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');

/**
 * @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() {

}

/**
 * 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'),
      'module' => '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/tripal_contact' ]= array(
    'title' => 'Contacts',
    'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of contacts'),
    'page callback' => 'theme',
    'page arguments' => array('tripal_contact_admin'),
    'access arguments' => array('administer tripal contacts'),
    'type' => MENU_NORMAL_ITEM
  );
  
  $items['admin/tripal/tripal_contact/sync'] = array(
    'title' => ' Sync Contacts',
    '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_NORMAL_ITEM,
  );
  
  return $items;
}
  
/**
 * Implements hook_theme(): Register themeing functions for this module
 *
 *
 * @return
 *   An array of themeing functions to register
 *
 */
function tripal_contact_theme() {

  return array(
    'tripal_contact_base' => array(
      'arguments' => array('node' => NULL),
    ),
    'tripal_contact_properties' => array(
      'arguments' => array('node' => NULL)
    ),
    'tripal_contact_relationships' => array(
      'arguments' => array('node' => NULL)
    ),
    'tripal_contact_admin' => array(
      'template' => 'tripal_contact_admin',  
      'arguments' =>  array(NULL),  
      'path' => drupal_get_path('module', 'tripal_contact') . '/theme' 
    ),
  );
}

/**
 * Implement hook_perm().
 */
function tripal_contact_perm() {
  return array(
    'access chado_contact content',
    'create chado_contact content',
    'delete chado_contact content',
    'edit chado_contact content',
    'administer tripal contacts',
  );
}

/**
 * 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 $account
 *  A user object representing the user for whom the operation is to be performed
 *
 *  @return
 *  TRUE
 *
 */
function chado_contact_access($op, $node, $account ) {
  if ($op == 'create') {
    if (!user_access('create chado_contact content', $account)) {
      return FALSE;
      }
  }

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

/**
 * Implementation of tripal_contact_form().
 *
 *
 *
 *  @parm &$node
 *    The node that is created when the database is initialized
 *
 *  @parm $form_state
 *    The state of the form, that has the user entered information that is neccessary for, setting
 *    up the database tables for the contact
 *
 *  @return $form
 *    The information that was enterd allong with
 *
 */
function chado_contact_form(&$node, $form_state) {

  $form = array();

  $contact = $node->contact;

  // get the contact default values.  When this module was first created
  // the contact description was incorrectly stored in the $node->body field.
  // It is better to store it in the Chado tables.  However, the 'description'
  // field of the contact table is only 255 characters.  So, we are going
  // to follow the same as the contact module and store the description in
  // the contactprop table and leave the contact.description field blank.
  // however, for backwards compatibitily, we check to see if the description
  // is in the $node->body field. If it is we'll use that.  When the node is
  // edited the text will be moved out of the body and into the contactprop
  // table where it should belong.
  if ($node->body) {
    $contact_description = $node->body;
  }
  else {
    $contact_description = $node->contact_description;
  }
  if (!$contact_description) {
    $contactprop = tripal_contact_get_property($contact->contact_id, 'contact_description');
    $contact_description = $contactprop->value;
  }

  $form['contact_id'] = array(
    '#type' => 'hidden',
    '#value' => (isset($node->contact_id)) ? $node->contact_id->contact_id : NULL ,
  );
  
  $sql = "
    SELECT CVTS.cvterm_id, CVTS.name
    FROM {cvtermpath} CVTP
      INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
      INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
      INNER JOIN {cv} CV       ON CVTO.cv_id = CV.cv_id
    WHERE 
      CV.name = 'tripal_contact' AND 
      CVTO.name = 'Contact Type' AND
      CVTP.pathdistance = 1      
    ORDER BY CVTS.name ASC 
  ";
  $results = chado_query($sql);
  $contact_types = array();
  $default_type = '';
  while ($contact_type = db_fetch_object($results)) {
    $contact_types[$contact_type->cvterm_id] = $contact_type->name;
    if (strcmp($contact_type->name,"Person") == 0) {
      $default_type = $contact_type->cvterm_id;
    }
  }
  $form['type_id'] = array(
    '#type' => 'select',
    '#title' => t('Contact Type'),
    '#options' => $contact_types,
    '#required' => TRUE,
    '#default_value' => isset($contact->contact_id->type_id) ? $contact->contact_id->type_id : $default_type,
  );
  
  $form['title']= array(
    '#type'          => 'textfield',
    '#title'         => t('Contact Name'),
    '#description'   => t('Enter the name of this contact'),
    '#required'      => TRUE,
    '#default_value' => $contact->name,
    '#weight'        => 1
  );

  $form['contact_description']= array(
    '#type'          => 'textarea',
    '#title'         => t('Contact Description'),
    '#description'   => t('A brief description of the contact'),
    '#required'      => TRUE,
    '#default_value' => $contact_description,
    '#weight'        => 5
  );
  return $form;

}


/**
 * Implementation of tripal_contact_insert().
 *
 * This function inserts user entered information pertaining to the contact instance into the
 * 'contactauthor', 'contactprop', 'chado_contact', 'contact' talble of the database.
 *
 *  @parm $node
 *    Then node which contains the information stored within the node-ID
 *
 *
 */
function chado_contact_insert($node) {
 
  // if a contact_id already exists for this node then it already exists in Chado and 
  // we get here because we are syncing the node.  Therefore, we can skip the insert
  if ($node->contact_id) {
    $contact['contact_id'] = $node->contact_id;
  }
  else {
    // check to see if this contact name already exists.    
    $values =  array('name' => $node->contact_name);
    $options = array('statement_name' => 'sel_contact_na');
    $contact = tripal_core_chado_select('contact', array('contact_id'), $values, $options);
    if (count($contact) > 0) {
      drupal_set_message(t('A contact with this name already exists.', 'error'));
      watchdog('tripal_contact','Insert Contact: A contact with this name already exists. %name',
        array('%name' => $node->contact_name), WATCHDOG_ERROR);
      return FALSE;  
    }
    else {
      $values =  array(
        'name' => $node->title,
        'description' => '',
        'type_id' => $node->type_id
      );
      $options = array('statement_name' => 'ins_contact_nadety');
      $contact = tripal_core_chado_insert('contact', $values, $options);
      if (!$contact) {
        drupal_set_message(t('Could not add the contact'), 'error');
        watchdog('tripal_contact','Could not add the contact',
          array(), WATCHDOG_ERROR);
        return FALSE; 
      }
    }
  }

  if ($contact) {   
   
    // add the description property
    tripal_contact_insert_property($contact['contact_id'], 'contact_description',
      $node->contact_description, TRUE);
    
    // make sure the entry for this contact doesn't already exist in the chado_contact table
    // if it doesn't exist then we want to add it.
    $contact_id = chado_get_id_for_node('contact', $node) ;
    if (!$contact_id) {
       // next add the item to the drupal table
      $sql = "INSERT INTO {chado_contact} (nid, vid, contact_id) ".
             "VALUES (%d, %d, %d)";
      db_query($sql, $node->nid, $node->vid, $contact['contact_id']);
    }
  }
  else {
    drupal_set_message(t('Unable to add contact.', 'warning'));
    watchdog('tripal_contact', 'Insert contact: Unable to create contact where values: %values',
      array('%values' => print_r($values, TRUE)), WATCHDOG_WARNING);
  }
  return TRUE;
}

/*
 *
 * Implements hook_update
 *
 * The purpose of the function is to allow the module to take action when an edited node is being
 * updated. It updates any name changes to the database tables that werec reated upon registering a contact.
 * As well, the database will be changed, so the user changed information will be saved to the database.
 *
 * @param $node
 *   The node being updated
 *
 * @ingroup tripal_contact
 */
function chado_contact_update($node) {
  if ($node->revision) {
    // there is no way to handle revisions in Chado but leave
    // this here just to make not we've addressed it.
  }
  
  $contact_id = chado_get_id_for_node('contact', $node) ;
  
  // check to see if this contact name doens't already exists.    
  $sql = "SELECT contact_id FROM {contact} WHERE NOT contact_id = %d AND name = '%s'";
  $contact = db_fetch_object(chado_query($sql, $contact_id, $node->contact_name));
  if ($contact) {
    drupal_set_message(t('A contact with this name already exists. Cannot perform update.'), 'warning');
    return;  
  }    
  
  // update the contact record
  $match = array(
     'contact_id' => $contact_id,
  );
  $values = array(
    'name' => $node->title,
    'description' => '',
    'type_id' => $node->type_id
  );
  $status = tripal_core_chado_update('contact', $match, $values);
  tripal_contact_update_property($contact_id, 'contact_description', $node->contact_description, 1);
}


/**
 * Implementation of tripal_contact_load().
 *
 *
 * @param $node
 *   The node that is to be accessed from the database
 *
 * @return $node
 *   The node with the information to be loaded into the database
 *
 */
function chado_contact_load($node) {
  // get the feature details from chado
  $contact_id = chado_get_id_for_node('contact', $node);

  $values = array('contact_id' => $contact_id);
  $contact = tripal_core_generate_chado_var('contact', $values); 

  $additions = new stdClass();
  $additions->contact = $contact;
  return $additions;

}

/**
 * Implementation of tripal_contact_delete().
 *
 * This function takes a node and if the delete button has been chosen by the user, the contact
 * and it's details will be removed.Following,given the node-ID, the instance will be deleted from
 * the 'chado_contact' table.
 *
 *  @parm $node
 *    Then node which contains the information stored within the node-ID
 *
 */
function chado_contact_delete(&$node) {

  $contact_id = chado_get_id_for_node('contact', $node);

  // if we don't have a contact id for this node then this isn't a node of
  // type chado_contact or the entry in the chado_contact table was lost.
  if (!$contact_id) {
    return;
  }

  // Remove data from {chado_contact}, {node} and {node_revisions} tables of
  // drupal database
  $sql_del = "DELETE FROM {chado_contact} ".
             "WHERE nid = %d ".
             "AND vid = %d";
  db_query($sql_del, $node->nid, $node->vid);
  $sql_del = "DELETE FROM {node_revisions} ".
             "WHERE nid = %d ".
             "AND vid = %d";
  db_query($sql_del, $node->nid, $node->vid);
  $sql_del = "DELETE FROM {node} ".
             "WHERE nid = %d ".
             "AND vid = %d";
  db_query($sql_del, $node->nid, $node->vid);

  // Remove data from contact and contactprop tables of chado database as well
  chado_query("DELETE FROM {contactprop} WHERE contact_id = %d", $contact_id);
  chado_query("DELETE FROM {contact} WHERE contact_id = %d", $contact_id);
}
/**
 *
 *
 * @ingroup tripal_contact
 */
function tripal_contact_preprocess_tripal_contact_relationships(&$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 = %d
  ";
  $as_subject = chado_query($sql, $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 = %d
  ";
  $as_object = chado_query($sql, $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 ($relationship = db_fetch_object($as_object)) {

     // 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 ($relationship = db_fetch_object($as_subject)) {

     // 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;
}