tripal/tripal_library/tripal_library.module

<?php
/**
 * @file
 * Integrates the Chado Library module with Drupal Nodes & Views
 */

/**
 * @defgroup tripal_library Library Module
 * @ingroup tripal_modules
 * @{
 * Integrates the Chado Library module with Drupal Nodes & Views
 * @}
 */

require_once 'api/tripal_library.DEPRECATED.inc';

require_once 'theme/tripal_library.theme.inc';

require_once 'includes/tripal_library.admin.inc';
require_once 'includes/tripal_library.chado_node.inc';

/**
 * Implements hook_permission().
 *
 * Set the permission types that the chado module uses.  Essentially we
 * want permissionis that protect creation, editing and deleting of chado
 * data objects
 *
 * @ingroup tripal_library
 */
function tripal_library_permission() {
  return array(
    'access chado_library content' => array(
      'title' => t('View Libraries'),
      'description' => t('Allow users to view library pages.'),
    ),
    'create chado_library content' => array(
      'title' => t('Create Libraries'),
      'description' => t('Allow users to create new library pages.'),
    ),
    'delete chado_library content' => array(
      'title' => t('Delete Libraries'),
      'description' => t('Allow users to delete library pages.'),
    ),
    'edit chado_library content' => array(
      'title' => t('Edit Libraries'),
      'description' => t('Allow users to edit library pages.'),
    ),
    'administer tripal library' => array(
      'title' => t('Administer Libraries'),
      'description' => t('Allow users to administer all libraries.'),
    ),
  );
}

/**
 * Implements hook_menu().
 *
 * Menu items are automatically added for the new node types created
 * by this module to the 'Create Content' Navigation menu item.  This function
 * adds more menu items needed for this module.
 *
 * @ingroup tripal_library
 */
function tripal_library_menu() {
  $items = array();
  // The administative settings menu
  $items['admin/tripal/chado/tripal_library'] = array(
    'title' => 'Libraries',
    'description' => 'Any biological library. Examples of genomic libraries include BAC, cDNA, FOSMID, etc.',
    'page callback' => 'tripal_library_admin_libraries_listing',
    'access arguments' => array('administer tripal library'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/tripal/chado/tripal_library/help'] = array(
    'title' => 'Help',
    'description' => 'Basic Description of Tripal Library Module Functionality',
    'page callback' => 'theme',
    'page arguments' => array('tripal_library_help'),
    'access arguments' => array('administer tripal library'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );

  $items['admin/tripal/chado/tripal_library/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Configure the Tripal Library module',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_library_admin'),
    'access arguments' => array('administer tripal library'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5
  );
  $items['admin/tripal/chado/tripal_library/sync'] = array(
    'title' => ' Sync',
    'description' => 'Create pages on this site for libraries stored in Chado',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('chado_node_sync_form', 'tripal_library', 'chado_library'),
    'access arguments' => array('administer tripal library'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 2
  );

  $items['admin/tripal/chado/tripal_library/views/libraries/enable'] = array(
    'title' => 'Enable Library Administrative View',
    'page callback' => 'tripal_enable_view',
    'page arguments' => array('tripal_library_admin_libraries', 'admin/tripal/chado/tripal_library'),
    'access arguments' => array('administer tripal library'),
    'type' => MENU_CALLBACK,
  );

  return $items;
}

/**
 * Implements hook_search_biological_data_views().
 *
 * Adds the described views to the "Search Data" Page created by Tripal Views
 */
function tripal_library_search_biological_data_views() {
  return array(
    'tripal_library_user_library' => array(
      'machine_name' => 'tripal_library_user_library',
      'human_name' => 'Libraries',
      'description' => 'Biological library including BAC, cDNA, FOSMID, etc.',
      'link' => 'chado/library'
    ),
  );
}

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

/**
 *  Implements hook_theme().
 *
 * We need to let drupal know about our theme functions and their arguments.
 *  We create theme functions to allow users of the module to customize the
 *  look and feel of the output generated in this module
 *
 * @ingroup tripal_library
 */
function tripal_library_theme($existing, $type, $theme, $path) {
  $core_path = drupal_get_path('module', 'tripal_core');

  $items = array(
    'node__chado_library' => array(
      'template' => 'node--chado-generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$core_path/theme/templates",
    ),

    // tripal_library templates
    'tripal_library_base' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_library_base',
      'path' => "$path/theme/templates",
    ),
    'tripal_library_features' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_library_features',
      'path' => "$path/theme/templates",
    ),
    'tripal_library_properties' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_library_properties',
      'path' => "$path/theme/templates",
    ),
    'tripal_library_publications' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_library_publications',
      'path' => "$path/theme/templates",
    ),
    'tripal_library_references' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_library_references',
      'path' => "$path/theme/templates",
    ),
    'tripal_library_synonyms' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_library_synonyms',
      'path' => "$path/theme/templates",
    ),
    'tripal_library_terms' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_library_terms',
      'path' => "$path/theme/templates",
    ),
    'tripal_library_help' => array(
      'template' => 'tripal_library_help',
      'variables' =>  array(NULL),
      'path' => "$path/theme/templates",
    ),

    // teaser
    'tripal_library_teaser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_library_teaser',
      'path' => "$path/theme/templates",
    ),

    // tripal_organism templates
    'tripal_organism_libraries' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_organism_libraries',
      'path' => "$path/theme/templates",
    ),

    // tripal_feature templates
    'tripal_feature_libraries' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_feature_libraries',
      'path' => "$path/theme/templates",
    ),

  );
  return $items;
}

/**
 * Implements hook_help().
 * Adds a help page to the module list
 *
 * @ingroup tripal_library
 */
function tripal_library_help ($path, $arg) {
  if ($path == 'admin/help#tripal_library') {
    return theme('tripal_library_help', array());
  }
}

/**
 * Implementation of hook_form_alter().
 *
 * @param $form
 * @param $form_state
 * @param $form_id
 *
 * @ingroup tripal_library
 */
function tripal_library_form_alter(&$form, &$form_state, $form_id) {

  if ($form_id == "chado_library_node_form") {
    // turn of preview button for insert/updates
    $form['actions']['preview']['#access'] = FALSE;

    //remove the body field
    unset($form['body']);
  }
}