tripal/tripal_natural_diversity/tripal_natural_diversity.module

<?php

require_once('api/tripal_natural_diversity.api.inc');
require_once('includes/tripal_natural_diversity.schema.inc');
require_once('includes/tripal_natural_diversity.nd_geolocation.inc');
require_once('includes/tripal_natural_diversity.admin.inc');

/**
 *  @file
 * This file contains the basic functions needed for this drupal module.
 * The drupal tripal_natural_diversity module maps directly to the chado X module.
 *
 * For documentation regarding the Chado X module:
 * @see http://gmod.org/wiki/Chado_General_Module
 *
 * @defgroup tripal_natural_diversity Natural Diversity Module
 * @ingroup tripal_modules
 */

/*************************************************************************
 * Implements hook_views_api()
 * Purpose: Essentially this hook tells drupal that there is views support for
 *  for this module which then includes tripal_natural_diversity.views.inc where all the
 *  views integration code is
 *
 * @ingroup tripal_natural_diversity
 */
function tripal_natural_diversity_views_api() {
  return array(
      'api' => 2.0,
  );
}

/**
 * Implements hook_theme
 *
 * @ingroup tripal_natural_diversity
 */
function tripal_natural_diversity_theme() {
  return array(
    'tripal_feature_nd_genotypes' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_feature_nd_genotypes',
    ),
    'tripal_stock_nd_genotypes' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_nd_genotypes',
    ),
    'tripal_stock_nd_phenotypes' => array(
      'arguments' => array('node' => NULL),
      'template' => 'tripal_stock_nd_phenotypes',
    ),
    'tripal_nd_geolocation_base' => array(
        'arguments' => array('node' => NULL),
        'template' => 'tripal_nd_geolocation_base',
    ),
    'tripal_nd_geolocation_properties' => array(
        'arguments' => array('node' => NULL),
        'template' => 'tripal_nd_geolocation_properties',
    ),
    'tripal_natural_diversity_admin' => array(
        'template' => 'tripal_natural_diversity_admin',
        'arguments' =>  array(NULL),
        'path' => drupal_get_path('module', 'tripal_natural_diversity') . '/theme'
    ),
  );
}

/**
 * Implements hook_nodeapi().
 *
 * @ingroup tripal_natural_diversity
 */
function tripal_natural_diversity_nodeapi(&$node, $op, $teaser, $page){
  switch ($op) {
    case 'view':
      if ($node->type == 'chado_feature') {
        // the tripal_genetic module provides a tripal_feature_genotype
        // template.  The only difference between them is the addition of
        // natural_diversity information by this module's template.  Therefore,
        // if the tripal_genetic content is present get rid of as this
        // module superceeds it.
        if (array_key_exists('tripal_feature_genotypes', $node->content)) {
          unset($node->content['tripal_feature_genotypes']);
        }
        $node->content['tripal_feature_nd_genotypes'] = array(
           '#value' => theme('tripal_feature_nd_genotypes', $node),
        );
      }
      if ($node->type == 'chado_stock') {
        $node->content['tripal_stock_nd_genotypes'] = array(
           '#value' => theme('tripal_stock_nd_genotypes', $node),
        );
        $node->content['tripal_stock_nd_phenotypes'] = array(
           '#value' => theme('tripal_stock_nd_phenotypes', $node),
        );
      }
      break;
  }
}

/**
 *
 *
 * @ingroup tripal_natural_diversity
 */
function tripal_natural_diversity_preprocess_tripal_stock_nd_genotypes(&$variables){

}

/**
 * Implements hook_menu
 *
 * @ingroup tripal_natural_diversity
 */
function tripal_natural_diversity_menu() {
  $items[ 'admin/tripal/tripal_natural_diversity' ]= array(
    'title' => 'Natural Diversity',
    'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of natural_diversity data'),
    'page callback' => 'theme',
    'page arguments' => array('tripal_natural_diversity_admin'),
    'access arguments' => array('administer site configuration'),
    'type' => MENU_NORMAL_ITEM
  );

  $items[ 'admin/tripal/tripal_natural_diversity/configuration' ]= array(
    'title' => 'Configuration',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_natural_diversity_admin'),
    'access arguments' => array('administer site configuration'),
    'type' => MENU_NORMAL_ITEM
  );

  return $items;
}

/**
 * Implements hook_perm()
 *
 *  This function sets the permission for the user to access the information in the database.
 *  This includes creating, inserting, deleting and updating of information in the database
 *
 *
 * @ingroup tripal_natural_diversity
 */
function tripal_natural_diversity_perm() {
  return array(
      'access chado_nd_geolocation content',
      'create chado_nd_geolocation content',
      'delete chado_nd_geolocation content',
      'edit chado_nd_geolocation content',
      'adminster tripal natural_diversity',
  );
}

/**
 * Implement hook_access().
 *
 * This hook allows node modules to limit access to the node types they define.
 *
 *  @param $op
 *  The operation to be performed
 *
 *  @param $node
 *  The node on which the operation is to be performed, or, if it does not yet exist, the
 *  type of node to be created
 *
 *  @param $account
 *  A user object representing the user for whom the operation is to be performed
 *
 *  @return
 *  If the permission for the specified operation is not set then return FALSE. If the
 *  permission is set then return NULL as this allows other modules to disable
 *  access.  The only exception is when the $op == 'create'.  We will always
 *  return TRUE if the permission is set.
 *
 * @ingroup tripal_natural_diversity
 */
function chado_natural_diversity_access($op, $node, $account) {

  if ($op == 'create') {
    if (!user_access('create chado_nd_geolocation content', $account)) {
      return FALSE;
    }
    return TRUE;
  }
  if ($op == 'update') {
    if (!user_access('edit chado_nd_geolocation content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'delete') {
    if (!user_access('delete chado_nd_geolocation content', $account)) {
      return FALSE;
    }
  }
  if ($op == 'view') {
    if (!user_access('access chado_nd_geolocation content', $account)) {
      return FALSE;
    }
  }
  return NULL;
}

/**
 * Implementation of hook_node_info().
 *
 * This node_info, is a simple node that describes the functionallity of the module. It specifies
 * that the title(Project Name) and body(Description) set to true so that they information can be
 * entered
 *
 *
 * @ingroup tripal_natural_diversity
 */
function tripal_natural_diversity_node_info() {
  return array(
      'chado_nd_geolocation' => array(
          'name' => t('ND Geolocation'),
          'module' => 'chado_nd_geolocation',
          'description' => t('A module for interfacing the GMOD chado database with Drupal, providing viewing of nd_geolocation'),
          'has_title' => TRUE,
          'title_label' => t('ND Geolocation'),
          'had_body' => FALSE,
          'body_label' => t('Full Description'),
      )
  );
}