tripal/tripal_phylogeny/tripal_phylogeny.module

<?php

/**
 * @file
 * Integrates the Chado Phylotree module with Drupal Nodes & Views
 */

/**
 * @defgroup tripal_phylogeny Phylotree Module
 * @ingroup tripal_modules
 * @{
 * Integrates the Chado Phylotree module with Drupal Nodes
 * @}
 */
require_once 'api/tripal_phylogeny.api.inc';
require_once 'theme/tripal_phylogeny.theme.inc';
require_once 'includes/tripal_phylogeny.admin.inc';
require_once 'includes/tripal_phylogeny.chado_node.inc';
require_once 'includes/tripal_phylogeny.import_tree.inc';
require_once 'includes/tripal_phylogeny.taxonomy.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_phylogeny
 */
function tripal_phylogeny_permission() {
  return array(
    'access chado_phylotree content' => array(
      'title' => t('View Phylotrees'),
      'description' => t('Allow users to view phylotree pages.'),
    ),
    'administer tripal phylotree' => array(
      'title' => t('Administer Phylotrees'),
      'description' => t('Allow users to administer all phylotrees.'),
    ),
  );
}

/**
 * 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_phylogeny
 */
function tripal_phylogeny_menu() {
  $items = array();

  // administration landing page. currently has no content but is
  // apparently required for the Sync and Help links to work.
  $items['admin/tripal/chado/tripal_phylogeny'] = array(
    'title' => 'Phylogeny and Taxonomy',
    'description' => 'Phylogenetic and taxonomic trees.',
    'page callback' => 'tripal_phylogeny_admin_phylotrees_listing',
    'access arguments' => array('administer tripal phylotree'),
    'type' => MENU_NORMAL_ITEM,
  );

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

  // configuration menu item
  $items['admin/tripal/chado/tripal_phylogeny/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Configure the Tripal Phylotree module',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_phylogeny_admin'),
    'access arguments' => array('administer tripal phylotree'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 1
  );

  $items['admin/tripal/chado/tripal_phylogeny/plots'] = array(
    'title' => 'Plot Defaults',
    'description' => 'Set defaults for the trees',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_phylogeny_default_plots_form'),
    'access arguments' => array('administer tripal phylotree'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 2
  );

  // sync menu item (will be rendered as a tab by tripal)
  $items['admin/tripal/chado/tripal_phylogeny/sync'] = array(
    'title' => ' Sync',
    'description' => 'Create pages on this site for phylotrees stored in Chado',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('chado_node_sync_form', 'tripal_phylogeny', 'chado_phylotree'),
    'access arguments' => array('administer tripal phylotree'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 3
  );

  // Enable admin view
  $items['admin/tripal/chado/tripal_phylogeny/views/phylotree/enable'] = array(
    'title' => 'Enable Phylotree Administrative View',
    'page callback' => 'tripal_enable_view',
    'page arguments' => array('tripal_phylogeny_admin_phylotree', 'admin/tripal/chado/tripal_phylogeny'),
    'access arguments' => array('administer tripal phylotree'),
    'type' => MENU_CALLBACK,
  );

  $items['chado_phylotree/%'] = array(
    'page callback' => 'phylotree_by_name',
    'page arguments' => array(1),
    // allow all anonymous http clients
    'access callback' => TRUE
  );

   // create a route for viewing json of all phylonodes having this phylotree_id
   $items['chado_phylotree/%/json'] = array(
    'page callback' => 'phylotree_json',
    'page arguments' => array(1),
     // allow all anonymous http clients
    'access callback' => TRUE
   );

   // Data Loaders
   $items['admin/tripal/loaders/newic_phylotree_loader'] = array(
     'title' => 'Phylogenetic Trees (Newic format)',
     'description' => 'Loads phylogenetic trees in Newic format. (Redirects to create a phylogenetic tree content type)',
     'page callback' => 'drupal_goto',
     'page arguments' => array('node/add/chado-phylotree'),
     'access arguments' => array('administer tripal phylotree'),
     'type' => MENU_NORMAL_ITEM,
   );

   $items['admin/tripal/loaders/ncbi_taxonomy_loader'] = array(
     'title' => 'NCBI Taxonomy Loader',
     'description' => 'Loads taxonomic details about installed organisms.',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_phylogeny_taxonomy_load_form'),
     'access arguments' => array('administer tripal phylotree'),
     'file' => '/includes/tripal_phylogeny.taxonomy.inc',
     'type' => MENU_NORMAL_ITEM,
   );

   $items['taxonomy_view'] = array(
     'title' => 'Site Taxonomy',
     'description' => 'A taxonomy viewer for the species on this site.',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_phylogeny_taxonomy_viewer'),
     'access arguments' => array('access taxonomy content'),
     'file' => '/includes/tripal_phylogeny.taxonomy.inc',
     'type' => MENU_NORMAL_ITEM,
   );

  return $items;
}

/**
 * Implements hook_search_biological_data_views().
 *
 * Adds the described views to the "Search Data" Page created by Tripal Views
 */
function tripal_phylogeny_search_biological_data_views() {
  return array(
      'tripal_phylogeny_user_phylotree' => array(
          'machine_name' => 'tripal_phylogeny_user_phylotree',
          'human_name' => 'Phylogenetic Trees',
          'description' => 'Gene trees, species trees, etc.',
          'link' => 'chado/phylotree'
      ),
  );
}

/**
 * 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_phylogeny
 */
function tripal_phylogeny_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_phylogeny
 */
function tripal_phylogeny_theme($existing, $type, $theme, $path) {
  $core_path = drupal_get_path('module', 'tripal_core');
  $items = array(
    // built-in theme
    'node__chado_phylotree' => array(
      'template' => 'node--chado-generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$core_path/theme/templates",
    ),
    // base template for this page (default tab) includes the phylogram
    'tripal_phylogeny_base' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_phylogeny_base',
      'path' => "$path/theme/templates",
    ),
    // Template for the phylogram.
    'tripal_phylogeny_phylogram' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_phylogeny_phylogram',
      'path' => "$path/theme/templates",
    ),
    // Template for the taxonomic tree.
    'tripal_phylogeny_taxonomic_tree' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_phylogeny_taxonomic_tree',
      'path' => "$path/theme/templates",
    ),
    // partial for organisms block
    'tripal_phylogeny_organisms' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_phylogeny_organisms',
      'path' => "$path/theme/templates",
    ),
    // partial for cross references block
    'tripal_phylogeny_references' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_phylogeny_references',
      'path' => "$path/theme/templates",
    ),
    // partial for cross references block
    'tripal_phylogeny_analysis' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_phylogeny_analysis',
      'path' => "$path/theme/templates",
    ),
    // partial for teaser view
    'tripal_phylogeny_teaser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_phylogeny_teaser',
      'path' => "$path/theme/templates",
    ),

    // FORM THEMES
    // Theme function for the project table in admin projects form
    'tripal_phylogeny_admin_org_color_tables' => array(
      'render element' => 'element',
    )
  );
  return $items;
}

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

// hack to suppress the 'Submitted by...' info drupal adds to nodes
$variables['display_submitted'] = FALSE;