tripal/tripal_bulk_loader/tripal_bulk_loader.module

<?php

/**
 * @file
 * The functions for the Tripal bulk loader.
 *
 * @defgroup tripal_bulk_loader Tripal Bulk Loader Module
 * @ingroup tripal_modules
 */
include('includes/tripal_bulk_loader.loader.inc');
include('includes/tripal_bulk_loader.constants.inc');

// Administration
include('includes/tripal_bulk_loader.admin.inc');
include('includes/tripal_bulk_loader.admin.templates.inc');

// API
include('api/tripal_bulk_loader.api.templates.inc');

/**
 * Implements hook_init
 * Used to add stylesheets and javascript files to the header
 *
 * @ingroup tripal_bulk_loader
 */
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
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_menu() {
  $items = array();
  // 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 tripal_bulk_loader'),
    'type' => MENU_CALLBACK,
  );
  $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 tripal_bulk_loader'),
    'type' => MENU_CALLBACK,
  );

  // Admin pages -----------------
  $items['admin/tripal/loaders/bulk'] = array(
    'title' => 'Bulk Loader',
    'description' => 'Templates for loading tab-delimited data',
    'page callback' => 'tripal_bulk_loader_admin_jobs_listing',
    'access arguments' => array('administer tripal_bulk_loader'),
    'type' => MENU_NORMAL_ITEM,
  );
  $items['admin/tripal/loaders/bulk/configure'] = array(
    'title' => 'Configure',
    'description' => 'Configuration of global options related to bulk loading jobs',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_bulk_loader_configuration_form'),
    'access arguments' => array('administer tripal_bulk_loader'),
    'weight' => 8,
    'type' => MENU_LOCAL_TASK,
  );
  $items['admin/tripal/loaders/bulk/help'] = array(
    'title' => 'Help',
    'description' => "A description of the Tripal Bulk Loader module including a short description of it's usage.",
    'page callback' => 'tripal_bulk_loader_admin_manage_templates',
    'access arguments' => array('administer tripal_bulk_loader'),
    'weight' => 10,
    'type' => MENU_LOCAL_TASK,
  );

  // Enable View Callbacks
  $items['admin/tripal/loaders/bulk/views/jobs/enable'] = array(
    'title' => 'Enable Jobs Administrative View',
    'description' => 'Enable Jobs Administrative View',
    'page callback' => 'tripal_bulk_loader_admin_enable_view',
    'page arguments' => array('tripal_bulk_loading_jobs'),
    'access arguments' => array('administer tripal_bulk_loader'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/loaders/bulk/views/templates/enable'] = array(
    'title' => 'Enable Templates Administrative View',
    'description' => 'Enable Templates Administrative View',
    'page callback' => 'tripal_bulk_loader_admin_enable_view',
    'page arguments' => array('tripal_bulk_loader_templates'),
    'access arguments' => array('administer tripal_bulk_loader'),
    'type' => MENU_CALLBACK,
  );

  // Create/Edit Template --------
  $items['admin/tripal/loaders/bulk/template/create'] = array(
    'title' => 'Create 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 tripal_bulk_loader'),
    'weight' => -8,
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/loaders/bulk/template/%tblid/edit'] = array(
    'title' => 'Edit 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',5),
    'access arguments' => array('administer tripal_bulk_loader'),
    'type' => MENU_CALLBACK,
  );
  /**
  $items['admin/tripal/loaders/bulk/template/edit'] = array(
    'title' => 'Edit 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',FALSE),
    'access arguments' => array('administer tripal_bulk_loader'),
    'weight' => -6,
    'type' => MENU_CALLBACK,
  );
  */

  // Add/Edit Record -----
  $items['admin/tripal/loaders/bulk/template/%tblid/add_record'] = 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_template_field_form','create_record',5,FALSE),
    'access arguments' => array('administer tripal_bulk_loader'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/loaders/bulk/template/%tblid/edit_record/%tblid'] = 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',5,7),
    'access arguments' => array('administer tripal_bulk_loader'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/loaders/bulk/template/%tblid/delete_record/%tblid'] = array(
    'title' => 'Delete Template Record',
    'description' => 'Delete a record in an existing tripal bulk loader template.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_bulk_loader_delete_template_record_form',5,7),
    'access arguments' => array('administer tripal_bulk_loader'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/loaders/bulk/template/%tblid/duplicate_record/%tblid'] = array(
    'title' => 'Duplicate Template Record',
    'description' => 'Duplicate a record in an existing tripal bulk loader template.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_bulk_loader_duplicate_template_record_form',5,7),
    'access arguments' => array('administer tripal_bulk_loader'),
    'type' => MENU_CALLBACK,
  );

  // Add/Edit Field ------
  $items['admin/tripal/loaders/bulk/template/%tblid/add_field/%tblid'] = 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_template_field_form','create',5,7),
    'access arguments' => array('administer tripal_bulk_loader'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/loaders/bulk/template/%tblid/edit_field/%tblid/%tblid'] = 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_template_field_form','edit',5,7,8),
    'access arguments' => array('administer tripal_bulk_loader'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/loaders/bulk/template/%tblid/delete_field/%tblid/%tblid'] = array(
    'title' => 'Delete Template Field',
    'description' => 'Delete an existing field from a tripal bulk loader template.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_bulk_loader_delete_template_field_form',5,7,8),
    'access arguments' => array('administer tripal_bulk_loader'),
    'type' => MENU_CALLBACK,
  );

  // Delete Template -----
  $items['admin/tripal/loaders/bulk/template/%tblid/delete'] = array(
    'title' => 'Delete Template',
    'description' => 'Delete bulk loader template',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_bulk_loader_delete_template_base_form',5),
    'access arguments' => array('administer tripal_bulk_loader'),
    'weight' => -4,
    'type' => MENU_CALLBACK,
  );
  // Import/Export ---------
  $items['admin/tripal/loaders/bulk/templates/import'] = array(
    'title' => 'Import Template',
    'description' => 'Import Loaders',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_bulk_loader_import_template_form'),
    'access arguments' => array('administer tripal_bulk_loader'),
    'weight' => 2,
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/loaders/bulk/template/%tblid/export'] = array(
    'title' => 'Export Template',
    'description' => 'Export Loaders',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_bulk_loader_export_template_form', 5),
    'access arguments' => array('administer tripal_bulk_loader'),
    'weight' => 4,
    'type' => MENU_CALLBACK,
  );

  return $items;
}

function tblid_to_arg($arg, $map, $index) {
  if (preg_match('/^\d+$/', $arg)) {
    return $arg;
  }
}

/**
 * Implements hook_views_api()
 *
 * Purpose: Essentially this hook tells drupal that there is views support for
 *  for this module which then includes tripal_views.views.inc where all the
 *  views integration code is
 *
 * @ingroup tripal_views
 */
function tripal_bulk_loader_views_api() {
  return array(
    'api' => 3.0,
  );
}

/**
 * Implements hook_theme
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_theme() {
  return array(
    'node__tripal_bulk_loader' => array(
      'template' => 'node--tripal-bulk-loader',
      'path' => drupal_get_path('module', 'tripal_bulk_loader') . '/theme',
      'render element' => 'node',
      'base hook' => 'node',
    ),
    'tripal_bulk_loader_template' => array(
      'variables' => array('template_id' => NULL),
      'template' => 'tripal_bulk_loader_template',
      'path' => drupal_get_path('module', 'tripal_bulk_loader') . '/theme',
    ),
    'tripal_bulk_loader_modify_template_base_form' => array(
      'template' => 'tripal_bulk_loader_modify_template_base_form',
      'path' => drupal_get_path('module', 'tripal_bulk_loader') . '/theme',
      'render element' => 'form'
    ),
    'tripal_bulk_loader_field_regex_fieldset' => array(
      'file' => 'theme/tripal_bulk_loader.theme.inc',
      'function' => 'tripal_bulk_loader_field_regex_fieldset',
      'render element' => 'element'
    ),
    'tripal_bulk_loader_admin' => array(
      'template' => 'tripal_bulk_loader_admin',
      'path' => drupal_get_path('module', 'tripal_bulk_loader') . '/theme',
    ),
  );
}

/**
 * Implement hook_access().
 *
 * This hook allows node modules to limit access to the node types they define.
 *
 *  @param $op
 *  The operation to be performed
 *
 *  @param $node
 *  The node on which the operation is to be performed, or, if it does not yet exist, the
 *  type of node to be created
 *
 *  @param $account
 *  A user object representing the user for whom the operation is to be performed
 *
 *  @return
 *  If the permission for the specified operation is not set then return FALSE. If the
 *  permission is set then return NULL as this allows other modules to disable
 *  access.  The only exception is when the $op == 'create'.  We will always
 *  return TRUE if the permission is set.
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_node_access($node, $op, $account) {
  if ($op == 'create') {
    if (!user_access('create tripal_bulk_loader', $account)) {
      return NODE_ACCESS_DENY;
    }
    return NODE_ACCESS_ALLOW;
  }
  if ($op == 'update') {
    if (!user_access('edit tripal_bulk_loader', $account)) {
      return NODE_ACCESS_DENY;
    }
    return NODE_ACCESS_ALLOW;
  }
  if ($op == 'delete') {
    if (!user_access('delete tripal_bulk_loader', $account)) {
      return NODE_ACCESS_DENY;
    }
    return NODE_ACCESS_ALLOW;
  }
  if ($op == 'view') {
    if (!user_access('access tripal_bulk_loader', $account)) {
      return NODE_ACCESS_DENY;
    }
    return NODE_ACCESS_ALLOW;
  }
  return NODE_ACCESS_IGNORE;
}

/**
 * Implements hook_perm
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_permission() {
  return array(
      'access tripal_bulk_loader' => array(
        'title' => t('View Tripal Bulk Loading Jobs'),
        'description' => t('Permission to view Tripal Bulk Loader Nodes')
      ),
      'create tripal_bulk_loader' => array(
        'title' => t('Create Tripal Bulk Loading Jobs'),
        'description' => t('Permission to create Tripal Bulk Loader Nodes')
      ),
      'edit tripal_bulk_loader' => array(
        'title' => t('Edit Tripal Bulk Loading Jobs'),
        'description' => t('Permission to edit Tripal Bulk Loader Nodes')
      ),
      'delete tripal_bulk_loader' => array(
        'title' => t('Delete Tripal Bulk Loading Jobs'),
        'description' => t('Permission to delete Tripal Bulk Loader Nodes')
      ),
      'administer tripal_bulk_loader' => array(
        'title' => t('Administrate Tripal Bulk Loader'),
        'description' => t('Permission to administrate the Tripal Bulk Loader including template management.')
      ),
  );
}

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

/**
 * Implements hook_node_info
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_node_info() {
  $nodes = array();
  $nodes['tripal_bulk_loader'] = array(
      'name' => t('Bulk Loading Job'),
      'base' => '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
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_form($node, $form_state) {
  $form = array();

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

  $results = db_select('tripal_bulk_loader_template', 't')
              ->fields('t', array('template_id','name'))
              ->execute();
  $templates = array();
  foreach ($results as $template) {
    $templates [$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'),
  );

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

  $form['loader']['template_id'] = array(
    '#type' => 'select',
    '#title' => t('Template'),
    '#description'   => t('Please specify a template for this loader'),
    '#options'       => $templates,
    '#weight'        => -9,
    '#required'      => TRUE,
    '#default_value' => (isset($node->template_id)) ? $node->template_id : current($templates),
  );

  $form['loader']['file']= array(
    '#type'          => 'textfield',
    '#title'         => t('Data File'),
    '#description'   => t('Please specify the data file to be loaded. This must be a tab-delimited text file with UNIX line endings.'),
    '#weight'        => -8,
    '#default_value' => (isset($node->file)) ? $node->file : '',
    '#maxlength'     => 1024,
  );

  $form['loader']['has_header'] = array(
    '#type' => 'radios',
    '#title' => t('File has a Header'),
    '#options' => array( 1 => 'Yes', 2 => 'No'),
    '#weight' => -7,
    '#default_value' => (isset($node->file_has_header)) ? $node->file_has_header : 1,
  );

  $form['loader']['keep_track_inserted'] = array(
    '#type' => 'radios',
    '#title' => t('Keep track of inserted record IDs'),
    '#description' => t('This enables the ability to revert an entire loading job even if '
      .'it completed successfully. Furthermore, it displays the number of records '
      .'successfully inserted into each table.'),
    '#options' => array( 1 => 'Yes', 0 => 'No'),
    '#weight' => -7,
    '#default_value' => (isset($node->keep_track_inserted)) ? $node->keep_track_inserted : variable_get('tripal_bulk_loader_keep_track_inserted', 0),
  );

  return $form;
}


/**
 * Implements node_load
 *
 * D7 Changes: now loads all $nodes at once so need to add loops
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_load($nodes) {

  // Loading Job Details
  // Add fields from the tripal_bulk_loader
  $result = db_select('tripal_bulk_loader', 'tbl')
    ->fields('tbl')
    ->condition('nid',array_keys($nodes),'IN')
    ->execute();
  foreach ($result as $record) {
    $nodes[$record->nid]->loader_name = $record->loader_name;
    $nodes[$record->nid]->template_id = $record->template_id;
    $nodes[$record->nid]->file = $record->file;
    $nodes[$record->nid]->job_id = $record->job_id;
    $nodes[$record->nid]->job_status = $record->job_status;
    $nodes[$record->nid]->file_has_header = $record->file_has_header;
    $nodes[$record->nid]->keep_track_inserted = $record->keep_track_inserted;

    $nodes[$record->nid]->exposed_fields = array();
    $nodes[$record->nid]->constants = array();
  }

  // Job Details
  // Add fields from tripal_jobs
  $result = db_query('SELECT tbl.nid, tj.* FROM {tripal_jobs} tj '
    . 'LEFT JOIN {tripal_bulk_loader} tbl ON tbl.job_id=tj.job_id '
    . 'WHERE tbl.nid IN (:nids)',
    array(':nids' => array_keys($nodes))
  );
  foreach ($result as $record) {
    $nodes[$record->nid]->job = $record;
  }

  // Add the Loader Template
  // Add fields from tripal_bulk_loader_template
  $result = db_query('SELECT tbl.nid, tblt.* FROM {tripal_bulk_loader_template} tblt '
    . 'LEFT JOIN {tripal_bulk_loader} tbl ON tbl.template_id=tblt.template_id '
    . 'WHERE tbl.nid IN (:nids)',
    array(':nids' => array_keys($nodes))
  );
  foreach ($result as $dbrecord) {
    $nodes[$dbrecord->nid]->template = $dbrecord;
    $nodes[$dbrecord->nid]->template->template_array = unserialize($dbrecord->template_array);

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

  // Add inserted records
  // Add fields from tripal_bulk_loader_inserted
  $result = db_query('SELECT tbli.* FROM {tripal_bulk_loader_inserted} tbli '
    . 'WHERE tbli.nid IN (:nids)',
    array(':nids' => array_keys($nodes))
  );
  foreach ($result as $record) {
    $record->num_inserted = sizeof(preg_split('/,/', $record->ids_inserted));
    $nodes[$record->nid]->inserted_records->{$record->table_inserted_into} = $record;
  }

  // Add constants
  // Add fields from tripal_bulk_loader_constants
  $result = db_query('SELECT tblc.* FROM {tripal_bulk_loader_constants} tblc '
    . 'WHERE tblc.nid IN (:nids) '
    . 'ORDER BY group_id, record_id, field_id',
    array(':nids' => array_keys($nodes))
  );
  foreach ($result as $record) {
    $nodes[$record->nid]->constants[$record->group_id][$record->record_id][$record->field_id] = array(
      'constant_id' => $record->constant_id,
      'group_id' => $record->group_id,
      'chado_table' => $record->chado_table,
      'chado_field' => $record->chado_field,
      'record_id' => $record->record_id,
      'field_id' => $record->field_id,
      'value' => $record->value
    );
  }

}

/**
 * Implements node_insert
 * Insert the data from the node form on Create content
 *
 * D7 Changes: seems to need db_insert; not recommended to change $node
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_insert($node) {

  $node->title = $node->loader_name;
  db_insert('tripal_bulk_loader')->fields(array(
    'nid' => $node->nid,
    'loader_name' => $node->loader_name,
    'template_id' => $node->template_id,
    'file' => $node->file,
    'file_has_header' => $node->has_header,
    'job_status' => 'Initialized',
    'keep_track_inserted' => $node->keep_track_inserted
  ))->execute();
  drupal_set_message(t('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
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_delete($node) {
  $tables = array();
  $tables[] = 'tripal_bulk_loader';
  $tables[] = 'tripal_bulk_loader_constants';
  $tables[] = 'tripal_bulk_loader_inserted';
  foreach($tables as $table) {
    db_delete($table)
      ->condition('nid',$node->nid)
      ->execute();
  }
}

/**
 * Implements node_update
 * Updates the data submitted by the node form on edit
 *
 * D7 Changes: db_update is much easier
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_update($node) {

  // Update tripal_bulk_loader
  db_update('tripal_bulk_loader')->fields(array(
    'nid' => $node->nid,
    'loader_name' => $node->loader_name,
    'template_id' => $node->template_id,
    'file' => $node->file,
    'file_has_header' => $node->has_header,
    'keep_track_inserted' => $node->keep_track_inserted
  ))->condition('nid',$node->nid)->execute();

  // Add a job if the user want to load the data
  /**
  No job checkbox in the form
  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)));
    }
  }
  */

}

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

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

  $resource = db_select('tripal_bulk_loader_template','t')
    ->fields('t')
    ->condition('template_id', $variables['template_id'])
    ->execute();
  $template = $resource->fetchObject();
  $template->template_array = unserialize($template->template_array);
  $variables['template'] = $template;

}

/**
 * Get the progress of the current constant set from the progress file
 *
 * When transactions are used, database updates to drupal cannot be made. Thus a separate
 * method to keep track of progress was implemented: save a period to the file for each
 * record successfully inserted; each line in the file represents a processed line.
 *
 * @param $job_id
 *   The id of the tripal job to check the progress of
 * @param $node
 *   The tripal_bulk_loader node associated with the job
 *
 * @return
 *   An array with the following keys:
 *     num_lines = the number of lines in the file processed so far
 *     total_lines = the total number of lines in the input file
 *     percent_file = the percent the input file has been loaded
 *     num_records = the number of records successfully inserted
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_progess_file_get_progress($job_id, $update_progress = TRUE) {
  $filename = '/tmp/tripal_bulk_loader_progress-' . $job_id . '.out';
  if (!file_exists($filename)) {
    return (object) array();
  }

  $num_lines = trim(`wc --lines < $filename`);
  $num_records = trim(`grep -o "." $filename | wc --lines`);

  $job = db_query("SELECT j.*, b.file, b.file_has_header, c.num as num_constant_sets
                              FROM {tripal_jobs} j
                              LEFT JOIN {tripal_bulk_loader} b ON b.job_id=j.job_id
                              LEFT JOIN (
                                  SELECT nid, count(distinct(group_id)) as num
                                  FROM {tripal_bulk_loader_constants}
                                  GROUP BY nid
                                ) c ON c.nid=b.nid
                              WHERE j.job_id=:job", array(':job' =>$job_id))->execute();
  if ($job->num_constant_sets) {
    $num_constant_sets_loaded = round($job->progress / (100 / $job->num_constant_sets), 4);

    // If the next constant set has started loading
    if ($job->num_constant_sets != $num_constant_sets_loaded) {

      // total lines in input file
      $total_lines = trim(`wc --lines < $job->file`);
      if ($job->file_has_header) {
        $total_lines--;
      }

      // percent of the current constant set loaded
      $percent = round($num_lines/$total_lines * 100, 2);

      // percent of the total job = (<# fully loaded constant sets> * 100 )
      //                           + <percent of current constant set>
      //                           / <total number of constant sets>
      $total_percent = (($num_constant_sets_loaded * 100) + $percent) / $job->num_constant_sets;

      // update the progress of the job
      if ($update_progress AND ($percent != 0 OR $percent != 100)) {
        tripal_job_set_progress($job_id, round($total_percent, 0));
      }
    }
  }

  return (object) array(
    'num_lines' => $num_lines,
    'total_lines' => $total_lines,
    'percent_file' => $percent,
    'num_constant_sets_loaded' => $num_constant_sets_loaded,
    'total_percent' => $total_percent,
    'num_records' => $num_records
  );
}

/**
 * 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 $args
 *   The arguements passed into tripal_add_job()
 * @return
 *   An array where keys are the human readable headers describing each arguement
 *   and the value is the aguement passed in after formatting
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_job_describe_args($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;
  }

}

/**
 * Implements hook_coder_ignore().
 * Defines the path to the file (tripal_bulk_loader.coder_ignores.txt) where ignore rules for coder are stored
 *
 * @ingroup tripal_bulk_loader
 */
function tripal_bulk_loader_coder_ignore() {
  return array(
    'path' => drupal_get_path('module', 'tripal_bulk_loader'),
    'line prefix' => drupal_get_path('module', 'tripal_bulk_loader'),
  );
}