tripal_phylotree.module

<?php

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

/**
 * @defgroup tripal_phylotree Phylotree Module
 * @ingroup tripal_modules
 * @{
 * Integrates the Chado Phylotree module with Drupal Nodes
 * @}
 */
require_once 'theme/tripal_phylotree.theme.inc';
require_once 'includes/tripal_phylotree.admin.inc';
require_once 'includes/tripal_phylotree.chado_node.inc';
require_once 'includes/tripal_phylotree_userinfo_block.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_phylotree
 */
function tripal_phylotree_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_phylotree
 */
function tripal_phylotree_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/extension/tripal_phylotree'] = array(
    'title' => 'Phylotrees',
    'description' => 'Phylogenetic trees & gene families',
    'page callback' => 'tripal_phylotree_admin_phylotrees_listing',
    'access arguments' => array('administer tripal phylotree'),
    'type' => MENU_NORMAL_ITEM,
  );

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

  // configuration menu item
  $items['admin/tripal/extension/tripal_phylotree/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Configure the Tripal Phylotree module',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_phylotree_admin'),
    'access arguments' => array('administer tripal phylotree'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5
  );

  // sync menu item (will be rendered as a tab by tripal)
  $items['admin/tripal/extension/tripal_phylotree/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_phylotree', 'chado_phylotree'),
    'access arguments' => array('administer tripal phylotree'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 2
  );

  // menu hook to fetch gene tree by name
   $items['chado_phylotree/%'] = array(
    'page callback' => 'phylotree_by_name',
    'page arguments' => array(1),
    'access callback' => TRUE // allow all anonymous http clients
   );

   // A menu hook to redirect to gene tree and hilight corresponding
   // node name (polypeptide) for the given gene name
   // /chado_gene_phylotree_v2?gene_name=C.cajan_38960_gene
   // or comma separated list of gene names
   // /chado_gene_phylotree_v2?gene_name=Araip.8X95G,Araip.JJJ8N,Araip.B0L4D
   $items['chado_gene_phylotree_v2'] = array(
    'page callback' => 'phylotree_redirect_by_gene',
    'access callback' => TRUE, // allow all anonymous http clients
   );

   $items['chado_gene_phylotree/%/text'] = array(
    'page callback' => 'phylotree_by_genename_text',
    // found this strategy described here: http://stackoverflow.com/questions/2285944/returning-untemplated-output-in-drupal-from-menu-callback-function
    // not sure if it has advantages over the simpler approach described in the top answer, but seemed worth exploring
    'delivery callback' => 'tripal_phylotree_text_deliver',
    'page arguments' => array(1),
    'access callback' => TRUE // allow all anonymous http clients
   );
  
   // route for viewing json of all phylonodes having this phylotree_id
   $items['chado_phylotree/%/json'] = array(
    'page callback' => 'phylotree_json_endpoint',
    'page arguments' => array(1),
    'access callback' => TRUE // allow all anonymous http clients
   );

   // route for static scripts/ content; this is the aurelia-cli build folder.
   $items['chado_phylotree/scripts/%'] = array(
       'page callback' => 'phylotree_static_scripts',
       'page arguments' => array(2),
       'access callback' => TRUE // allow all anonymous http requests
   );

   // route for getting text of msa
   $items['chado_phylotree_msa/%/text'] = array(
    'page callback' => 'phylotree_msa_download',
    'delivery callback' => 'tripal_phylotree_text_deliver',
    'page arguments' => array(1),
    'access callback' => TRUE // allow all anonymous http clients
   );

   
   return $items;
}

/**
 * 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_phylotree
 */
function tripal_phylotree_views_api() {
    $path = drupal_get_path('module', 'tripal_phylotree');
    return array(
        'api' => 3.0,
        'path' => $path . '/includes/views',
        'template path' => $path .'/themes'
    );
}

/**
 * Implements hook_search_biological_data_views().
 * Adds the described views to the "Search Data" Page created by Tripal Views
 *
 * @ingroup tripal_phylotree
 */

function tripal_phylotree_search_biological_data_views() {
  return array(
      'tripal_phylotree_user_phylotree' => array(
          'machine_name' => 'tripal_phylotree_user_phylotree',
          'human_name' => 'Phylotrees',
          'description' => 'Gene trees, species trees, etc.',
          'link' => 'chado/phylotree'
    ),
  );
}

/**
 *  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_phylotree
 */
function tripal_phylotree_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_phylotree_base' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_phylotree_base',
      'path' => "$path/theme/templates",
    ),
    // partial for cross references block
    'tripal_phylotree_references' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_phylotree_references',
      'path' => "$path/theme/templates",
    ),
    // partial for analysis block
    'tripal_phylotree_analysis' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_phylotree_analysis',
      'path' => "$path/theme/templates",
    ),
    // partial for teaser view
    'tripal_phylotree_teaser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_phylotree_teaser',
      'path' => "$path/theme/templates",
    ),
  );
  return $items;
}


/**
  * hook_form_alter
  *
  * Add a validator to the search form.
* */

function tripal_phylotree_form_alter(&$form, &$form_state, $form_id) {
//drupal_set_message("Form ID is: $form_id"); ?~@~S uncomment to verify form name
if ($form_id == 'views_exposed_form') { $form['#validate'][] = 'tripal_phylotree_form_validate';
//drupal_set_message("Validation is set to " . var_export($form['#validate'], true)); -- uncomment to verify validator was added 
 }
}
/**
  * Form validator for search form.
  * Use this to trim whitespace from text fields.
  */
function tripal_phylotree_form_validate($form, &$form_state) {
//drupal_set_message("Form values are " . var_export($form_state['values'], true)); -- uncomment to see form field names 
$form_state['values']['phylotree_name'] = trim($form_state['values']['phylotree_name']);
$form_state['values']['phylotree_comment'] = trim($form_state['values']['phylotree_comment']);
$form_state['values']['domains_con'] = trim($form_state['values']['domains_con']);
}


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

function tripal_phylotree_text_deliver($page_callback_result) {
	print $page_callback_result;
	drupal_exit();
}


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