Implements hook_menu(). Registers all menu items associated with this module

Related topics

File

tripal_cv/tripal_cv.module, line 43

Provides functions for managing chado controlled vocabularies which are used ubiquitously throughout chado.

Code

function tripal_cv_menu() {
  $items = array();

  $items['admin/tripal/chado/tripal_cv'] = array(
    'title' => 'Controlled Vocabularies',
    'description' => 'Controlled Vocabularies control the terms available for various chado fields.',
    'page callback' => 'tripal_cv_admin_cv_listing',
    'access arguments' => array('administer controlled vocabularies'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/tripal/chado/tripal_cv/defaults'] = array(
    'title' => 'Defaults',
    'description' => 'Set the default vocabularies for properties and relationships.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_cv_admin_set_defaults_form'),
    'access arguments' => array('administer controlled vocabularies'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5
  );

  $items['admin/tripal/chado/tripal_cv/help'] = array(
    'title' => 'Help',
    'description' => "A description of the Tripal Controlled Vocabulary module including a short description of it's usage.",
    'page callback' => 'theme',
    'page arguments' => array('tripal_cv_admin'),
    'access arguments' => array('administer controlled vocabularies'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );

  // The OBO loader will be available in two places
  $items['admin/tripal/chado/tripal_cv/obo_loader'] = array(
    'title' => 'OBO File Loader',
    'description' => 'Load an ontology in OBO format chado as a controlled vocabulary.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_cv_obo_form'),
    'access arguments' => array('administer controlled vocabularies'),
    'type' => MENU_CALLBACK,
  );

  $items['admin/tripal/loaders/obo_loader'] = array(
    'title' => 'OBO File Loader',
    'description' => 'Load an ontology in OBO format into chado as a controlled vocabulary.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_cv_obo_form'),
    'access arguments' => array('administer controlled vocabularies'),
    'type' => MENU_NORMAL_ITEM,
  );

  /*
   * Menu for updating the cvtermpath
   */

  $items['admin/tripal/chado/tripal_cv/cvtermpath'] = array(
    'title' => 'Update Chado cvtermpath table',
    'description' => 'The Chado cvtermpath table provides lineage for terms and is useful for quickly finding any ancestor parent of a term.  However, this table must be populated.  This page allows for populating of this table one vocabulary at a time',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_cv_cvtermpath_form'),
    'access arguments' => array('administer controlled vocabularies'),
    'type' => MENU_CALLBACK,
  );

  /*
   * Menu items for adding and editing CVs
   */
  $items['admin/tripal/chado/tripal_cv/cv/edit/%'] = array(
    'title' => 'Edit a Controlled Vocabulary',
    'description' => 'Edit the details such as name and description for an existing controlled vocabulary.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_cv_cv_edit_form', 6),
    'access callback' => 'user_access',
    'access arguments' => array('administer controlled vocabularies'),
    'type' => MENU_CALLBACK,
  );

  $items['admin/tripal/chado/tripal_cv/cv/add'] = array(
    'title' => 'Add a Controlled Vocabulary',
    'description' => 'Manually a new controlled vocabulary.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_cv_cv_add_form'),
    'access callback' => 'user_access',
    'access arguments' => array('administer controlled vocabularies'),
    'type' => MENU_CALLBACK,
  );

  /*
   * Menu items for adding and editing CVterms
   */
  $items['admin/tripal/chado/tripal_cv/cv/%/cvterm/add'] = array(
    'title' => 'Add a Controlled Vocabulary Term',
    'description' => 'Add a new controlled vocabulary term.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_cv_cvterm_add_form', 5),
    'access arguments' => array('administer controlled vocabularies'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/chado/tripal_cv/cvterm/add'] = array(
    'title' => 'Add a Controlled Vocabulary Term',
    'description' => 'Add a new controlled vocabulary term.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_cv_cvterm_add_form'),
    'access arguments' => array('administer controlled vocabularies'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/chado/tripal_cv/cv/%/cvterm/edit/%'] = array(
    'title' => 'Edit a Controlled Vocabulary Term',
    'description' => 'Edit an existing controlled vocabulary term.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_cv_cvterm_edit_form', 5, 8),
    'access arguments' => array('administer controlled vocabularies'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/chado/tripal_cv/cvterm/auto_name/%/%'] = array(
    'page callback' => 'tripal_autocomplete_cvterm',
    'page arguments' => array(6, 7),
    'access arguments' => array('administer controlled vocabularies'),
    'type' => MENU_CALLBACK,
  );
  /*
   * Menu items for enabling views
   */
  $items['admin/tripal/chado/tripal_cv/views/cvs/enable'] = array(
    'title' => 'Enable Vocabulary Administrative View',
    'page callback' => 'tripal_enable_view',
    'page arguments' => array('tripal_cv_admin_cvs', 'admin/tripal/chado/tripal_cv'),
    'access arguments' => array('administer controlled vocabularies'),
    'type' => MENU_CALLBACK,
  );
  $items['admin/tripal/chado/tripal_cv/views/cvterms/enable'] = array(
    'title' => 'Enable Vocabulary Terms Administrative View',
    'page callback' => 'tripal_enable_view',
    'page arguments' => array('tripal_cv_admin_cvterms', 'admin/tripal/chado/tripal_cv'),
    'access arguments' => array('administer controlled vocabularies'),
    'type' => MENU_CALLBACK,
  );

  /*
   * Charts
   */
  $items['tripal_cv_chart'] = array(
    'path' => 'tripal_cv_chart',
    'page callback' => 'tripal_cv_chart',
    'page arguments' => array(1),
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK
  );


  /*
   * Menu items for working with CV Trees
   */
  $items['cv_browser'] = array(
    'page callback' => 'tripal_cv_show_browser',
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK
  );

  $items['tripal_cv_tree'] = array(
    'path' => 'tripal_cv_tree',
    'page callback' => 'tripal_cv_tree',
    'page arguments' => array(1),
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK
  );

  $items['tripal_cv_init_browser'] = array(
    'path' => 'tripal_cv_init_browser',
    'page callback' => 'tripal_cv_init_browser',
    'page arguments' => array(1),
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK
  );

  // menu item for interaction with the tree
  $items['tripal_cv_update_tree'] = array(
    'path' => 'tripal_cv_update_tree',
    'page callback' => 'tripal_cv_update_tree',
    'page arguments' => array(2, 3),
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK
  );

  // menu items for working with terms
  $items['tripal_cv_cvterm_info'] = array(
    'path' => 'tripal_cv_cvterm_info',
    'title' => 'CV Term Viewer',
    'page callback' => 'tripal_cv_cvterm_info',
    'page arguments' => array(1),
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK
  );

  return $items;
}