tripal/tripal_organism/tripal_organism.module

<?php

require_once "api/tripal_organism.api.inc";
require_once "includes/tripal_organism.admin.inc";
require_once "includes/tripal_organism.chado_node.inc";

/**
 * @defgroup tripal_organism Organism Module
 * @ingroup tripal_modules
 * @{
 * Provides functions for managing chado organisms including creating details pages for each one
 * @}
 */

/**
 *
 * @ingroup tripal_organism
 */
function tripal_organism_init() {

  // add the jGCharts JS and CSS
  drupal_add_css(drupal_get_path('module', 'tripal_organism') . '/theme/css/tripal_organism.css');
  drupal_add_js(drupal_get_path('module', 'tripal_organism') . '/theme/js/tripal_organism.js');
}



/**
 *
 * @ingroup tripal_organism
 */
function tripal_organism_block_info() {

  $blocks['base']['info'] = t('Tripal Organism Details');
  $blocks['base']['cache'] = DRUPAL_NO_CACHE;

  return $blocks;

}
/**
 *
 * @ingroup tripal_organism
 */
function tripal_organism_block_view($delta = '') {

  if (user_access('access chado_feature content') and arg(0) == 'node' and is_numeric(arg(1))) {
    $nid = arg(1);
    $node = node_load($nid);

    $block = array();
    switch ($delta) {
      case 'base':
        $block['subject'] = t('Organism Details');
        $block['content'] = theme('tripal_organism_base', $node);
        break;
      default:
    }
    return $block;
  }
}
/**
 *  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_organism
 */
function tripal_organism_menu() {
  $items = array();

  // the administative settings menu
  $items['admin/tripal/chado/tripal_organism'] = array(
    'title' => 'Organisms',
    'description' => 'Any living biological entity, such as an animal, plant, fungus, or bacterium.',
    'page callback' => 'tripal_organism_admin_organism_view',
    'access arguments' => array('adminster tripal organism'),
    'type' => MENU_NORMAL_ITEM,
  );

  $items['admin/tripal/chado/tripal_organism/help'] = array(
    'title' => 'Help',
    'description' => "A description of the Tripal Organism module including a short description of it's usage.",
    'page callback' => 'theme',
    'page arguments' => array('tripal_organism_help'),
    'access arguments' => array('adminster tripal organism'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );

  $items['admin/tripal/chado/tripal_organism/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Manage integration of Chado organisms including associated features',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_organism_admin'),
    'access arguments' => array('adminster tripal organism'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5
  );

  $items['admin/tripal/chado/tripal_organism/sync'] = array(
    'title' => ' Sync',
    'description' => 'Create pages on this site for organisms stored in Chado',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_core_chado_node_sync_form', 'tripal_organism', 'chado_organism'),
    'access arguments' => array('administer tripal organism'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 2
  );

  $items['admin/tripal/chado/tripal_organism/views/organisms/enable'] = array(
    'title' => 'Enable Organism Administrative View',
    'page callback' => 'tripal_views_admin_enable_view',
    'page arguments' => array('tripal_organism_admin_organisms', 'admin/tripal/chado/tripal_organism'),
    'access arguments' => array('administer tripal organism'),
    'type' => MENU_CALLBACK,
  );


  return $items;
}

/**
 * Implements hook_help()
 * Purpose: Adds a help page to the module list
 */
function tripal_organism_help ($path, $arg) {
  if ($path == 'admin/help#tripal_organism') {
    return theme('tripal_organism_help', array());
  }
}

/**
 *  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_organism
 */
function tripal_organism_theme($existing, $type, $theme, $path) {
  $core_path = drupal_get_path('module', 'tripal_core');

  $items = array(
    'node__chado_organism' => array(
      'template' => 'node--chado-generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$core_path/theme",
    ),
    'tripal_organism_base' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_organism_base',
      'path' => "$path/theme/tripal_organism",
    ),
    'tripal_organism_teaser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_organism_teaser',
      'path' => "$path/theme/tripal_organism",
    ),
    'tripal_organism_help' => array(
      'template' => 'tripal_organism_help',
      'variables' =>  array(NULL),
      'path' => "$path/theme",
    ),
  );
  return $items;
}

/**
  *  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_organism
  */
function tripal_organism_permission() {
  return array(
    'access chado_organism content' => array(
      'title' => t('View Organisms'),
      'description' => t('Allow users to view organism pages.'),
    ),
    'create chado_organism content' => array(
      'title' => t('Create Organisms'),
      'description' => t('Allow users to create new organism pages.'),
    ),
    'delete chado_organism content' => array(
      'title' => t('Delete Organisms'),
      'description' => t('Allow users to delete organism pages.'),
    ),
    'edit chado_organism content' => array(
      'title' => t('Edit Organisms'),
      'description' => t('Allow users to edit organism pages.'),
    ),
    'adminster tripal organism' => array(
      'title' => t('Administer Organisms'),
      'description' => t('Allow users to administer all organisms.'),
    ),
  );
}
/**
 * Implements hook_views_api()
 * Purpose: 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_organism
 */
function tripal_organism_views_api() {
  return array(
    'api' => 2.0,
  );
}
/**
 *
 *
 * @ingroup tripal_organism
 */
function tripal_organism_job_describe_args($callback, $args) {

  $new_args = array();
  if ($callback == 'tripal_organism_sync_organisms') {
    $organism = tripal_core_chado_select('organism', array('genus', 'species'), array('organism_id' => $args[0]));
    $new_args['Organism'] = $organism[0]->genus . " " . $organism[0]->species;
  }
  return $new_args;
}


/**
 * Implementation of hook_form_alter()
 *
 * @param $form
 * @param $form_state
 * @param $form_id
 */
function tripal_organism_form_alter(&$form, &$form_state, $form_id) {
  // turn of preview button for insert/updates
  if ($form_id == "chado_organism_node_form") {
    $form['actions']['preview']['#access'] = FALSE;
  }
}