tripal/tripal_chado_views/tripal_chado_views.module

<?php
/**
 * @file
 * Basic Tripal Views functionality
 */

/**
 * @defgroup tripal_chado_views Tripal Chado Views Module
 * @ingroup tripal_modules
 * @{
 * Provides functions for integrating chado with Drupal Views.
 * @}
 */

require_once 'api/tripal_chado_views.api.inc';
//require_once 'api/tripal_chado_views.DEPRECATED.inc';

require_once 'tripal_chado_views.views.inc';

require_once 'includes/tripal_chado_views_integration.inc';
require_once 'includes/tripal_chado_views_integration_UI.inc';
require_once 'includes/tripal_chado_views_integration_port.inc';

/**
 * Implements hook_menu().
 * This hook provides details about new menu items added by this module
 *
 * @ingroup tripal_chado_views
 */
function tripal_chado_views_menu() {
  $items = array();

//   $items['chado'] = array(
//     'title' => 'Search Data',
//     'description' => 'Listings of the various biological data available categorized by type.',
//     'page callback' => 'theme',
//     'page arguments' => array('tripal_chado_views_search_biological_content'),
//     'access arguments' => array('access content'),
//     'expanded' => TRUE,
//     'type' => MENU_NORMAL_ITEM,
//   );

  // TODO: should the views integration be moved into the tripal_chado module?
  $items['admin/tripal/storage/chado/views-integration'] = array(
    'title' => 'Views Integration',
    'description' => 'Integration of all the chado tables and fields with Drupal Views.',
    'page callback' => 'tripal_chado_views_admin_integration_view',
    'access arguments' => array('manage tripal_views_integration'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => 10
  );

  /**
  $items['admin/tripal/storage/chado/views-integration/list'] = array(
    'title' => 'List of Integrated Tables',
    'description' => 'Provide a list of all integrated tables and allows for adding new tables or editing already integrated tables.',
    'page callback' => 'tripal_chado_views_integration_setup_list',
    'access arguments' => array('manage tripal_views_integration'),
    'type' => MENU_NORMAL_ITEM,
    'weight' => 0,
  );
  */

  $items['admin/tripal/storage/chado/views-integration/new'] = array(
    'title' => 'Integrate A Table',
    'description' => 'Describe to Tripal Views how to integrate a new chado table or materialized view.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_views_integration_form'),
    'access arguments' => array('manage tripal_views_integration'),
    'type' => MENU_CALLBACK,
    'weight' => 1,
  );

  $items['admin/tripal/storage/chado/views-integration/edit/%'] = array(
    'title' => 'Edit Views Integration',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_chado_views_integration_form', 6),
    'access arguments' => array('manage tripal_views_integration'),
    'type' => MENU_CALLBACK,
  );

  $items['admin/tripal/storage/chado/views-integration/delete/%'] = array(
    'title' => 'Delete Views Integration',
    'page callback' => 'tripal_chado_views_integration_delete',
    'page arguments' => array(6),
    'access arguments' => array('manage tripal_views_integration'),
    'type' => MENU_CALLBACK,
  );

  $items['admin/tripal/storage/chado/views-integration/delete-all/confirm'] = array(
    'title' => 'Delete ALL Views Integration',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_chado_views_integration_delete_all_form'),
    'access arguments' => array('manage tripal_views_integration'),
    'type' => MENU_CALLBACK,
  );

  $items['admin/tripal/storage/chado/views-integration/import'] = array(
    'title' => 'Import Views Integration',
    'description' => 'Import a Chado Views Integration from another site.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_chado_views_integration_import_form'),
    'access arguments' => array('manage tripal_views_integration'),
    'type' => MENU_CALLBACK,
    'weight' => 2,
  );

  $items['admin/tripal/storage/chado/views-integration/export/%'] = array(
    'title' => 'Export Views Integration',
    'description' => 'Export a Chado Views Integration for use in another Tripal site',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_chado_views_integration_export_form', 6),
    'access arguments' => array('manage tripal_views_integration'),
    'type' => MENU_CALLBACK,
  );

  $items['admin/tripal/storage/chado/views-integration/help'] = array(
    'title' => 'Help',
    'description' => "A description of the Tripal Chado Views module including a short description of it's usage.",
    'page callback' => 'theme',
    'page arguments' => array('tripal_chado_views_help'),
    'access arguments' => array('manage tripal_views_integration'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10,
  );

  $items['admin/tripal/storage/chado/views-integrations/views/integrations/enable'] = array(
    'title' => 'Enable Integrations Administrative View',
    'page callback' => 'tripal_enable_view',
    'page arguments' => array('tripal_chado_views_admin_integrations', 'admin/tripal/storage/chado/views-integration'),
    'access arguments' => array('manage tripal_views_integration'),
    'type' => MENU_CALLBACK,
  );

  return $items;
}

/**
 * Implements hook_init().
 *
 * @ingroup tripal_chado_views
 */
function tripal_chado_views_init() {
return;
  // Need to ensure that all chado tables are integrated w/out making
  // the user go to views UI. It would be ideal to do this in a hook called only once
  // directly after install/enabling of the module but such a hook doesn't
  // exist in Drupal 6
  $tripal_views = db_query("SELECT true as has_rows FROM {tripal_views}");
  $tripal_views = $tripal_views->fetchObject();
  if (isset($tripal_views)) {
    if (!$tripal_views->has_rows) {
      tripal_rebuild_views_integrations();
    }
  }
}

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

/**
 * Implements hook_permissions().
 *
 * Set the permission types that the chado module uses.
 *
 * @ingroup tripal_chado_views
 */
function tripal_chado_views_permission() {
  return array(
    'manage tripal_views_integration' => array(
      'title' => t('Administrate Tripal Chado Views Integration'),
      'description' => t('Permission to manage Tripal Chado Views Integration.')
    ),
  );
}

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

/**
 * Implements hook_theme().
 *
 * This hook provides details about themable objects added by
 *   this module
 *
 * @ingroup tripal_chado_views
 */
function tripal_chado_views_theme($existing, $type, $theme, $path) {
  return array(
    'tripal_chado_views_integration_form' => array(
      'template'  => 'tripal_chado_views_integration_fields_form',
      'render element'=> 'form',
    ),
    'file_upload_combo' => array(
      'variables' => array('element' => NULL)
    ),
    'sequence_combo' => array(
      'variables' => array('element' => NULL)
    ),
    // instructions page for the views module
    'tripal_chado_views_help' => array(
      'template' => 'tripal_chado_views_help',
      'variables' =>  array(NULL),
      'path' => drupal_get_path('module', 'tripal_chado_views') . '/theme'
    ),
    // search biological content page
    'tripal_chado_views_search_biological_content' => array(
      'template' => 'tripal_chado_views_search_biological_content',
      'variables' =>  array(NULL),
      'path' => drupal_get_path('module', 'tripal_chado_views') . '/theme'
    ),
  );
}

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

/**
 * A landing page for all views of chado content. Simply lists all menu items that
 * are children of it.
 *
 * @ingroup tripal_chado_views
 */
function tripal_chado_views_biological_data_page() {
  $output = '';

  $item = menu_get_item();
  $content = system_admin_menu_block($item);

  $output .= '<dl class="admin-list">';
  foreach ($content as $item) {
    $output .= '<dt>'. l($item['title'], $item['href'], $item['localized_options']) .'</dt>';
    $output .= '<dd>'. $item['description'] .'</dd>';
  }
  $output .= '</dl>';

  return $output;
}

/**
 * Admin launchpad
 *
 * @ingroup tripal_chado_views
 */
function tripal_chado_views_admin_integration_view() {
  $output = '';

  // set the breadcrumb
  $breadcrumb = array();
  $breadcrumb[] = l('Home', '<front>');
  $breadcrumb[] = l('Administration', 'admin');
  $breadcrumb[] = l('Tripal', 'admin/tripal');
  $breadcrumb[] = l('Data Storage', 'admin/tripal/storage');
  $breadcrumb[] = l('Chado', 'admin/tripal/storage/chado');
  $breadcrumb[] = l('Views Integration', 'admin/tripal/storage/chado/views-integration');
  drupal_set_breadcrumb($breadcrumb);

  // Add the view
  $view = views_embed_view('tripal_views_admin_integrations','default');
  if (isset($view)) {
    $output .= $view;
  }
  else {
    $output .= '<p>The Tripal Chado Views Module uses primarily views to provide an '
      . 'administrative interface. Currently one or more views needed for this '
      . 'administrative interface are disabled. <strong>Click each of the following links to '
      . 'enable the pertinent views</strong>:</p>';
    $output .= '<ul>';
      $output .= '<li>'.l('Tripal Views Admin', 'admin/tripal/storage/chado/views-integration/views/integrations/enable').'</li>';
    $output .= '</ul>';
  }

  return $output;
}