tripal/tripal_bulk_loader/tripal_bulk_loader.module.orig

<?php

include('tripal_bulk_loader.loader.inc');
include('tripal_bulk_loader.constants.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,
   );
   // Bulk Loading Job Node
   $items['node/%node/constants/%/edit'] = array(
      'title' => 'Edit Constant Set',
      'description' => 'Edit a group of constants associated with the current bulk loader',
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_bulk_loader_edit_constant_set_form', 1, 3),
      'access arguments' => array('administer site configuration'),
      'type' => MENU_CALLBACK,
<<<<<<< HEAD
      'file' => 'tripal_bulk_loader.constants.inc',
=======
		  'file' => 'tripal_bulk_loader.constants.inc',
>>>>>>> 6.x-0.4-dev
   );
   $items['node/%node/constants/%/delete'] = array(
      'title' => 'Delete Constant Set',
      'description' => 'Delete a group of constants associated with the current bulk loader',
      'page callback' => 'drupal_get_form',
      'page arguments' => array('tripal_bulk_loader_delete_constant_set_form', 1, 3),
      'access arguments' => array('administer site configuration'),
      'type' => MENU_CALLBACK,
<<<<<<< HEAD
      'file' => 'tripal_bulk_loader.constants.inc',
=======
		  'file' => 'tripal_bulk_loader.constants.inc',
>>>>>>> 6.x-0.4-dev
   );

   // 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,
<<<<<<< HEAD
      'file' => 'tripal_bulk_loader.admin.inc',
  );
  // Create/Edit Template -------
=======
		  'file' => 'tripal_bulk_loader.admin.inc',
	);
   $items['admin/tripal/tripal_bulk_loader_template/configure'] = array(
      'title' => 'Configuration',
      'description' => 'Configure the Tripal Bulk Loader Module',
    	'page callback' => 'drupal_get_form',
    	'page arguments' => array('tripal_bulk_loader_configuration_form'),
      'access arguments' => array('administer site configuration'),
      'type' => MENU_NORMAL_ITEM,
		  'file' => 'tripal_bulk_loader.admin.inc',
	);

	// Create/Edit Template -------
>>>>>>> 6.x-0.4-dev
  $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,
<<<<<<< HEAD
    'file' => 'tripal_bulk_loader.admin.inc',
=======
		'file' => 'tripal_bulk_loader.admin.inc',
>>>>>>> 6.x-0.4-dev
  );
  $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,
<<<<<<< HEAD
      'file' => 'tripal_bulk_loader.admin.inc',
=======
		  'file' => 'tripal_bulk_loader.admin.inc',
>>>>>>> 6.x-0.4-dev
  );
  $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,
<<<<<<< HEAD
    'file' => 'tripal_bulk_loader.admin.inc',
  );
  $items['admin/tripal/tripal_bulk_loader_template/add_field'] = array(
=======
		'file' => 'tripal_bulk_loader.admin.inc',
	);
	$items['admin/tripal/tripal_bulk_loader_template/add_field'] = array(
>>>>>>> 6.x-0.4-dev
      '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,
<<<<<<< HEAD
    'file' => 'tripal_bulk_loader.admin.inc',
  );
  $items['admin/tripal/tripal_bulk_loader_template/edit_field'] = array(
=======
		'file' => 'tripal_bulk_loader.admin.inc',
	);
	$items['admin/tripal/tripal_bulk_loader_template/edit_field'] = array(
>>>>>>> 6.x-0.4-dev
      '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,
<<<<<<< HEAD
    'file' => 'tripal_bulk_loader.admin.inc',
  );
  // Delete Template -----
  $items['admin/tripal/tripal_bulk_loader_template/delete'] = array(
=======
		'file' => 'tripal_bulk_loader.admin.inc',
	);
	// Delete Template -----
	$items['admin/tripal/tripal_bulk_loader_template/delete'] = array(
>>>>>>> 6.x-0.4-dev
      '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,
<<<<<<< HEAD
    'file' => 'tripal_bulk_loader.admin.inc',
  );
  // Import/Export ---------
=======
		'file' => 'tripal_bulk_loader.admin.inc',
	);
	// Import/Export ---------
>>>>>>> 6.x-0.4-dev
  $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,
<<<<<<< HEAD
      'file' => 'tripal_bulk_loader.admin.inc',
=======
		  'file' => 'tripal_bulk_loader.admin.inc',
>>>>>>> 6.x-0.4-dev
  );
  $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,
<<<<<<< HEAD
      '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',
  );
=======
		  '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',
	);
>>>>>>> 6.x-0.4-dev

  return $items;
}


/**
 * Implements hook_theme
 */
function tripal_bulk_loader_theme() {
  return array(
    'tripal_bulk_loader_set_constants_form' => array(
      'arguments' => array('form' => NULL),
    ),
    '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 = '';

<<<<<<< HEAD
  $header = array('', 'Status', 'Loader', 'File');
=======
  $header = array('','Status','Loader','File');
>>>>>>> 6.x-0.4-dev
  $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_state) {
  $form = array();

  if (isset($form_state['values'])) {
    $node = $form_state['values'] + (array)$node;
    $node = (object) $node;
  }

  $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'] = array(
    '#type' => 'fieldset',
    '#title' => t('Basic Details'),
  );

  $form['loader']['loader_name'] = array(
    '#type'          => 'textfield',
    '#title'         => t('Loading Job Name'),
    '#weight'        => -10,
    '#required'      => TRUE,
    '#default_value' => $node->loader_name
  );

  $form['loader']['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['loader']['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['loader']['has_header'] = array(
    '#type' => 'radios',
    '#title' => t('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));

<<<<<<< HEAD
  $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;
=======
	$node->title = 'Bulk Loading Job: '.$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;
>>>>>>> 6.x-0.4-dev

  // 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)) {
<<<<<<< HEAD
    $r->num_inserted = sizeof(preg_split('/,/', $r->ids_inserted));
=======
    $r->num_inserted = sizeof(preg_split('/,/',$r->ids_inserted));
>>>>>>> 6.x-0.4-dev
    $node->inserted_records->{$r->table_inserted_into} = $r;
  }

  // Add exposed field list
  $node->exposed_fields = array();
  if ($template) {
    foreach ($template as $record_id => $record) {
      foreach ($record['fields'] as $field_id => $field) {
        if ($field['exposed']) {
          $node->exposed_fields[] = array(
            'record_id' => $record_id,
            'field_id' => $field_id,
            'title' => $field['title'],
          );
        }
      }
    }

    if (empty($node->exposed_fields)) {
      $node->exposed_fields[] = array();
    }
  }


  // Add constants
  $sql = 'SELECT * FROM {tripal_bulk_loader_constants} WHERE nid=%d ORDER BY group_id, record_id, field_id';
  $resource = db_query($sql, $node->nid);
  while ($r = db_fetch_object($resource)) {
    $node->constants[$r->group_id][$r->record_id][$r->field_id] = array(
      'constant_id' => $r->constant_id,
      'group_id' => $r->group_id,
<<<<<<< HEAD
      'chado_table' => $r->chado_table,
      'chado_field' => $r->chado_field,
      'record_id' => $r->record_id,
      'field_id' => $r->field_id,
      'value' => $r->value
=======
      'chado_table'=>$r->chado_table,
      'chado_field'=>$r->chado_field,
      'record_id'=>$r->record_id,
      'field_id'=>$r->field_id,
      'value'=>$r->value
>>>>>>> 6.x-0.4-dev
    );
  }
  if (!$node->constants) {
    $node->constants[] = array();
  }

<<<<<<< HEAD
  return $node;
=======
	return $node;
>>>>>>> 6.x-0.4-dev
}

/**
 * Implements node_insert
 * Insert the data from the node form on Create content
 */
<<<<<<< HEAD
function tripal_bulk_loader_insert($node) {
=======
function tripal_bulk_loader_insert ($node) {
>>>>>>> 6.x-0.4-dev

  // Insert into tripal_bulk_loader
  $sql = "INSERT INTO {tripal_bulk_loader} (nid, loader_name, template_id, file, file_has_header, job_status) VALUES (%d, '%s', %d, '%s', %d, '%s')";
  db_query($sql, $node->nid, $node->loader_name, $node->template_id, $node->file, $node->has_header, 'Initialized');

<<<<<<< HEAD
  // Update title
  $node->title =$node->loader_name;
  drupal_write_record('node', $node, 'nid');
  drupal_write_record('node_revision', $node, 'nid');
=======
	// Update title
	$node->title =$node->loader_name;
	drupal_write_record('node',$node,'nid');
	drupal_write_record('node_revision',$node,'nid');
>>>>>>> 6.x-0.4-dev

  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
 */
<<<<<<< HEAD
function tripal_bulk_loader_update($node) {

  // Update tripal_bulk_loader
  $sql = "UPDATE {tripal_bulk_loader} SET nid = %d, loader_name = '%s', template_id = %d, file = '%s', file_has_header = '%s' WHERE nid = %d";
  db_query($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(t("Can not open %file. Job not scheduled.", array('%file' => $node->file)));
    }
  }
=======
function tripal_bulk_loader_update ($node) {

  // Update tripal_bulk_loader
	$sql = "UPDATE {tripal_bulk_loader} SET nid = %d, loader_name = '%s', template_id = %d, file = '%s', file_has_header = '%s' WHERE nid = %d";
	db_query($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.");
		}
	}
>>>>>>> 6.x-0.4-dev

}

///////////////////////////////////////////////////////////

/**
 * 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;

<<<<<<< HEAD
=======
	$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;

>>>>>>> 6.x-0.4-dev
}

/**
 * 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;
  }

}