'user_password'  => $node->user_password,
    'gbrowse_name'  => $node->gbrowse_name,
    'gbrowse_link' => $node->gbrowse_link,
    'config_file' => $node->config_file,
    'library_id'=>$node->library_id,
    'nid' => $node->nid,
    'vid' => $node->vid,
  );
  
  //Pulling out the configuration file
  $config_file = $node->config_file;
    
  if(strcmp($old_config_file, $config_file)!=0){
  	//Removing configuration file from the directory
  	$command = "mv " .$old_config_file ." ".$config_file;
  	exec($command);
	}

	if($old_database_name != $node->database_name){
    tripal_gbrowse_database_modification($node,$old_database_name);
	}		

	drupal_write_record('tripal_gbrowse_instances', $values, $match);

}


/**
* Implementation of tripal_gbrowse_load().
*
*
* @param $node
*   The node that is to be accessed from the database
*
* @return $node
*   The node with the information to be loaded into the database 
*
*/
function tripal_gbrowse_load($node) {
	
	$result = db_fetch_object(db_query('SELECT gbrowse_id,database_name,database_user,user_password,
	gbrowse_name,gbrowse_link,config_file FROM {tripal_gbrowse_instances} WHERE nid=%d AND vid=%d',$node->nid, $node->vid));
	
  $node->gbrowse = $result;
	
  return $node;
}


//-----------------------------------------------------------------------------
//  SECTION: Configuration form
//-----------------------------------------------------------------------------


/**
* Implemets hook_menu(): Adds menu items for the tripal_gbrowse module
*
* This form creates a specific Configuration File directory and sets a specific
* GBrowse web address for later access 
*
* @return
*   An array of menu items '$form' 
*/
function tripal_gbrowse_administration_form () {
 
  //Creating Fieldset for multiple fields in form
  $form['configuration_features'] = array(
    '#type' => 'fieldset',
    '#title' => t('Module Configuration Fields'),
  );
 
  //Configuration File Directory
  $form['configuration_features']['configuration_file'] = array(
    '#type' => 'textfield',
    '#title' => t('Set Default Configuration File Directory'),
    '#size' => 30,
    '#maxlength' => 64,
    '#description' => t('Specific Configuration File Directory'),
    '#default_value' => variable_get('tripal_gbrowse_configuration_file_path', ''),
  );
  
  //GBrowse Web Address
  $form['configuration_features']['gbrowse_address'] = array(
    '#type' => 'textfield',
    '#title' => t('Set Default GBrowse Web Address'),
    '#size' => 30,
    '#maxlength' => 64,
     '#description' => t('Desired GBrowse web address'),
     '#default_value' => variable_get('tripal_gbrowse_gbrowse_address_stub', ''),
  );
  
  //A box if checked creates GBrowse Instances(.conf file and database)
	$form['configuration_features']['delete_check_box'] = array(
		'#type' => 'checkbox',
		'#title' => t('Delete Instance'),
		'#description' => t('Delete GBrowse Configuration file and Database  '),
		'#default_value'=>variable_get('tripal_gbrowse_delete_all', ''),	
	);

  $form['configuration_features']['submit'] = array(
    '#type' => 'submit', 
    '#weight' => 10,
    '#value' => t('Submit')
  );
 
  return $form;
}


/**
 * Validate User-submitted data for Register GBrowse Instances Form
 *
 * This function validates the user input for each form element in the Register GBrowse 
 * instances form that is a text field. Validations checked include:
 *    -parse_url-checks that the url can be parsed
 *
 * @param $form
 *   The form that the user submitted and whose input is being validated
 * @param $form_state
 *   An array containing the state of the form being validated including user-input
 */
function tripal_gbrowse_administration_form_validate ($form, $form_state) {
  
  if ( !valid_url($form_state['values']['gbrowse_address'])) {
    form_set_error('gbrowse_address', 'Invalid URL');
  }
}


/**
*
* Configuration-Form
*
* @param $form
*    -The submitted form containing the user entered infromation
* @param $form_state 
*    -Is the state of the form: i.e what button was pressed, what infromation was entered,etc.
*    The key is the 'values'
*/
function tripal_gbrowse_administration_form_submit ($form, $form_state) {

  if(!preg_match('/\/$/', $form_state['values']['configuration_file'])) {
      $form_state['values']['configuration_file'] = $form_state['values']['configuration_file'] . "/";
  }

  variable_set('tripal_gbrowse_configuration_file_path',$form_state['values']['configuration_file'] );
  drupal_set_message('Configuration File Path set to: '.variable_get('tripal_gbrowse_configuration_file_path', ''));
    
        
  variable_set('tripal_gbrowse_gbrowse_address_stub',$form_state['values']['gbrowse_address'] );
  drupal_set_message('GBrowse Default Address set to: '.variable_get('tripal_gbrowse_gbrowse_address_stub', ''));
  
  if($form_state['values']['delete_check_box']==1){									
  	variable_set('tripal_gbrowse_delete_all',$form_state['values']['delete_check_box'] );
  	drupal_set_message('Selected GBrowse instance will be deleted: '.variable_get('tripal_gbrowse_delete_all', 'NOT SET'));
  }

}


//-----------------------------------------------------------------------------
//  SECTION: Register-GBrowse-Instance 
//-----------------------------------------------------------------------------


/**
*
* Register & Create GBrowse instance ( called by the node form )
*
* This form submit takes it's fields from the form for registering a GBrowse instance. The 'sed'command
* is used to select certain lines of a template 'conf' file and replaces them with the user specified GBrowse instance
* and data base name. It then removes the temporary file that was created. This function utilizes the MySQL database
* and uses the commands for MySQL to create a database for the registered GBrowse instance, appropriate warnings
* are issued if there are problems connecting/registering/accessing the database.
*
* @param $form
*    -The submitted form containing the user entered infromation
*
* @param $form_state 
*    This is the state of the form: i.e what button was pressed.The key is 
*    the name of the fields in database 
*
*/
function tripal_gbrowse_create_gbrowse_instance($values) {
    
    global $user;    //make current user details available so access of user id is available 
        
  //checking for existance of configuration file, if allready created a warning is issued
	if ( file_exists($values['config_file']) ){
		drupal_set_message('Configuration File Already Exists', 'warning');
	}else{ 
	
		$config_path = variable_get('tripal_gbrowse_configuration_file_path', '');
		
		if(empty($config_path)){   
			drupal_set_message( "Invalid or Non-Existent Configuration Path (Check Configuration Menu Defaults)", 'error');
		}
				
		$temp_file = '/tmp/temporary_gbrowse_'.time().'.conf';
		
		// Using 'sed' to select the second line of the template.config substitute <#gbrowse_name>
		//for .$values['gbrowse_name'] 
		$command = "sed '2 s/<#gbrowse_name#>/".$values['gbrowse_name']."/' ".$config_path."template.conf > ".$temp_file; 

		exec($command);
		
		// Using 'sed' to select the fifth line of the template.config substitute <#database_name>
		//for .$values['database_name']
		 $command = "sed '5 s/<#database_name#>/".$values['database_name']."/' ".$temp_file." > ".$values['config_file'];

		exec($command);
		
		// Check configuration file is there
		if (file_exists($values['config_file'])) {
			drupal_set_message('Configuration File created successfully');
		} else {
			drupal_set_message('Unable to create configuration file','error');
		}

		//To create a database use the mysql_query() function to execute an SQL query
		$link = mysql_connect('localhost', $values['database_user'],$values['user_password']);
	
		if (!$link) {
			drupal_set_message('Could not connect: ' . mysql_error());
			return false;
		}

		$sql = 'CREATE DATABASE ' . $values['database_name'];

		if (mysql_query($sql, $link)) {	
			drupal_set_message( "Database created successfully\n");
		} else {
			drupal_set_message( 'Error creating database: ' . mysql_error() . "\n");
			return false;
		}
	
		mysql_query( "GRANT SELECT ON " .$values['database_name'].".* TO 'www-data'@'localhost'",$link);
								
		mysql_close($link);

		$job_args=array($values['database_name'],$values['database_user'],$values['user_password'],$values['library_id'],TRUE);
			
		//registering a job with the tripal system, this job calls the function when executed
		$job_id = tripal_add_job('Loading Features Into GBrowse', 'tripal_gbrowse','tripal_gbrowse_load_library_features_into_gbrowse', $job_args, $user->uid);

		drupal_set_message(' The Backbone needs to be loaded into GBrowse (done by executing Tripal Jobs Loading script), 
		Before loaded libraries or GBrowse Instance will be displayed. ');

  	}
  
}


//-----------------------------------------------------------------------------
//  SECTION: Un-Register Existing GBrowse Instances
//-----------------------------------------------------------------------------


/**
* Un-Register GBrowse Instance Form Submit
*
* This is the Form-Submit section of the Un-Register GBrowse instance function. Depending on 
* which instance was selected, it will be removed from the database. A check box is provided
* which, if checked is true, will delete all data/files that was associated with the selected
* GBrowse instance.SQL commands are used in order to remove the selected instances from the 
* SQL database.
*
* @param $form
*    the submitted form containing the user entered infromation
* @param $form_state 
*    The state of the form: i.e if check-box was checked and what gbrowse_instance was selected to be deleted
*    The key is the 'values'
*
* @return
*    true or false, depending wheater the check box had been selected, if true, the 
*   selected GBrowse instance will be deleted
*/
function tripal_gbrowse_delete_gbrowse_instance($gbrowse) {
    
  // Retrieve current gbrowse instance details
  $gbrowse_instance = db_fetch_object(
  db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $gbrowse->gbrowse_id )
  );
     
    //Pulling out the configuration file
    $config_file = $gbrowse->config_file;
      
    //Removing configuration file from the directory
    $command = "rm ".$config_file;

    exec($command);
    
    if (file_exists($config_file)) {
      drupal_set_message('Configuration File ('.$config_file.') not removed!', 'error');
    } else {
      drupal_set_message('Configuration File removed successfully');
    }
      
    $user_name = $gbrowse->database_user;
    
    $user_password = $gbrowse->user_password;

    $link = mysql_connect('localhost', $user_name,$user_password);
      
    if (!$link) {     
      drupal_set_message('Could not connect: ' . mysql_error(), 'error');
      return false;
    }

    $sql = 'DROP DATABASE ' . $gbrowse->database_name;
      
    if(mysql_query($sql, $link)){    
      drupal_set_message( "Database removed successfully\n"); 
    }else{
      drupal_set_message( 'Error removing database: ' . mysql_error(), 'error');
      return false;
    }
      
    mysql_close($link);
  
}


//-----------------------------------------------------------------------------
//  SECTION: Load Library features into GBrowse Form & Form Submit
//-----------------------------------------------------------------------------


/**
* Implements hook_form
*
* This function creates a form for the database name, user name for database operation and a 
* password for access.The module uses these features to access information regarding the user's 
* operations and needs.
*
* @return
*   An array describing the form to be rendered
*/
function tripal_gbrowse_load_library_features_form() {
 
  $new_array=array();
   
  $result = tripal_core_chado_select ( 'library', array('library_id','name'), array() );
  
  foreach ($result as $value) {
    $new_array[$value->library_id]=$value->name;        //options for the select list
  }
  
  //Creating Fieldset for multiple fields in form
  $form['load_features'] = array(
    '#type' => 'fieldset'
  );
 
  //Library ID
  $form['load_features']['library_id'] = array(
      '#type' => 'select',
      '#title' => t('Libraries'),
      '#options' => $new_array,
      '#description' => t('Library of Genetic Sequences.'),
  );
    
  //Sending query to the database
  $resource = db_query('SELECT * FROM {tripal_gbrowse_instances}');

    $items = array();
  
    while($record = db_fetch_object($resource)){
      $items[$record->gbrowse_id]= $record->gbrowse_name;
    }
   
  //GBrowse Instances
  $form['load_features']['gbrowse_id'] = array(
    '#type' => 'select',
    '#title' => t('GBrowse Instances'),
    '#options' => $items,
    '#description' => t('Selected GBrowse Instances to be Loaded.'),
  );
    
  //A checkbox to update features for the gbrowse
  $form['load_features']['check_box'] = array(
    '#type' => 'checkbox',
    '#title' => t('Update Features'),
    '#description' => t('Existing Same Name Features Updated Accordingly.'),
  );

  $form['load_features']['submit'] = array(
   '#type' => 'submit', 
   '#weight' => 10,
   '#value' => t('Submit Job')
   );
  
  return $form;
}


/**
* Load-Features-Form
*
* @param $form
*    -The submitted form containing the user entered infromation
* @param $form_state 
*    -Is the state of the form: i.e what button was pressed, what infromation was entered,etc.
*    The key is the 'values'
*/
function tripal_gbrowse_load_library_features_form_submit($form,$form_state) {
    
	global $user;    //needed to make the current users details available so access of user id is available 
				
	$record = db_fetch_object(db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $form_state['values']['gbrowse_id']));
	
	$name = $record->database_name;

	$user_name = $record->database_user;

	$password= $record->user_password;

	$job_args = array($name,$user_name,$password,$form_state['values']['library_id'], FALSE);   
								
	//Checking state of check box, if checked delete features from GBrowse
	if($form_state['values']['check_box']==1){
		//registering a delete job with the tripal system, this job calls the function when executed
			$job_id = tripal_add_job('Deleting Features From GBrowse', 'tripal_gbrowse', 
			'tripal_gbrowse_delete_library_features_from_gbrowse', $job_args, $user->uid);
	}
	
  //registering a job with the tripal system, this job calls the function when executed
	$job_id = tripal_add_job('Loading Features Into GBrowse', 'tripal_gbrowse', 
	'tripal_gbrowse_load_library_features_into_gbrowse', $job_args, $user->uid);

}


//-----------------------------------------------------------------------------
//  SECTION:Load Library Features into GBrowse
//-----------------------------------------------------------------------------


/**
 * Load Library features into database 
 *
 * This loading function firstly creates a output GFF3 format file for verification purposes. Then, a 'Chado' table
 * is selected,depending which table the user is interested in, from this table specific infromation 
 * is taken out and placed in the GFF3 file.The Featurelocation(fmin) & featurelocation (fmax) are used  
 * to set the featureloc.feature_id = feature.feature_id, the fmin = start & fmax = end of the desired gene.
 * The testing if the phase is empty is done, if so a '.' is inserted into $phase variable. If the parent 
 * feature is indicated in feature location for the child feature will be set.The Attributes section 
 * sets the, ID, Name, Alias, Dbrexf to variables to be put into a CONF file.The strand is either a 
 * positive, negative, or zero value and is represented by +/./- accordingley.
 *
 * @param $name
 *   name of GBrowse database
 *
 * @param $user_name
 *   GBrowse MySQL user name 
 *
 * @param $password
 *   user password for GBrowse
 *
 * @param $library_id
 *   GBrowse MySQL user name 
 *
 * @param $clear_database
 *   Used to clear the database of its backbone structure
 */
function tripal_gbrowse_load_library_features_into_gbrowse($database_name, $user_name, $password, $library_id,$clear_database){

  //A test file created to verify output
  $myFile = "/tmp/temporaryGBrowse_".time().".gff3";
  
  //Test opening the file, will print warning if file is not able to be opened
  $fh = fopen($myFile, 'w') or die("WARNING: Can not open file");

  print "Creating GFF3 file of features for library...\n";
 
  if (!preg_match('/^\d+$/', $library_id)) {
   print "ERROR: Invalid Library ID supplied (Library ID = ".$library_id.")\n";  
   return false;
  }
  
  // Selecting all features
  $values = array('library_id' => $library_id);
   
  $prime_result = tripal_core_chado_select ( 'library_feature', array('feature_id'), $values );

  // Select Table:library; column:uniquename
  $result = tripal_core_chado_select ( 'library', array('uniquename'), $values );

  $source = $result[0]->uniquename ;
  
  // Check source: ERROR

  //For each feature, type id form feature table, specific record the feature id containing $feature_id
  foreach ($prime_result as $value) {

    $feature_id = $value->feature_id;
     
    if (!preg_match('/^\d+$/', $feature_id)) {
      print "ERROR: Invalid feature ID (".$feature_id.") associated with Library (Library ID = ".$library_id.")\n";
    }
   
    $result = tripal_core_chado_select('feature', array('type_id'), array('feature_id'=>$feature_id));
   
    $type_id = $result[0]->type_id;
     
    if (empty($type_id)) {
      print "ERROR: No Type associated with Feature (Feature ID = ".$feature_id.")\n";
    }
   
    //Taking the cvterm name from the cvterm table given the type-id($type_id)
    $result = tripal_core_chado_select('cvterm', array('name'), array('cvterm_id'=>$type_id));

    //The extracted cvterm name
    $type = $result[0]->name;
    
    if (empty($type)) {
      print "ERROR: Type associated with Feature (".$type_id.") doesn't exist in cvterm table (Feature ID = ".$feature_id.")\n";
    }
    
    //Featureloc.fmin & featureloc.fmax ( where featureloc.feature_id = feature.feature_id )
    //fmin = start & fmax = end
    $result = tripal_core_chado_select('featureloc', array('fmin','fmax', 'strand', 'phase', 'srcfeature_id'), array('feature_id'=>$feature_id));
  
    $start = $result[0]->fmin;
    if (!preg_match('/^\d+$/', $start)) {
      print "ERROR: Invalid Start (".$start.") of Feature (Feature ID= ".$feature_id.")\n";
    }
  
    $end = $result[0]->fmax;
    if (!preg_match('/^\d+$/', $end)) {
      print "ERROR: Invalid End (".$end.") of Feature (Feature ID= ".$feature_id.")\n";
    }
    
    $score = '.';


    //Converting from +1/0/-1 to +/./- as there are only three possible values
    if ($result[0]->strand < 0) {
    
      $strand= '-';
    } elseif ($result[0]->strand == 0) {
    
      $strand = '.';
    } elseif($result[0]->strand > 0) {
    
      $strand = '+';
    } else{
    
      $strand = '.';
    }
  
    //Testing if phase is empty, if so a '.' is inserted into $phase variable
    $phase = $result[0]->phase;
    if(empty($phase)){
      $phase = '.';
    }
  
    //This is the parent feature as indicated in feature location for the child feature and 
    //the current line described the child feature
    $srcfeature_id = $result[0]->srcfeature_id;

    if (empty($srcfeature_id)) {
      print "ERROR: No Parent associated with Feature Location (Feature ID = ".$feature_id.")\n";
    }
  
    $result = tripal_core_chado_select('feature', array('name'), array('feature_id'=>$srcfeature_id));
  
    $seqid = $result[0]->name;

    if (empty($seqid)) {
      print "ERROR: Parent (Parent Feature ID = ".$seqid.") associated with Feature doesn't exist in feature table (Feature ID =".$feature_id."\n";
    }

    
    //Attributes section, ID, Name, Alias, Dbrexf  
    $result = tripal_core_chado_select('feature', array('uniquename', 'name'), array('feature_id'=>$feature_id));
  
    $id = $result[0]->uniquename;
  
    if (empty($id)) {
      print "ERROR: Missing Unique Name for Feature (Feature ID = ".$feature_id.")\n";
    }

    $name = $result[0]->name;
  
    if (empty($name)) {
      print "WARNING: Missing Name for Feature (Feature ID = ".$feature_id.")\n";
    }
    
    //Synonym
    $result = tripal_core_chado_select('feature_synonym', array('synonym_id'), array('feature_id'=>$feature_id));

    $synonyms = array();
    foreach ($result as $obj){
  
      $synonym_id = $obj->synonym_id;
    
      $sub_result = tripal_core_chado_select('synonym', array('name'), array('synonym_id'=>$synonym_id));

      // check that $sub_result[0]->name isn't empty
      if (empty($sub_result[0]->name)) {
        print "ERROR: Synonym (".$synonym_id.") associated with feature not found in synonym table (Feature ID = ".$feature_id.")\n";
      } else {
        $synonyms[] = $sub_result[0]->name;
      }

    }
    
    // Additional Dbxref's
    $result = tripal_core_chado_select('feature_dbxref', array('dbxref_id'), array('feature_id'=>$feature_id));
    $dbxref = array();
    
    foreach ($result as $obj){
    
      $dbxref_id = $obj->dbxref_id;
  
      if (!empty($dbxref_id)) {
        $sub1_result = tripal_core_chado_select('dbxref', array('db_id', 'accession'), array('dbxref_id'=>$dbxref_id));
    
        $dbxref_accession = $sub1_result[0]->accession;
        
        $db_id = $sub1_result[0]->db_id;
        
        if (!empty($db_id)) {
          $sub_sub_result =tripal_core_chado_select('db', array('name'), array('db_id'=>$db_id));
        
          $db_name = $sub_sub_result[0]->name;    
      
          if (empty($db_name)) {
            print "ERROR: Database (".$db_id.") associated with database reference not in db table (Database Reference ID = ".$dbxref_id.")\n";
          } elseif (empty($dbxref_accession)) {
            print "WARNING: Missing Accession for Database Reference (Database Reference ID = ".$dbxref_id.")\n";
          } else {
            $dbxref[] = $db_name . ':' . $dbxref_accession;
          }
        }
      }
    }

    //Main Dbxref
    $result = tripal_core_chado_select('feature', array('dbxref_id'), array('feature_id'=>$feature_id));
  
    $dbxref_id = $result[0]->dbxref_id;
  
    if (empty($dbxref_id)) {
      print "WARNING: No Database Reference associated directly with Feature (Feature ID = ".$feature_id.")\n";
    }

    $result = tripal_core_chado_select('dbxref', array('accession','db_id'), array('dbxref_id'=>$dbxref_id));
      
    $dbxref_accession = $result[0]->accession;

    //checking $dbrexf_accession for emptyness 
    if(!empty($dbxref_accession)){

      $db_id = $result[0]->db_id;
    
      $sub_sub_result =tripal_core_chado_select('db', array('name'), array('db_id'=>$db_id));

      $db_name = $sub_sub_result[0]->name;
  
      $dbxref[] = $db_name . ':' . $dbxref_accession;

    } else {
      print "WARNING: Missing Accession for Database Reference (Database Reference ID = ".$dbxref_id.")\n";
    }

    //attributes array is assigned given elements based on previous initializations
    $attributes = array();

    $attributes[] = 'ID='.$id;

    if (!empty($name)) { $attributes[] = 'Name='.$name; }

    if (!empty($synonyms)) { $attributes[] = 'Alias='.implode(',',$synonyms); }

    if (!empty($dbxref)) { $attributes[] = 'Dbxref=' .implode(',', $dbxref); }

    //write to string for printing
    $stringData = implode("\t", array($seqid,$source,$type,$start,$end,$score,$strand,$phase,
  
    implode(';',$attributes)))."\n";
    
    //Write concatinated data ($stringData) to file    
    fwrite($fh, $stringData);
  }

  //Closing file
  fclose($fh);


  if($clear_database){    

    //The loading script: bp_seqfeature_load.pl, allows loading of data to specific file 
    $command= "bp_seqfeature_load.pl -c -u '" .$user_name. "' -p '" .$password. "' -d " .$database_name. " " . $myFile;

  }else{

    //The loading script: bp_seqfeature_load.pl, allows loading of data to specific file 
    $command= "bp_seqfeature_load.pl -u '" .$user_name. "' -p '" .$password. "' -d " .$database_name. " " . $myFile;
  }

  //optional 'print' statement to verify that the above comman is being called and executed properly
  print 'Executing Command:'.$command."\n";

  exec($command, $out_put, $return_var);


} 


//-----------------------------------------------------------------------------
//  SECTION: Delete library features from database Form & Form submit
//-----------------------------------------------------------------------------


/**
*
* This form's purpose is to delete library featues from a selected GBrowse insatance. By selecting
* a Library of genetic sequences and a GBrowse instance, the instance will be removed as will all the 
* associated libraries. This form allows access to a specified database and will delete any
* selected Library features. It will return the form that contains all of the neccessary
* information to send to the 'form_submit' function.
*
* @return $form
*   An array of menu items allowing deletion of features from the library
*/
function tripal_gbrowse_delete_library_features_from_gbrowse_form() {

  $form = array();
  
  $result = tripal_core_chado_select ( 'library', array('library_id','name'), array() );

  foreach ($result as $value){
    $newArray[$value->library_id]=$value->name;        //options for the select list
  }
    
  //Creating Fieldset for multiple fields in form
  $form['delete_gbrowse'] = array(
    '#type' => 'fieldset',
    '#title' => t(''),
  );
     
   //Library ID
   $form['delete_gbrowse']['library_id'] = array(
    '#type' => 'select',
    '#title' => t('Libraries'),
    '#options' => $newArray,
    '#description' => t('Genetic Sequences.'),
  );
    
  //Sending query to the database
  $resource = db_query('SELECT * FROM {tripal_gbrowse_instances}');

  $items = array();
  
  while($record = db_fetch_object($resource)){  
    $items[$record->gbrowse_id]= $record->gbrowse_name;  
  }

  $form['delete_gbrowse']['gbrowse_id'] = array(
    '#type' => 'select',
    '#title' => t('GBrowse Instances'),
    '#options' => $items,
    '#description' => t('Selected Instances to be Removed.'),
  );
  
  //Delete button to remove Library
  $form['delete_gbrowse']['submit'] = array(
     '#type' => 'submit', 
     '#weight' => 10,
     '#value' => t('Delete')
   );
    
  return $form;

}


/**
* This 'form_submit' function uses MySQL commands to select the GBrowse instance from a selected database.
* Then the selected features are deleted from the library.
*
*
* @param $form
*    The submitted form that 
*
* @param $form_state 
*    The state of the form, includes the selected library and the GBrowse instance to be removed
*    The key is the 'values'
*/
function tripal_gbrowse_delete_library_features_from_gbrowse_form_submit($form, $form_state) {
  
  global $user;    //needed to make the current users details available so access of user id is available 
          
  $record = db_fetch_object(db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $form_state['values']['gbrowse_id']));
    
  $name = $record->database_name;
  
  $user_name = $record->database_user;
  
  $password= $record->user_password;
  
  $job_args = array($name,$user_name,$password,$form_state['values']['library_id']);   
                  
  //Checking state of submit button, if selected delete features from library
  if($form_state['values']['op'] == 'Delete'){

    //registering a delete job with the tripal system, this job calls the function when executed
    $job_id = tripal_add_job('Deleting Library Features From GBrowse', 'tripal_gbrowse', 'tripal_gbrowse_delete_library_features_from_gbrowse', $job_args, $user->uid);
        
  }
    
}


//-----------------------------------------------------------------------------
//  SECTION: Delete Library Features from GBrowse
//-----------------------------------------------------------------------------


/**
* Delete-GBrowse-Feature
*
* This form Removes features from library that the user has specified. The form allows the user
* to select a desired instance. Once the library and instance are selected and deleted, the selected 
* libraries 
*
*
*
* @param $database_name
*   name of GBrowse database
* @param $user_name
*   GBrowse MySQL user name 
* @param $password
*   user password for GBrowse
* @param $library_id
*   The id of the library that is being selected from
*
*/
function tripal_gbrowse_delete_library_features_from_gbrowse($database_name, $user_name, $password, $library_id){

  $result = tripal_core_chado_select ( 'library', array('name'), array('library_id' => $library_id) 
  
  );

  $library_name = $result[0]->name;
  
  print "Removing Features of all types related to the ".$library_name." library...\n";

  $sql = 'SELECT cvterm.name FROM feature JOIN cvterm cvterm ON cvterm.cvterm_id=feature.type_id 
  
  JOIN library_feature library_feature ON library_feature.feature_id=feature.feature_id JOIN library 
  
  library ON library.library_id=library_feature.library_id WHERE library.library_id=%d GROUP BY 
  
  cvterm.name';

  $previous_db = tripal_db_set_active('chado');
  
  $resource = db_query($sql, $library_id);
  
  tripal_db_set_active($previous_db);
  
  while($record = db_fetch_object($resource)){
  
    $type = $record->name;
    
    //The loading script: bp_seqfeature_delete.pl, allows removal of data to specific file 
    $command= "bp_seqfeature_delete.pl -u '".$user_name."' -p '".$password."' -d '" .$database_name. "' -t '" .$type. ":".$library_name."'";
    
    print "Executing Command: ".$command."\n";
    
    //exec() allows for execution of a external program: given the input
    exec($command);
  
  }

}


//-----------------------------------------------------------------------------
//  SECTION: Load analyses into GBrowse Form and Form Submit
//-----------------------------------------------------------------------------


/**
* Implements hook_form
*
* This function creates a form for the database name, user name for database operation and a 
* password for access.The module uses these analyses to access information regarding the user's 
* operations and needs.
*
* @return
*   An array describing the form to be rendered
*/
function tripal_gbrowse_load_analyses_form(){
 
  $newArray=array();
  
  $result = tripal_core_chado_select ( 'analysis', array('analysis_id','name'), array() );
  
  foreach ($result as $value) {
    $newArray[$value->analysis_id]=$value->name;        //options for the select list
  }
  
  //Creating Fieldset for multiple fields in form
  $form['load_analyses'] = array(
    '#type' => 'fieldset',
  );
 
  //Library ID
  $form['load_analyses']['analysis_id'] = array(
      '#type' => 'select',
      '#title' => t('Analyses'),
      '#options' => $newArray,
      '#description' => t('Analyses.'),
  );
    
  //Sending query to the database
  $resource = db_query('SELECT * FROM {tripal_gbrowse_instances}');

    $items = array();
  
    while($record = db_fetch_object($resource)){
      $items[$record->gbrowse_id]= $record->gbrowse_name;
  }
  
  //GBrowse Instances
  $form['load_analyses']['gbrowse_id'] = array(
      '#type' => 'select',
      '#title' => t('GBrowse Instances'),
      '#options' => $items,
      '#description' => t('Selected GBrowse Instances to be Loaded.'),
  );
    
  //A checkbox to update features for the gbrowse
  $form['load_analyses']['check_box'] = array(
    '#type' => 'checkbox',
    '#title' => t('Update Analyses'),
    '#description' => t('Existing Same Name Analyses Updated Accordingly.'),
  );

  $form['load_analyses']['submit'] = array(
   '#type' => 'submit', 
   '#weight' => 10,
   '#value' => t('Submit Job')
   );
  
  return $form;
}


/**
* Load-Features-Form
*
* @param $form
*    -The submitted form containing the user entered infromation
*
* @param $form_state 
*    -Is the state of the form: i.e what button was pressed, what infromation was entered,etc.
*    The key is the 'values'
*/
function tripal_gbrowse_load_analyses_form_submit($form, $form_state) {
    
    global $user;    //needed to make the current users details available so access of user id is available 
          
    $record = db_fetch_object(db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $form_state['values']['gbrowse_id']));
    
    $name = $record->database_name;
  
    $user_name = $record->database_user;
  
    $password= $record->user_password;
 
    $job_args = array($name,$user_name,$password,$form_state['values']['analysis_id'], FALSE);   
                 
    //Checking state of check box, if checked delete features from GBrowse
    if($form_state['values']['check_box']==1){
        //registering a delete job with the tripal system, this job calls the function when executed
        $job_id = tripal_add_job('Deleting Features From GBrowse', 'tripal_gbrowse', 
        'tripal_gbrowse_delete_analysis_features_from_gbrowse', $job_args, $user->uid);
    }
    
    //registering a job with the tripal system, this job calls the function when executed
    $job_id = tripal_add_job('Loading Features Into GBrowse', 'tripal_gbrowse', 
    'tripal_gbrowse_load_analysis_features_into_gbrowse', $job_args, $user->uid);

}


//-----------------------------------------------------------------------------
//  SECTION:Load Analysis Features into GBrowse
//-----------------------------------------------------------------------------


/**
 * Load Analysis features into database 
 *
 * This loading function firstly creates a output GFF3 format file for verification purposes. Then, a 'Chado' table
 * is selected,depending which table the user is interested in, from this table specific infromation 
 * is taken out and placed in the GFF3 file.The Featurelocation(fmin) & featurelocation (fmax) are used  
 * to set the featureloc.feature_id = feature.feature_id, the fmin = start & fmax = end of the desired gene.
 * The testing if the phase is empty is done, if so a '.' is inserted into $phase variable. If the parent 
 * feature is indicated in feature location for the child feature will be set.The Attributes section 
 * sets the, ID, Name, Alias, Dbrexf to variables to be put into a CONF file.The strand is either a 
 * positive, negative, or zero value and is represented by +/./- accordingley.
 *
 * @param $name
 *   name of GBrowse database
 *
 * @param $user_name
 *   GBrowse MySQL user name
 *
 * @param $password
 *   user password for GBrowse
 *
 * @param $library_id
 *   GBrowse MySQL user name 
 *
 * @param $clear_database
 *   Used to clear the database of its backbone structure
 */
function tripal_gbrowse_load_analysis_features_into_gbrowse($database_name, $user_name, $password, $analysis_id,$clear_database){

	//print 'Analysis ID: '.$analysis_id.".\n";

  //A test file created to verify output
  $myFile = "/tmp/temporaryGBrowse_".time().".gff3";
  
  //Test opening the file, will print warning if file is not able to be opened
  $fh = fopen($myFile, 'w') or die("WARNING: Can not open file");

  print "Creating GFF3 file of features for Analysis...\n";
 
  if (!preg_match('/^\d+$/', $analysis_id)) {
   print "ERROR: Invalid Analysis ID supplied (Analysis ID= ".$analysis_id.")\n";  
   return false;
  }
  
  // Selecting all analyses
  $values = array('analysis_id' => $analysis_id);
      
  $prime_result = tripal_core_chado_select ( 'analysisfeature', array('feature_id'), $values);

  // Select Table:library; column:uniquename
  $result = tripal_core_chado_select ( 'analysis', array('name'), $values );

  $source = $result[0]->name ;
  
  // Check source: ERROR
  //For each feature, type id form feature table, specific record the feature id containing $feature_id
  foreach ($prime_result as $value) {

    $feature_id = $value->feature_id;
     
    if (!preg_match('/^\d+$/', $feature_id)) {
      print "ERROR: Invalid feature ID (".$feature_id.") associated with Library (Library ID = ".$analysis_id.")\n";
    }
   
    $result = tripal_core_chado_select('feature', array('type_id'), array('feature_id'=>$feature_id));
   
    $type_id = $result[0]->type_id;
     
    if (empty($type_id)) {
      print "ERROR: No Type associated with Feature ( Feature ID = ".$feature_id.")\n";
    }
   
    //Taking the cvterm name from the cvterm table given the type-id($type_id)
    $result = tripal_core_chado_select('cvterm', array('name'), array('cvterm_id'=>$type_id));

    //The extracted cvterm name
    $type = $result[0]->name;
    
    if (empty($type)) {
      print "ERROR: Type associated with Feature (".$type_id.") doesn't exist in cvterm table (Feature ID = ".$feature_id.")\n";
    }
    
    //Featureloc.fmin & featureloc.fmax ( where featureloc.feature_id = feature.feature_id )
    //fmin = start & fmax = end
    $result = tripal_core_chado_select('featureloc', array('fmin','fmax', 'strand', 'phase', 'srcfeature_id'), array('feature_id'=>$feature_id));
  
    $start = $result[0]->fmin;
    if (!preg_match('/^\d+$/', $start)) {
      print "ERROR: Invalid Start (".$start.") of Feature (Feature ID= ".$feature_id.")\n";
    }
  
    $end = $result[0]->fmax;
    if (!preg_match('/^\d+$/', $end)) {
      print "ERROR: Invalid End (".$end.") of Feature (Feature ID= ".$feature_id.")\n";
    }
    
    $score = '.';

    //Converting from +1/0/-1 to +/./- as there are only three possible values
    if ($result[0]->strand < 0) {
      $strand= '-';
    } elseif ($result[0]->strand == 0) {
      $strand = '.';
    } elseif($result[0]->strand > 0) {
      $strand = '+';
    } else{
      $strand = '.';
    }
  
    //Testing if phase is empty, if so a '.' is inserted into $phase variable
    $phase = $result[0]->phase;
    if(empty($phase)){
      $phase = '.';
    }
  
    //This is the parent feature as indicated in feature location for the child feature and 
    //the current line described the child feature
    $srcfeature_id = $result[0]->srcfeature_id;

    if (empty($srcfeature_id)) {
      print "ERROR: No Parent associated with Feature Location (Feature ID = ".$feature_id.")\n";
    }
  
    $result = tripal_core_chado_select('feature', array('name'), array('feature_id'=>$srcfeature_id));
  
    $seqid = $result[0]->name;

    if (empty($seqid)) {
      print "ERROR: Parent (Parent Feature ID = ".$seqid.") associated with Feature doesn't exist in feature table (Feature ID =".$feature_id."\n";
    }

    //Attributes section, ID, Name, Alias, Dbrexf  
    $result = tripal_core_chado_select('feature', array('uniquename', 'name'), array('feature_id'=>$feature_id));
  
    $id = $result[0]->uniquename;
  
    if (empty($id)) {
      print "ERROR: Missing Unique Name for Feature (Feature ID = ".$feature_id.")\n";
    }

    $name = $result[0]->name;
  
    if (empty($name)) {
      print "WARNING: Missing Name for Feature (Feature ID = ".$feature_id.")\n";
    }
    
    //Synonym
    $result = tripal_core_chado_select('feature_synonym', array('synonym_id'), array('feature_id'=>$feature_id));

    $synonyms = array();
    foreach ($result as $obj){
  
      $synonym_id = $obj->synonym_id;
    
      $sub_result = tripal_core_chado_select('synonym', array('name'), array('synonym_id'=>$synonym_id));

      // check that $sub_result[0]->name isn't empty
      if (empty($sub_result[0]->name)) {
        print "ERROR: Synonym (".$synonym_id.") associated with feature not found in synonym table (Feature ID = ".$feature_id.")\n";
      } else {
        $synonyms[] = $sub_result[0]->name;
      }

    }
    
    // Additional Dbxref's
    $result = tripal_core_chado_select('feature_dbxref', array('dbxref_id'), array('feature_id'=>$feature_id));
    $dbxref = array();
    
    foreach ($result as $obj){
    
      $dbxref_id = $obj->dbxref_id;
  
      if (!empty($dbxref_id)) {
        $sub1_result = tripal_core_chado_select('dbxref', array('db_id', 'accession'), array('dbxref_id'=>$dbxref_id));
    
        $dbxref_accession = $sub1_result[0]->accession;
        
        $db_id = $sub1_result[0]->db_id;
        
        if (!empty($db_id)) {
          $sub_sub_result =tripal_core_chado_select('db', array('name'), array('db_id'=>$db_id));
        
          $db_name = $sub_sub_result[0]->name;    
      
          if (empty($db_name)) {
            print "ERROR: Database (".$db_id.") associated with database reference not in db table (Database Reference ID = ".$dbxref_id.")\n";
          } elseif (empty($dbxref_accession)) {
            print "WARNING: Missing Accession for Database Reference (Database Reference ID = ".$dbxref_id.")\n";
          } else {
            $dbxref[] = $db_name . ':' . $dbxref_accession;
          }
        }
      }
    }

    //Main Dbxref
    $result = tripal_core_chado_select('feature', array('dbxref_id'), array('feature_id'=>$feature_id));
  
    $dbxref_id = $result[0]->dbxref_id;
  
    if (empty($dbxref_id)) {
      print "WARNING: No Database Reference associated directly with Feature (Feature ID = ".$feature_id.")\n";
    }

    $result = tripal_core_chado_select('dbxref', array('accession','db_id'), array('dbxref_id'=>$dbxref_id));
      
    $dbxref_accession = $result[0]->accession;

    //checking $dbrexf_accession for emptyness 
    if(!empty($dbxref_accession)){

      $db_id = $result[0]->db_id;
    
      $sub_sub_result =tripal_core_chado_select('db', array('name'), array('db_id'=>$db_id));

      $db_name = $sub_sub_result[0]->name;
  
      $dbxref[] = $db_name . ':' . $dbxref_accession;

    } else {
      print "WARNING: Missing Accession for Database Reference (Database Reference ID = ".$dbxref_id.")\n";
    }

    //attributes array is assigned given elements based on previous initializations
    $attributes = array();

    $attributes[] = 'ID='.$id;

    if (!empty($name)) { 
      $attributes[] = 'Name='.$name; 
    }

    if (!empty($synonyms)) { 
      $attributes[] = 'Alias='.implode(',',$synonyms); 
    }

    if (!empty($dbxref)) { 
      $attributes[] = 'Dbxref=' .implode(',', $dbxref); 
    }

    //write to string for printing
    $stringData = implode("\t", array($seqid,$source,$type,$start,$end,$score,$strand,$phase,
  
    implode(';',$attributes)))."\n";
    
    //Write concatinated data ($stringData) to file    
    fwrite($fh, $stringData);
  }

  //Closing file
  fclose($fh);


  if($clear_database){    
    //The loading script: bp_seqfeature_load.pl, allows loading of data to specific file 
    $command= "bp_seqfeature_load.pl -c -u '" .$user_name. "' -p '" .$password. "' -d " .$database_name. " " . $myFile;
  }else{
    //The loading script: bp_seqfeature_load.pl, allows loading of data to specific file 
    $command= "bp_seqfeature_load.pl -u '" .$user_name. "' -p '" .$password. "' -d " .$database_name. " " . $myFile;
  }

  //optional 'print' statement to verify that the above comman is being called and executed properly
  print 'Executing Command:'.$command."\n";

  exec($command, $out_put, $return_var);
} 


//-----------------------------------------------------------------------------
//  SECTION: Delete analysis features from database Form & Form submit
//-----------------------------------------------------------------------------


/**
* This form's purpose is to delete analysis featues from a selected GBrowse insatance. By selecting
* a Library of analyses and a GBrowse instance, the instance will be removed as will all the 
* associated analysis library. This form allows access to a specified database and will delete any
* selected Analysis features. It will return the form that contains all of the neccessary
* information to send to the 'form_submit' function.
*
* @return $form
*   An array of menu items allowing deletion of features from the library
*/
function tripal_gbrowse_delete_analysis_features_from_gbrowse_form() {

  $form = array();
  
  $result = tripal_core_chado_select ( 'analysis', array('analysis_id','name'), array() );

  foreach ($result as $value){
    $newArray[$value->analysis_id]=$value->name;        //options for the select list
  }
    
  //Creating Fieldset for multiple fields in form
  $form['delete_analysis'] = array(
    '#type' => 'fieldset',
    '#title' => t(''),
  );
     
   //Library ID
   $form['delete_analysis']['analysis_id'] = array(
    '#type' => 'select',
    '#title' => t('Analysis Features'),
    '#options' => $newArray,
    '#description' => t('Analysis.'),
  );
    
  //Sending query to the database
  $resource = db_query('SELECT * FROM {tripal_gbrowse_instances}');

  $items = array();
  
  while($record = db_fetch_object($resource)){
    $items[$record->gbrowse_id]= $record->gbrowse_name;
  }
  
  $form['delete_analysis']['gbrowse_id'] = array(
    '#type' => 'select',
    '#title' => t('GBrowse Instances'),
    '#options' => $items,
    '#description' => t('Selected Instances to be Removed.'),
  );
  
  //Delete button to remove Library
  $form['delete_analysis']['submit'] = array(
     '#type' => 'submit', 
     '#weight' => 10,
     '#value' => t('Delete')
   );
    
  return $form;
}


/**
* This 'form_submit' function uses MySQL commands to select the GBrowse instance from a selected database.
* Then the selected features are deleted from the library.
*
*
* @param $form
*    The submitted form that 
*
* @param $form_state 
*    The state of the form, includes the selected library and the GBrowse instance to be removed
*    The key is the 'values'
*/
function tripal_gbrowse_delete_analysis_features_from_gbrowse_form_submit($form, $form_state) {
  
  global $user;    //needed to make the current users details available so access of user id is available 
          
  $record = db_fetch_object(db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $form_state['values']['gbrowse_id']));
    
  $name = $record->database_name;
  
  $user_name = $record->database_user;
  
  $password= $record->user_password;
  
  $job_args = array($name,$user_name,$password,$form_state['values']['analysis_id']);
                  
  //Checking state of submit button, if selected delete features from library
  if($form_state['values']['op'] == 'Delete'){
    //registering a delete job with the tripal system, this job calls the function when executed
    $job_id = tripal_add_job('Deleting Analysis Features From GBrowse', 'tripal_gbrowse', 'tripal_gbrowse_delete_analysis_features_from_gbrowse', $job_args, $user->uid);
  }
    
}


//-----------------------------------------------------------------------------
//  SECTION: Delete Analysis Features from GBrowse
//-----------------------------------------------------------------------------


/**
* Delete-GBrowse-Feature
*
* This form Removes features from Analysis that the user has specified. The form allows the user
* to select a desired instance. Once the analysis and instance are selected and deleted, the selected 
* analyses will be disassociated with the specified instance. 
*
* @param $database_name
*   name of GBrowse database
*
* @param $user_name
*   GBrowse MySQL user name 
*
* @param $password
*   user password for GBrowse
*
* @param $library_id
*   The id of the library that is being selected from
*
*/
function tripal_gbrowse_delete_analysis_features_from_gbrowse($database_name, $user_name, $password, $analysis_id){

  $result = tripal_core_chado_select ( 'analysis', array('name'), array('analysis_id' => $analysis_id) 
  
  );
  
  $analysis_name = $result[0]->name;
  
  print "Removing Analysis Features of all types related to the ".$analysis_name." analysis...\n";

  $sql = 'SELECT cvterm.name FROM feature JOIN cvterm cvterm ON cvterm.cvterm_id=feature.type_id 
  
  JOIN analysisfeature analysisfeature ON analysisfeature.feature_id=feature.feature_id JOIN analysis 
  
  analysis ON analysis.analysis_id=analysisfeature.analysis_id WHERE analysis.analysis_id=%d GROUP BY 
  
  cvterm.name';

  $previous_db = tripal_db_set_active('chado');
  $resource = db_query($sql, $analysis_id);
  tripal_db_set_active($previous_db);
  
  while($record = db_fetch_object($resource)){
  
    $type = $record->name;
    
    //The loading script: bp_seqfeature_delete.pl, allows removal of data to specific file 
    $command= "bp_seqfeature_delete.pl -u '".$user_name."' -p '".$password."' -d '" .$database_name. "' -t '" .$type. ":".$analysis_name."'";
    
    print "Executing Command: ".$command."\n";
    
    //exec() allows for execution of a external program: given the input
    exec($command);
  }

}


//-----------------------------------------------------------------------------
//  SECTION: Add Tracks Form & Form submit
//-----------------------------------------------------------------------------


/**
* Add-GBrowse-Tracks
*      This Menu item is implemented to allow users to define and add tracks including their name,
*  glyph, colour (fore and back ground), size and link. By adding tracks, the user is able to
*  visually inspect the features of their genomic data. The Glyph library has been hardcoded 
*  into the software and represents the most used Glyph representations. The "Glyph" option  
*  determines the shape of each of the displayed genomic features associated with a specific  
*  GBrowse track. It presents a configurable set of parameters specific to its type allowing 
*  further control over the display features such as height, color (foreground & backround) etc.
*
*
* @return
*   An '$form' that is an array of menu items that allows the user to Register a GBrowse instance
*/
function tripal_gbrowse_add_tracks_form() {

  
  //Creating Fieldset for multiple fields in form
  $form['add_tracks_field_set'] = array(
    '#type' => 'fieldset',
    '#title' => t('Content-Related Fields'),
  );

  //Sending query to the database for GBrowse Instances
  $resource = db_query('SELECT * FROM {tripal_gbrowse_instances}');

  $items = array();
  
  while($record = db_fetch_object($resource)){
      
    $items[$record->gbrowse_id]= $record->gbrowse_name;
      
  }

  //GBrowse Instances
  $form['add_tracks_field_set']['gbrowse_instances'] = array(
    '#type' => 'select',
    '#title' => t('Registered GBrowse Instances'),
    '#options' => $items,
    '#description' => t('Selected GBrowse Instances to be Loaded.'),
    '#required' => TRUE,
  );

  //Feature Type
  $sql = 'SELECT name as type, cvterm_id '
          .'FROM cvterm '
          .'WHERE cvterm_id IN (SELECT type_id FROM feature)';
  $previous_db = tripal_db_set_active('chado');
  $resource = db_query($sql);
  tripal_db_set_active($previous_db);
  
  $items = array();
  
  while($record = db_fetch_object($resource)){
    
    $items[$record->type] = $record->type;
  }

  $form['add_tracks_field_set']['type_name'] = array(
    '#type' => 'select',
    '#title' => t('Feature Type'),
    '#options' => $items,
    '#description' => t('Selected GBrowse Instances to be Loaded.'),
    '#required' => TRUE,
  );

  //Populating Select list for  Library    
  $newArray['none'] = 'None';        //No option for select list
  $result = tripal_core_chado_select ( 'library', array('library_id','name'), array() );
  foreach ($result as $value) {
    $newArray[$value->name]=$value->name;        //options for the select list
  }
        
  //Library
  $form['add_tracks_field_set']['library_id'] = array(
    '#type' => 'select',
    '#title' => t('Library'),
    '#options' => $newArray,
    '#description' => t('Selected GBrowse Instances to be Loaded.'),
  );

  //Creating Fieldset for multiple fields in form
  $form['track_text'] = array(
    '#type' => 'fieldset',
    '#title' => 'Track-Specific Fields'
  );

  //Specify Track Identifier
  $form['track_text']['identifier'] = array(
    '#type' => 'textfield',
    '#title' => t('Track Identifier'),
    '#size' => 30,
    '#maxlength' => 64,
    '#description' => t('Specify Track Identifier (Must be Unique and Specific)'),
    '#required' => TRUE,
  );

  //Specify Track Name
  $form['track_text']['track_name'] = array(
    '#type' => 'textfield',
    '#title' => t('Track Name'),
    '#size' => 30,
    '#maxlength' => 64,
    '#description' => t('Specify Track Name (Must be Unique and Specific)'),
    '#required' => TRUE,
  );
  
  //Populating Array of Glyph List
  $item = array();
  $item[''] = 'Default Glyph';
  $item['generic'] = 'Generic';
  $item['allele_tower  '] = 'Allele Tower';
  $item['anchored_arrow'] = 'Anchored Arrow';
  $item['arrow'] = 'Arrow';
  $item['box'] = 'Box';
  $item['cds'] = 'CDS';
  $item['crossbox'] = 'Cross Box';
  $item['diamond'] = 'Diamond';
  $item['dna'] = 'DNA';
  $item['dot'] = 'Dot';
  $item['ellipse'] = 'Ellipse';
  $item['extending_arrow'] = 'Extending Arrow';
  $item['generic'] = 'Generic';
  $item['graded_segments'] = 'Graded Segments';
  $item['heterogeneous_segments  '] = 'Heterogeneous Segments';
  $item['image'] = 'Image';
  $item['line'] = 'Line';
  $item['primers'] = 'Primers';
  $item['processed_transcript'] = 'Processed Transcript';
  $item['rndrect'] = 'Rndrect';
  $item['ruler_arrow'] = 'Ruler Arrow';
  $item['segments'] = 'Segments';
  $item['span'] = 'Span';
  $item['toomany'] = 'Too Many';
  $item['transcript'] = 'Transcript';
  $item['transcript2'] = 'Transcript2';
  $item['translation'] = 'Translation';
  $item['triangle'] = 'Triangle';
  $item['wiggle_densit'] = 'Wiggle Densit';
  $item['wiggle_xyplot'] = 'Wiggle XYplot';
  $item['xyplot'] = 'XYplot';
      
      
  //Glyphs
  $form['track_text']['glyph'] = array(
    '#type' => 'select',
    '#title' => t('Glyph'),
    '#options' => $item,
    '#description' => t('Shape of Genomic Feature Track '),
  );

  //Modify The foreground colour of track
    $form['track_text']['foreground_colour'] = array(
    '#type' => 'textfield',
    '#title' => t('Foreground Colour'),
    '#size' => 30,
    '#maxlength' => 64,
    '#description' => t('Enter name/Hex-code for identifying foreground colour of glyph.
                        List of available colours here:'.l("GBrowse Colour Palette.pdf",
                        "http://gmod.org/mediawiki/images/a/ae/Gbrowse_Color_Palette.pdf")),
  );


  //Modify The Backround colour of track
  $form['track_text']['backround_colour'] = array(
    '#type' => 'textfield',
    '#title' => t('Background Colour'),
    '#size' => 30,
    '#maxlength' => 20,
    '#description' => t('Enter name/Hex-code for identifying background colour of glyph.
                        List of available colours here:'.l("GBrowse Colour Palette.pdf",
                        "http://gmod.org/mediawiki/images/a/ae/Gbrowse_Color_Palette.pdf")),
  );


  //Modify The Height of track
  $form['track_text']['track_height'] = array(
    '#type' => 'textfield',
    '#title' => t('Height'),
    '#size' => 30,
    '#maxlength' => 20,
    '#description' => t('Modify Track Height'),
  );

  //Specify Link
  $form['track_text']['link'] = array(
    '#type' => 'textfield',
    '#title' => t('Link'),
    '#size' => 30,
    '#maxlength' => 64,
    '#description' => t('Specify to Further details (HTML address)'),
  );

  //Register job submit button
  $form['create_instance']['submit'] = array(
     '#type' => 'submit',
     '#value' => t('Add Track')
  );
  
  return $form;

}


/**
 * Validate User-submitted data for Register GBrowse Instances 
 *
 * This function validates the user input for each form element in the Register GBrowse 
 * instances form that is a text field. Validations checked include:
 *   - database_name: contains only word characters not including punctuation 
 *       or white-space ([A-Z][a-z][0-1]_)
 *
 * @param $form
 *   The form that the user submitted and whose input is being validated
 *
 * @param $form_state
 *   An array containing the state of the form being validated including user-input
 */
function tripal_gbrowse_add_tracks_form_validate ($form, $form_state) {
  
  if (!empty($form_state['values']['foreground_colour'])) {
    // foreground colour is present and a valid colour
    if ( !preg_match('/^[\w#]+$/', $form_state['values']['foreground_colour'])) {
      
      form_set_error('foreground_colour',
      'The Foreground Colour should be either the name of a colour listed in the linked to pdf or a valid hex colour');
    }
  }
  
  if (!empty($form_state['values']['backround_colour'])) {
    if(!preg_match('/^[\w#]+$/', $form_state['values']['backround_colour'])){
      form_set_error('backround_colour','The Background Colour should be either the name of a colour listed in the linked to pdf or a valid hex colour');
    }
  }
  
  if (!empty($form_state['values']['track_height'])){
    if(!preg_match('/^\d*$/', $form_state['values']['track_height'])){
      form_set_error('track_height','The Track Height must be a positive integer');
    }
  }
  
  if(!preg_match('/^\w+$/', $form_state['values']['identifier'])){

    form_set_error('identifier','The Identifier must be composed of the following characters only: [A-Z][a-z][0-9] and _');
  
  }
  
  if (!empty($form_state['values']['link'])){
    if(!preg_match('/^http:/', $form_state['values']['link'])){
      form_set_error('link','The Link must be a conventional web site name, beginging with  http: ');
    }
  }

} 


/**
*Add-GBrowse-Tracks Form_Submit
*
* @param $form
*    The form for the information that the user has entered
*
* @param $form_state 
*    This is the state of the form: i.e what button was pressed.The key is 
*    the name of the fields in database 
*
* @return
*   An '$form' that is an array of menu items that allows the user to Register a GBrowse instance
*/
function tripal_gbrowse_add_tracks_form_submit($form, $form_state) {

  

  $string = "\n[".$form_state['values']['identifier']."]\n"
    ."key = ".$form_state['values']['track_name']."\n";
    
  if($form_state['values']['library_id'] == 'none'){    
    $string .= "feature =  ".$form_state['values']['type_name']."\n";
  } else {
    $string .= "feature =  ".$form_state['values']['type_name'].":" .$form_state['values']['library_id']."\n";
  }
  
  if (!empty($form_state['values']['glyph'])) {
    $string .= "glyph = ".$form_state['values']['glyph']."\n";
  }
  
  if (!empty($form_state['values']['track_height'])) {
    $string .= "height = ".$form_state['values']['track_height']."\n";
  }
  
  if (!empty($form_state['values']['foreground_colour'])) {
    $string .= "bgcolor = ".$form_state['values']['foreground_colour']."\n";
  }
  
  if (!empty($form_state['values']['backround_colour'])) {
    $string .= "fgcolor = ".$form_state['values']['backround_colour']."\n";
  }
  
  if (!empty($form_state['values']['link'])) {
    $string .= "link = ".$form_state['values']['link']."\n";
  }
  
  $string .= "\n";
       
  $record = db_fetch_object(db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $form_state['values']['gbrowse_instances']));
  
  $config_file = $record->config_file;
  
  $command = "echo '".$string."' >> ".$config_file;
  
  exec($command);

}


//-----------------------------------------------------------------------------
//  SECTION: Delete Tracks Form & Form submit
//-----------------------------------------------------------------------------


/**
*Delete-GBrowse-Tracks
*    
*    This Form allows selection for a specific GBrowse Instance to be removed in a multi-submit form outline.
*    Once the GBrowse instance is selected,the corresponding track list that corresponds to 
*    the selected GBrowse instance is deleted. This can be done one track at a time. As
*    there is no limit to the number of tracks that can be added to a particular GBrowse instance and
*    thus all the tracks that have bee added can be deleted, one track at a time. The track that is to 
*    be deleted is to be selected from the list. When selected and the delete button is pushed, 
*    the track that was selected is removed from the 'configuration' file.
*
* @param $form_state
*    The state of the form as it is setting the default value of $form_state is NULL
*
* @return
*   An '$form' that is an array of menu items that allows the user to Register a GBrowse instance
*/
function tripal_gbrowse_delete_tracks_form(&$form_state=NULL) {

  //Creating Fieldset for multiple fields in form
  $form['delete_tracks_field_set'] = array(
    '#type' => ($form_state['storage']['gbrowse_id']) ? 'hidden' : 'fieldset',
    '#title' => t('GBrowse Specific Fields'),
  );
  
  //Sending query to the database for GBrowse Instances
  $resource = db_query('SELECT * FROM {tripal_gbrowse_instances}');

  $items = array();
  
  while($record = db_fetch_object($resource)){
      
    $items[$record->gbrowse_id]= $record->gbrowse_name;
    
  }

  //GBrowse Instance Select List
  $form['delete_tracks_field_set']['gbrowse_instances'] = array(
    '#type' => 'select',
    '#title' => t('Registered GBrowse Instances'),
    '#options' => $items,
    '#description' => t('Selected GBrowse Instances to be Loaded.'),
    '#default_value' => $form_state['values']['gbrowse_instances'],
  );
  
  //Set Instance Submit button
  $form['delete_tracks_field_set']['submit_instance'] = array(
    '#type' => 'submit',
    '#value' => t('Set Instance')
  );

  //Creating Fieldset for multiple fields in form
  $form['delete_tracks'] = array(
    '#type' => ($form_state['storage']['gbrowse_id']) ? 'fieldset' : 'hidden',
    '#title' => t('Track Specific Fields'),
  );
  
  
  $gbrowse_id = $form_state['storage']['gbrowse_id'];
  
  if ($gbrowse_id){
  
    $items = track_name_options($gbrowse_id);
  
  }else {
    
    $items = array();
  
  }
  
  //Track Name Select List
  $form['delete_tracks']['track_line_number'] = array(
    '#type' => 'select',
    '#title' => t('Track Name'),
    '#options' => $items,
    '#description' => t('Name of Track to Remove '),
    '#default_value' => $form_state['values']['gbrowse_id'],
  );

  //Remove Track button
  $form['delete_tracks']['remove_track'] = array(
    '#type' => 'submit',
    '#value' => t('Remove Track')
  );

  return $form;

}


/**
*Delete-GBrowse-Tracks
*
*@param $form
*    The form that is completed in the above section
*
*  @param $form_state
*    The state of the form, as it is completed by the user and will contain all of the user's
*    selected infromation that is to be removed from the configuration file.    
*
*/
function tripal_gbrowse_delete_tracks_form_submit($form, &$form_state) {

  $form_state['storage']['gbrowse_id'] = $form_state['values']['gbrowse_instances'];
  
  //Checking that the "Remove Track" button was selected      
  if($form_state['clicked_button']['#value']=='Remove Track'){
        
    //selecting GBrowse-ID from the database
    $resource= db_fetch_object(db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $form_state['storage']['gbrowse_id']));
    
    //putting contents of the configuration file into an variable
    $config_file = (string) $resource->config_file;
          
    $read_file_handle = fopen($config_file,'r') or drupal_set_message("WARNING: Can not open file:" .$config_file, 'error');

    $track_number = $form_state['values']['track_line_number'];
  
    $line_num = 0;
  
    //create temp file 
    $new_conf_file = '/tmp/temp_config_file.temp';
          
    //making '.temp' file in the /tmp directory
    $command = 'touch /tmp/temp_config_file.temp';
          
    exec($command);
          
    //Checking that the newly created file is writable    
    if (is_writable($new_conf_file)) {
          
      //opening file for writing to
      $write_file_handle = fopen($new_conf_file, 'w') or drupal_set_message("WARNING: Can not open file:" .$new_conf_file, 'error');
          
     }else{
           
       drupal_set_message("WARNING: Attempting to create a temporary file -insufficient permissions: ".$new_conf_file, 'error');                   
     }    

    while(!feof($read_file_handle)){
  
      $file_line = fgets($read_file_handle);
            
      $line_num++;
      
      if($line_num == $track_number){
                          
        $remove_track = TRUE;
                  
       }
       
       if(preg_match('/^\s*$/',$file_line)){
                            
         $remove_track=FALSE;
                  
       }
       
       if($remove_track==FALSE){
                  
         fwrite($write_file_handle, $file_line);              
                  
       }
                                    
    }
          
    $command = 'cp '.$new_conf_file.'  '.$config_file  ; 
          
    exec($command);
          
    $command = 'rm '.$new_conf_file ;
          
    exec($command);
        
  }
      
}


/**
*  Populate Track-Name List
*
* This section  takes a GBrowse ID so the coresponding configuration file can be accessed. Once it has been
* obtained from the database, by the db_query() command. The configuration file is is searched for lines
* that start with "[ ]". This corresponds to the framework of the conf file, as the Track Names are
* enclosed within "[ ]". The file is then scanned from the spots that contain the "[ ]".  
*
*
*  @param gbrowse_id
*        The Selected GBrowse instance's identification
*
* @return
*    $items() and array with the tracks that are in the selected GBrowse instance.
*/
function track_name_options($gbrowse_id) {

  $items = array();

  // Use GBrowse ID to get configuration filename  
  $record = db_fetch_object(db_query('SELECT * FROM {tripal_gbrowse_instances} WHERE gbrowse_id=%d', $gbrowse_id));

  //putting contents of the configuration file into an variable
  $config_file = (string) $record->config_file;

  $config_array = array();
  
  //command to select the lines that begin with '[' and have characters within the '[ ]'
  $command = 'grep -n "^\[.*\]" ' .$config_file;
    
  //execution of the command
  exec($command , $config_array);
  
  $config_array_size = count($config_array);
        
  //while the end-of-file has not been reached
  for($i = 0 ; $i < $config_array_size; $i++){
    
    $file_line = $config_array[$i];      
          
        if ($is_track_definition){
        
            if(preg_match('/^(\d+):\[(.+)\]$/', $file_line, $matches)){
  
              $items[$matches[1]] = $matches[2];
              
            }
        
    }
        
        if(preg_match('/\[TRACK DEFAULTS\]/', $file_line)){
            
            $is_track_definition = TRUE;
        }
        
  }
  
  return $items;
}


//-----------------------------------------------------------------------------
//  END OF SOFTWARE
//-----------------------------------------------------------------------------