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.form.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() {

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

    // Themed Forms
    'chado_contact_node_form' => array(
      'arguments' => array('form'),
    ),
  );
}
/**
 * @ingroup tripal_library
 */
function tripal_contact_block_info() {

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

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

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

  $blocks['contpubs']['info'] = t('Tripal Cotact Publications');
  $blocks['contpubs']['cache'] = BLOCK_NO_CACHE;

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

  if (user_access('access chado_library 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'] = theme('tripal_contact_base', $node);
        break;
      case 'contprops':
        $block['subject'] = t('Properties');
        $block['content'] = theme('tripal_contact_properties', $node);
        break;
      case 'contrels':
        $block['subject'] = t('Relationships');
        $block['content'] = theme('tripal_contact_relationships', $node);
        break;
      case 'contpubs':
        $block['subject'] = t('Publications');
        $block['content'] = theme('tripal_contact_publications', $node);
        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.'),
    ),
  );
}

/**
 * Implement hook_access().
 *
 * This hook allows node modules to limit access to the node types they define.
 *
 *  @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 $op
 *  The operation to be performed
 *
 *  @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 $op == 'create'.  We will always
 *  return TRUE if the permission is set.
 *
 */
function chado_contact_node_access($node, $op, $account ) {
  if ($op == 'create') {
    if (!user_access('create chado_contact content', $account)) {
      return FALSE;
    }
    return TRUE;
  }

  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_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 {
    // we don't want to store the description in the description field as it may be longer than
    // 255 characters, so we'll use a property to store this value.
    $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;
    }

    // now add the properties
    $properties = array(); // stores all of the properties we need to add

    // get the list of properties for easy lookup (without doing lots of database queries
    $properties_list = array();
    $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
        NOT CVTO.name = 'Contact Type'
      ORDER BY CVTS.name ASC
    ";
    $prop_types = chado_query($sql);
    while ($prop = $prop_types->fetchObject()) {
      $properties_list[$prop->cvterm_id] = $prop->name;
    }

    // get the properties that should be added. Properties are in one of two forms:
    //  1) prop_value-[type id]-[index]
    //  2) new_value-[type id]-[index]
    //  3) new_id, new_value
    foreach ($node as $name => $value) {
      if (preg_match('/^new_value-(\d+)-(\d+)/', $name, $matches)) {
        $type_id = $matches[1];
        $index = $matches[2];
        $name = $properties_list[$type_id];
        $properties[$name][$index] = trim($value);
      }
    }
    if ($node->new_id and $node->new_value) {
      $type_id = $node->new_id;
      $index = count($properties[$name]);
      $name = $properties_list[$type_id];
      $properties[$name][$index] = trim($node->new_value);
    }
    // now add in the properties
    foreach ($properties as $property => $elements) {
      foreach ($elements as $rank => $value) {

        $status = tripal_contact_insert_property($contact['contact_id'], $property, $value, FALSE);
        if (!$status) {
          drupal_set_message("Error cannot add property: $property", "error");
          watchdog('t_contact', "Error cannot add property: %prop",
          array('%property' => $property), WATCHDOG_ERROR);
        }
      }
    }
  }

  // add the record to the chado_contact table in Drupal
  if ($contact) {

    // add the description property
    tripal_contact_insert_property($contact['contact_id'], 'contact_description',
      $node->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', $node->nid) ;
    if (!$contact_id) {
       // next add the item to the drupal table
      $sql = "INSERT INTO {chado_contact} (nid, vid, contact_id) ".
             "VALUES (:nid, :vid, :contact_id)";
      db_query($sql, array(':nid'=> $node->nid, ':vid' => $node->vid, ':contact_id' => $contact['contact_id']));
    }
  }
  else {
    drupal_set_message(t('Unable to add contact.', 'warning'));
    watchdog('tripal_contact', 'Insert contact: Unable to create contact where values: %values',
      array('%values' => print_r($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->nid) ;

  // check to see if this contact name doens't already exists.
  $sql = "SELECT contact_id FROM {contact} WHERE NOT contact_id = :contact_id AND name = :name";
  $contact = chado_query($sql, array(':contact_id' => $contact_id, ':name' => $node->contact_name))->fetchObject();
  if ($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, $values);
  if (!$status) {
    drupal_set_message("Error updating contact", "error");
    watchdog('t_contact', "Error updating contact", array(), WATCHDOG_ERROR);
    return;
  }

  // now update the properties
  $properties = array(); // stores all of the properties we need to add

  // get the list of properties for easy lookup (without doing lots of database queries
  $properties_list = array();
  $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
      NOT CVTO.name = 'Contact Type'
    ORDER BY CVTS.name ASC
  ";
  $prop_types = chado_query($sql);
  while ($prop = $prop_types->fetchObject()) {
    $properties_list[$prop->cvterm_id] = $prop->name;
  }

  // get the properties that should be added. Properties are in one of three forms:
  //  1) prop_value-[type id]-[index]
  //  2) new_value-[type id]-[index]
  //  3) new_id, new_value
  //  dpm($node);
  foreach ($node as $key => $value) {
    if (preg_match('/^prop_value-(\d+)-(\d+)/', $key, $matches)) {
      $type_id = $matches[1];
      $index = $matches[2];
      $name = $properties_list[$type_id];
      $properties[$name][$index] = trim($value);
    }
    if (preg_match('/^new_value-(\d+)-(\d+)/', $key, $matches)) {
      $type_id = $matches[1];
      $index = $matches[2];
      $name = $properties_list[$type_id];
      $properties[$name][$index] = trim($value);
    }
  }
  if ($node->new_id and $node->new_value) {
    $type_id = $node->new_id;
    $name = $properties_list[$type_id];
    $index = count($properties[$name]);
    $properties[$name][$index] = trim($node->new_value);
  }

  // now add in the properties by first removing any the contact
  // already has and adding the ones we have
  tripal_core_chado_delete('contactprop', array('contact_id' => $contact_id));
  foreach ($properties as $property => $elements) {
    foreach ($elements as $rank => $value) {
      $status = tripal_contact_insert_property($contact_id, $property, $value, FALSE);
      if (!$status) {
        drupal_set_message("Error cannot add property: '$property'", "error");
        watchdog('t_contact', "Error cannot add property: '%prop'",
        array('%prop' => $property), WATCHDOG_ERROR);
      }
    }
  }

  tripal_contact_update_property($contact_id, 'contact_description', $node->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->nid);

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

  // get the contact description and replace the contact.description field with this one
  $values = array(
    'contact_id' => $contact->contact_id,
    'type_id' => array(
      'name' => 'contact_description',
    ),
  );
  $options = array(
    'return_array' => 1,
    'include_fk' => array('type_id' => 1),
  );
  $description = tripal_core_generate_chado_var('contactprop', $values, $options);
  if (count($description) == 1) {
    $description = tripal_core_expand_chado_vars($description, 'field', 'contactprop.value');
    $contact->description = $description[0]->value;
  }


  $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->nid);

  // 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
  $sql_del = "DELETE FROM {chado_contact} WHERE nid = :nid AND vid = :vid";
  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
  $sql_del = "DELETE FROM {node_revision} WHERE nid = :nid AND vid = :vid";
  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
  $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
  db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));

  // Remove data from contact and contactprop tables of chado database as well
  chado_query("DELETE FROM {contactprop} WHERE contact_id = :contact_id", array(':contact_id' => $contact_id));
  chado_query("DELETE FROM {contact} WHERE contact_id = :contact_id", array(':contact_id' => $contact_id));
}
/**
 *
 *
 * @ingroup tripal_contact
 */
function tripal_contact_preprocess_tripal_contact_relationships(&$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 = :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;
  }
}