tripal/tripal_contact/tripal_contact.module

<?php

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

require('api/tripal_contact.api.inc');
require('includes/contact_sync.inc');
require('includes/tripal_contact.admin.inc');
require('includes/tripal_contact.chado_node.inc');

/**
 * @defgroup tripal_contact Contact Module
 * @ingroup tripal_modules
 * @{
 * Currently this module only provides support for integration with Drupal
 * views and some support for querying using the Tripal Core API.
 *
 * This module needs further development to support full management of
 * contact information within Chado, and full definitions for foreign
 * key relationships in Chado.
 * @}
 */


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

/**
 *
 * @ingroup tripal_contact
 */
function tripal_contact_init() {
  drupal_add_js(drupal_get_path('module', 'tripal_contact') . '/theme/js/tripal_contact.js');
  drupal_add_css(drupal_get_path('module', 'tripal_contact') . '/theme/css/tripal_contact.css');

}

/**
 * Implementation of hook_tripal_contact_node_info().
 *
 * This node_info, is a simple node that describes the functionallity of the module.
 *
 */
function tripal_contact_node_info() {

  return array(
    'chado_contact' => array(
      'name' => t('Contact'),
      'base' => 'chado_contact',
      'description' => t('A contact from the Chado database'),
      'title_label' => t('Article Title'),
      'body_label' => t('Abstract'),
      'has_title' => TRUE,
      'has_body' => FALSE,
    ),
  );
}

/**
 * Tripal-contact-Menu
 *
 * Implemets hook_menu(): Adds menu items for the tripal_contact module menu. This section
 * gives the outline for the main menu of the Tripal-contact module
 *
 * @return
 *   An array of menu items that is visible within the Drupal Menu, returned as soon
 *   as the program is ran
 */
function tripal_contact_menu() {

  $items = array();

  $items['admin/tripal/chado/tripal_contact']= array(
    'title' => 'Contacts',
    'description' => ('Model persons, institutes, groups, organizations, etc.'),
    'page callback' => 'tripal_contact_admin_contact_view',
    'access arguments' => array('administer tripal contacts'),
    'type' => MENU_NORMAL_ITEM
  );

  $items['admin/tripal/chado/tripal_contact/configuration'] = array(
    'title' => 'Settings',
    'description' => 'Integration of Chado contacts.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_contact_admin'),
    'access arguments' => array('administer tripal contact'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 5
  );

  $items['admin/tripal/chado/tripal_contact/help']= array(
    'title' => 'Help',
    'description' => ('Help with the contact module.'),
    'page callback' => 'theme',
    'page arguments' => array('tripal_contact_help'),
    'access arguments' => array('administer tripal contacts'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 10
  );

  $items['admin/tripal/chado/tripal_contact/sync'] = array(
    'title' => ' Sync',
    'description' => 'Sync contacts in Chado with Drupal',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_contact_sync_form'),
    'access arguments' => array('administer tripal contacts'),
    'type' => MENU_LOCAL_TASK,
    'weight' => 0
  );

  // AJAX calls for adding/removing properties to a contact
  $items['tripal_contact/properties/add'] = array(
    'page callback' => 'tripal_contact_property_add',
    'access arguments' => array('edit chado_contact content'),
    'type ' => MENU_CALLBACK,
  );
  $items['tripal_contact/properties/description'] = array(
    'page callback' => 'tripal_contact_property_get_description',
    'access arguments' => array('edit chado_contact content'),
    'type ' => MENU_CALLBACK,
  );
  $items['tripal_contact/properties/minus/%/%'] = array(
    'page callback' => 'tripal_contact_property_delete',
    'page arguments' => array(3, 4),
    'access arguments' => array('edit chado_contact content'),
    'type ' => MENU_CALLBACK,
  );

  return $items;
}

/**
 * Implements hook_theme(): Register themeing functions for this module
 *
 *
 * @return
 *   An array of themeing functions to register
 *
 */
function tripal_contact_theme($existing, $type, $theme, $path) {
  $core_path = drupal_get_path('module', 'tripal_core');
  
  $items = array(
    'node__chado_contact' => array(
      'template' => 'node--chado-generic',
      'render element' => 'node',
      'base hook' => 'node',
      'path' => "$core_path/theme",
    ),
    'tripal_contact_base' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_contact_base',
      'path' => "$path/theme/tripal_contact",
    ),
    'tripal_contact_properties' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_contact_properties',
      'path' => "$path/theme/tripal_contact",
    ),
    'tripal_contact_relationships' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_contact_relationships',
      'path' => "$path/theme/tripal_contact",
    ),
    'tripal_contact_publications' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_contact_publications',
      'path' => "$path/theme/tripal_contact",
    ),
    'tripal_contact_help' => array(
      'template' => 'tripal_contact_help',
      'variables' =>  array(NULL),
      'path' => "$path/theme",
    ),
    'tripal_contact_teaser' => array(
      'variables' => array('node' => NULL),
      'template' => 'tripal_contact_teaser',
      'path' => "$path/theme/tripal_contact",
    ),
  );
  return $items;
}
/**
 * @ingroup tripal_contact
 */
function tripal_contact_block_info() {

  $blocks['contbase']['info'] = t('Tripal Contact Details');
  $blocks['contbase']['cache'] = 'DRUPAL_NO_CACHE';

  $blocks['contprops']['info'] = t('Tripal Contact Properties');
  $blocks['contprops']['cache'] = 'DRUPAL_NO_CACHE';

  $blocks['contrels']['info'] = t('Tripal Contact Relationships');
  $blocks['contrels']['cache'] = 'DRUPAL_NO_CACHE';

  $blocks['contpubs']['info'] = t('Tripal Contact Publications');
  $blocks['contpubs']['cache'] = 'DRUPAL_NO_CACHE';

  return $blocks;
}
/**
 * @ingroup tripal_contact
 */
function tripal_contact_block_view($delta = '') {

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

    $block = array();
    switch ($delta) {
      case 'contbase':
        $block['subject'] = t('Details');
        $block['content'] = array(
          '#theme' => 'tripal_contact_base', 
          '#nodes' => $node,
          '#title' => '',
        );
        break;
      case 'contprops':
        $block['subject'] = t('Properties');
        $block['content'] = array(
          '#theme' => 'tripal_contact_properties', 
          '#nodes' => $node,
          '#title' => '',
        );
        break;
      case 'contrels':
        $block['subject'] = t('Relationships');
        $block['content'] = array(
          '#theme' => 'tripal_contact_relationships', 
          '#nodes' => $node,
          '#title' => '',
        );
        break;
      case 'contpubs':
        $block['subject'] = t('Publications');
        $block['content'] = array(
          '#theme' => 'tripal_contact_publications', 
          '#nodes' => $node,
          '#title' => '',
        );
        break;
      default :
    }
    return $block;
  }
}

/**
 * Implement hook_perm().
 */
function tripal_contact_permissions() {
  return array(
    'access chado_contact content' => array(
      'title' => t('View Contacts'),
      'description' => t('Allow users to view contact pages.'),
    ),
    'create chado_contact content' => array(
      'title' => t('Create Contacts'),
      'description' => t('Allow users to create new contact pages.'),
    ),
    'delete chado_contact content' => array(
      'title' => t('Delete Contacts'),
      'description' => t('Allow users to delete contact pages.'),
    ),
    'edit chado_contact content' => array(
      'title' => t('Edit Contacts'),
      'description' => t('Allow users to edit contact pages.'),
    ),
    'adminster tripal contact' => array(
      'title' => t('Administer Contacts'),
      'description' => t('Allow users to administer all contacts.'),
    ),
  );
}


/**
 *
 *
 * @ingroup tripal_contact
 */
function tripal_contact_preprocess_tripal_contact_relationships(&$variables) {
  // we want to provide a new variable that contains the matched contacts.
  $contact = $variables['node']->contact;

  // normally we would use tripal_core_expand_chado_vars to expand our
  // organism object and add in the relationships, however whan a large
  // number of relationships are present this significantly slows the
  // query, therefore we will manually perform the query
  $sql = "
    SELECT C.name, C.contact_id, CP.nid, CVT.name as rel_type
    FROM {contact_relationship} PR
      INNER JOIN {contact} C              ON PR.object_id  = C.contact_id
      INNER JOIN {cvterm} CVT             ON PR.type_id    = CVT.cvterm_id
      LEFT  JOIN public.chado_contact CP  ON C.contact_id  = CP.contact_id
    WHERE PR.subject_id = :contact_id
  ";
  $as_subject = chado_query($sql, array(':contact_id' => $contact->contact_id));
  $sql = "
    SELECT C.name, C.contact_id, CP.nid, CVT.name as rel_type
    FROM {contact_relationship} PR
      INNER JOIN {contact} C              ON PR.subject_id = C.contact_id
      INNER JOIN {cvterm} CVT             ON PR.type_id    = CVT.cvterm_id
      LEFT  JOIN public.chado_contact CP  ON C.contact_id  = CP.contact_id
    WHERE PR.object_id = :contact_id
  ";
  $as_object = chado_query($sql, array(':contact_id' => $contact->contact_id));

  // combine both object and subject relationshisp into a single array
  $relationships = array();
  $relationships['object'] = array();
  $relationships['subject'] = array();

  // iterate through the object relationships
  while ($relationship = $as_object->fetchObject()) {

     // get the relationship and child types
     $rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
     $sub_type = t(preg_replace('/_/', " ", $relationship->sub_type));

     if (!array_key_exists($rel_type, $relationships['object'])) {
       $relationships['object'][$rel_type] = array();
     }
     if (!array_key_exists($sub_type, $relationships['object'][$rel_type])) {
       $relationships['object'][$rel_type][$sub_type] = array();
     }
     $relationships['object'][$rel_type][$sub_type][] = $relationship;
  }

  // now add in the subject relationships
  while ($relationship = $as_subject->fetchObject()) {

     // get the relationship and child types
     $rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
     $obj_type = t(preg_replace('/_/', " ", $relationship->obj_type));

     if (!array_key_exists($rel_type, $relationships['subject'])) {
       $relationships['subject'][$rel_type] = array();
     }
     if (!array_key_exists($obj_type, $relationships['subject'][$rel_type])) {
       $relationships['subject'][$rel_type][$obj_type] = array();
     }
     $relationships['subject'][$rel_type][$obj_type][] = $relationship;
  }

  $contact->all_relationships = $relationships;
}

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

/**
 *
 * @ingroup tripal_feature
 */
function tripal_contact_node_view($node, $view_mode, $langcode) {
  switch ($node->type) {
    case 'chado_contact':
      // Show feature browser and counts
      if ($view_mode == 'full') {
        $node->content['tripal_contact_base'] = array(
          '#value' => theme('tripal_contact_base', array('node' => $node)),
        );
        $node->content['tripal_contact_properties'] = array(
          '#value' => theme('tripal_contact_properties', array('node' => $node)),
        );
        $node->content['tripal_contact_publications'] = array(
          '#value' => theme('tripal_contact_publications', array('node' => $node)),
        );
        $node->content['tripal_contact_relationships'] = array(
          '#value' => theme('tripal_contact_relationships', array('node' => $node)),
        );
      }
      if ($view_mode == 'teaser') {
        $node->content['tripal_contact_teaser'] = array(
          '#value' => theme('tripal_contact_teaser', array('node' => $node)),
        );
      }
      break;
  }
}