<?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;
}