tripal/modules/base/tripal_bulk_loader/tripal_bulk_loader.module

<?php

include('tripal_bulk_loader.loader.inc');

/**
 * Implements hook_init
 * Used to add stylesheets and javascript files to the header
 */
function tripal_bulk_loader_init(){
	// Add javascript and style sheet
	drupal_add_css(drupal_get_path('theme', 'tripal').'/css/tripal_bulk_loader.css');
	drupal_add_js(drupal_get_path('theme', 'tripal').'/js/tripal_bulk_loader.js');
}

/**
 * Implements hook_menu
 */
function tripal_bulk_loader_menu() {
  $items = array();
   // Show all loaders
   $items['tripal_bulk_loaders'] = array(
     'title' => 'Tripal Bulk Loaders',
     'description' => 'Tripal bulk loaders for loading tab-delimited file into chado database',
     'page callback' => 'tripal_bulk_loader_list',
     'access arguments' => array('access tripal_bulk_loader'),
     'type' => MENU_NORMAL_ITEM,
   );
   // Admin page to create the template
   $items['admin/tripal/tripal_bulk_loader_template'] = array(
      'title' => 'Bulk Loader Template',
      'description' => 'Templates for loading tab-delimited data',
    	'page callback' => 'tripal_bulk_loader_admin_template',
      'access arguments' => array('administer site configuration'),
      'type' => MENU_NORMAL_ITEM,   
		  'file' => 'tripal_bulk_loader.admin.inc',
	);
	// Create/Edit Template -------
  $items['admin/tripal/tripal_bulk_loader_template/create'] = array(
      'title' => 'Create Bulk Loader Template',
      'description' => 'Create loader template for loading tab-delimited data',
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_bulk_loader_modify_template_base_form', 'create'),
      'access arguments' => array('administer site configuration'),
      'type' => MENU_NORMAL_ITEM,   
		'file' => 'tripal_bulk_loader.admin.inc',
  );
  $items['admin/tripal/tripal_bulk_loader_template/edit'] = array(
      'title' => 'Edit Bulk Loader Template',
      'description' => 'Edit loader template for loading tab-delimited data',
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_bulk_loader_modify_template_base_form', 'edit'),
      'access arguments' => array('administer site configuration'),
      'type' => MENU_NORMAL_ITEM,   
		  'file' => 'tripal_bulk_loader.admin.inc',  
  );
	$items['admin/tripal/tripal_bulk_loader_template/edit_record'] = array(
      'title' => 'Edit Template Record',
      'description' => 'Edit a record in an existing tripal bulk loader template.',
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_bulk_loader_edit_template_record_form'),
      'access arguments' => array('administer site configuration'),
      'type' => MENU_CALLBACK,   
		'file' => 'tripal_bulk_loader.admin.inc',
	);
	$items['admin/tripal/tripal_bulk_loader_template/add_field'] = array(
      'title' => 'Add Template Field',
      'description' => 'Add a template field to an existing tripal bulk loader template.',
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_bulk_loader_add_template_field_form'),
      'access arguments' => array('administer site configuration'),
      'type' => MENU_CALLBACK,   
		'file' => 'tripal_bulk_loader.admin.inc',
	);
	$items['admin/tripal/tripal_bulk_loader_template/edit_field'] = array(
      'title' => 'Edit Template Field',
      'description' => 'Edit an existing field from a tripal bulk loader template.',
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_bulk_loader_edit_template_field_form'),
      'access arguments' => array('administer site configuration'),
      'type' => MENU_CALLBACK,   
		'file' => 'tripal_bulk_loader.admin.inc',
	);
	// Delete Template -----
	$items['admin/tripal/tripal_bulk_loader_template/delete'] = array(
      'title' => 'Delete Bulk Loader Template',
      'description' => 'Delete bulk loader template',
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_bulk_loader_delete_template_base_form'),
      'access arguments' => array('administer site configuration'),
      'type' => MENU_NORMAL_ITEM,   
		'file' => 'tripal_bulk_loader.admin.inc',
	);
	// Import/Export ---------
  $items['admin/tripal/tripal_bulk_loader_template/import'] = array(
      'title' => 'Import Bulk Loader Template',
      'description' => 'Import Loaders',
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_bulk_loader_import_export_template_form', 'import'),
      'access arguments' => array('administer site configuration'),
      'type' => MENU_NORMAL_ITEM,   
		  'file' => 'tripal_bulk_loader.admin.inc',  
  );	
  $items['admin/tripal/tripal_bulk_loader_template/export'] = array(
      'title' => 'Export Bulk Loader Template',
      'description' => 'Export Loaders',
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_bulk_loader_import_export_template_form', 'export'),
      'access arguments' => array('administer site configuration'),
      'type' => MENU_NORMAL_ITEM,   
		  'file' => 'tripal_bulk_loader.admin.inc',  
  );	
	// AHAH ---------
	$items['admin/tripal/tripal_bulk_loader_template/add_field_ahah'] = array(
      'page callback' => 'tripal_bulk_loader_add_field_ahah',
      'access arguments' => array('administer site configuration'),
      'type' => MENU_CALLBACK,   
		  'file' => 'tripal_bulk_loader.admin.inc',	
	);
	$items['admin/tripal/tripal_bulk_loader_template/edit_field_ahah'] = array(
      'page callback' => 'tripal_bulk_loader_edit_field_ahah',
      'access arguments' => array('administer site configuration'),
      'type' => MENU_CALLBACK,   
		  'file' => 'tripal_bulk_loader.admin.inc',	
	);
	
  return $items;
}

/**
 * Implements hook_theme
 */
function tripal_bulk_loader_theme() {
  return array(
    'tripal_bulk_loader_template' => array(
    	'arguments'=> array('template_id' => NULL),
    	'template' => 'tripal_bulk_loader_template'
    ),
    'tripal_bulk_loader_modify_template_base_form' => array(
    	'arguments' => array('form' => NULL),
    	'template' => 'tripal_bulk_loader_modify_template_base_form',
    ),
    'tripal_bulk_loader_edit_template_field_form' => array(
      'arguments' => array('form' => NULL),
      'template' => 'tripal_bulk_loader_edit_template_field_form',
    ),
    'tripal_bulk_loader_add_template_field_form' => array(
      'arguments' => array('form' => NULL),
      'template' => 'tripal_bulk_loader_add_template_field_form',
    ),
  );
}

/**
 *  Implements hook_access
 */
function tripal_bulk_loader_access($op, $node, $account){
	if ($op == 'create') {
		if(!user_access('create tripal_bulk_loader', $account)){
         return FALSE;
      }
	}
	if ($op == 'update') {
		if (!user_access('edit tripal_bulk_loader', $account)) {
			return FALSE;
		}
	}
	if ($op == 'delete') {
		if (!user_access('delete tripal_bulk_loader', $account)) {
			return FALSE;
		}
	}
	if ($op == 'view') {
		if (!user_access('access tripal_bulk_loader', $account)) {
			return FALSE;
		}
	}
	return NULL;
}

/**
 * Implements hook_perm
 */
function tripal_bulk_loader_perm(){
	return array(
      'access tripal_bulk_loader',
      'create tripal_bulk_loader',
      'delete tripal_bulk_loader',
      'edit tripal_bulk_loader',
	);
}

/**
 * Creates a listing page for all bulk loading jobs
 */
function tripal_bulk_loader_list () {
  $num_results_per_page = 50;
  $output = '';
  
  $header = array('','Status','Loader','File');
  $rows = array();
  
  $query = 'SELECT * FROM {tripal_bulk_loader} l '
    .'LEFT JOIN {node} n ON n.nid = l.nid '
    .'LEFT JOIN {tripal_bulk_loader_template} t ON t.template_id = cast(l.template_id as integer)';
  $resource = pager_query($query, $num_results_per_page, 0, NULL);
  while ($r = db_fetch_object($resource)) {
    $row = array(
      l($r->title, 'node/'.$r->nid),
      $r->job_status,
      $r->name,
      $r->file
    );
    $rows[] = $row;
  }
  
  $output .= theme('table', $header, $rows);
  return $output;
  
}

//////////////////////////////////////////////////////////////////////////////////////////////
// Node Functions
//////////////////////////////////////////////////////////////////////////////////////////////

/**
 * Implements hook_node_info
 */
function tripal_bulk_loader_node_info() {
	$nodes = array();
	$nodes['tripal_bulk_loader'] = array(
      'name' => t('Bulk Loading Job'),
      'module' => 'tripal_bulk_loader',
      'description' => t('A bulk loader for inserting tab-delimited data into chado database'),
      'has_title' => TRUE,
      'has_body' => FALSE,
      'locked' => TRUE
	);
	return $nodes;
}

/**
 * Implements node_form
 * Used to gather the extra details stored with a Bulk Loading Job Node
 */
function tripal_bulk_loader_form ($node){
   $form = array();
   $sql = "SELECT * FROM {tripal_bulk_loader_template}";
   $results = db_query($sql);
   $templates = array ();
   while ($template = db_fetch_object ($results)) {
   	$templates [$template->template_id] = $template->name;
   }
   
   if (!$templates) {
   	$form['label'] = array(
   	'#type' => 'item',
      '#description' => t("Loader template needs to be created before any bulk loader can be added. Go to 'Tripal Management > Bulk Loader Template' to create the template."),
      '#weight'        => -10,
		);
		
		return $form;
   }
   
   $form['loader_name'] = array(
   	'#type'          => 'textfield',
      '#title'         => t('Loading Job Name'),
      '#weight'        => -10,
      '#required'      => TRUE,
   	'#default_value' => $node->loader_name
   );
   
   $form['template_id'] = array(
      '#type' => 'select',
      '#title' => t('Template'),
   	'#description'   => t('Please specify a template for this loader'),
    	'#options'       => $templates,
   	'#weight'        => -9,
      '#required'      => TRUE,
   	'#default_value' => $node->template_id
   );
   
   $form['file']= array(
      '#type'          => 'textfield',
      '#title'         => t('Data File'),
      '#description'   => t('Please specify the data file to be loaded.'),
      '#weight'        => -8,
   	'#default_value' => $node->file
   );
   
   $form['has_header'] = array(
    '#type' => 'radios',
    '#title' => 'File has a Header',
    '#options' => array( 1 => 'Yes', 2 => 'No'),
    '#weight' => -7,
    '#default_value' => $node->file_has_header,
   );

   return $form;
}

/**
 * Implements node_load
 */
function tripal_bulk_loader_load($node){
	$sql = "SELECT * FROM {tripal_bulk_loader} WHERE nid = %d";
	$node = db_fetch_object(db_query($sql, $node->nid));

	$node->title = 'Bulk Loading Job: '.$node->loader_name;
	
	// Add the loader template
	$sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
	$results = db_fetch_object(db_query($sql, $node->template_id));
	$template = unserialize($results->template_array);
	$node->template = $results;
	$node->template->template_array = $template;

  // Add inserted records
  $sql = 'SELECT * FROM {tripal_bulk_loader_inserted} WHERE nid=%d';
  $resource = db_query($sql,$node->nid);
  while ($r = db_fetch_object($resource)) {
    $r->num_inserted = sizeof(preg_split('/,/',$r->ids_inserted)); 
    $node->inserted_records->{$r->table_inserted_into} = $r;
  }
  
	return $node;
}

/**
 * Implements node_insert
 * Insert the data from the node form on Create content
 */
function tripal_bulk_loader_insert ($node) {
  
	$sql = "INSERT INTO {tripal_bulk_loader} (nid, loader_name, template_id, file, file_has_header, job_status) VALUES (%d, '%s', %d, '%s', %d, '%s')";
	db_query($sql, $node->nid, $node->loader_name, $node->template_id, $node->file, $node->has_header, 'Initialized');
	$node->title =$node->loader_name;
	drupal_write_record('node',$node,'nid');
	drupal_write_record('node_revision',$node,'nid');	
	
	drupal_set_message('After reviewing the details, please Submit this Job (by clicking the "Submit Job" button below). No data will be loaded until the submitted job is reached in the queue.');

}

/**
 * Implements node_delete
 * Deletes the data when the delete button on the node form is clicked
 */
function tripal_bulk_loader_delete ($node) {
	$sql = "DELETE FROM {tripal_bulk_loader} WHERE nid = %d";
	db_query($sql, $node->nid);
}

/**
 * Implements node_update
 * Updates the data submitted by the node form on edit
 */
function tripal_bulk_loader_update ($node) {
	$sql = "UPDATE {tripal_bulk_loader} SET nid = %d, loader_name = '%s', template_id = %d, file = '%s', file_has_header = '%s' WHERE nid = %d";
	db_query($sql, $node->nid, $node->loader_name, $node->template_id, $node->file, $node->has_header, $node->nid);
	// Add a job if the user want to load the data
	global $user;
	if($node->job) {
		$job_args[0] =$node->loader_name;
		$job_args[1] = $node->template_id;
		$job_args[2] = $node->file;
		if (is_readable($node->file)) {
			$fname = preg_replace("/.*\/(.*)/", "$1", $node->file);
			tripal_add_job("Bulk Load: $fname",'tripal_bulk_loader', 'tripal_bulk_loader_load_data', $job_args, $user->uid);
		} else {
			drupal_set_message("Can not open $node->file. Job not scheduled.");
		}
	}
}

/**
 * Preprocessor function for the tripal_bulk_loader template
 */
function tripal_bulk_loader_preprocess_tripal_bulk_loader_template (&$variables) {

	$sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
	$template = db_fetch_object(db_query($sql, $variables['template_id']));
	$template->template_array = unserialize($template->template_array);	
	$variables['template'] = $template;
	
}

/**
 * Implements hook_job_describe_args()
 * Specifically to make viewing past tripal jobs more readable for jobs registered by this module
 *
 * @params $callback
 *   The callback passed into tripal_add_job()
 * @param $args
 *   The arguements passed into tripal_add_job()
 * @return 
 *   An array where keys are the human readable headers describing each arguement 
 *   and the value is the aguement passed in after formatting
 */
function tripal_bulk_loader_job_describe_args($callback,$args){

  $new_args = array();
  if($callback == 'tripal_bulk_loader_load_data'){
    //1st arg is the nid for a bulk loader node
    $node = node_load($args[0]);
    $new_args['Bulk Loading Job'] = l($node->title, 'node/'.$args[0]);
    return $new_args;
  }
  
}