<?php
/**
* @file
* Implements Tripal Stock Module hooks
*/
/**
* @defgroup tripal_stock Stock Module
* @{
* Provides functions for managing chado stocks including creating details pages for each stock
*
* The Tripal Stock Module provides functionality for adding, editing, deleting and accessing chado
* stocks. The stock module was designed to store information about stock collections in a
* laboratory. What is called a stock could also be called a strain or an accession. There is a lot
* in common between a Drosophila stock and a Saccharomyces strain and an Arabidopsis line. They all
* come from some taxon, have genotypes, physical locations in the lab, some conceivable
* relationship with a publication, some conceivable relationship with a sequence feature (such as a
* transgene), and could be described by some ontology term. For more information about the chado
* Stock Module see the GMOD Wiki Page (http://gmod.org/wiki/Chado_Stock_Module)
* @}
* @ingroup tripal_modules
*/
require("tripal_stock-administration.inc");
require("tripal_stock.api.inc");
require("other_module_api_functions.inc");
require("tripal_stock-secondary_tables.inc");
require("tripal_stock-properties.inc");
require("tripal_stock-relationships.inc");
require("tripal_stock-db_references.inc");
/**
* Implements hook_menu(): Adds menu items for the tripal_stock
*
* @return
* Menu definitions for the tripal_stock
*
* @ingroup tripal_stock
*/
function tripal_stock_menu() {
$items = array();
//Administrative settings menu-----------------
$items['admin/tripal/tripal_stock'] = array(
'title' => 'Stocks',
'description' => 'Basic Description of Tripal Stock Module Functionality',
'page callback' => 'tripal_stock_module_description_page',
'access arguments' => array('administer site configuration'),
'type' => MENU_NORMAL_ITEM
);
$items['admin/tripal/tripal_stock/configuration'] = array(
'title' => 'Configuration',
'description' => 'Settings for Chado Stocks',
'page callback' => 'drupal_get_form',
'page arguments' => array('tripal_stock_admin'),
'access arguments' => array('administer site configuration'),
'type' => MENU_NORMAL_ITEM
);
// Adding Secondary Properties-----------------
$items['node/%cs_node/properties'] = array(
'title' => 'Add Properties & Synonyms',
'description' => 'Settings for Chado Stocks',
'page callback' => 'tripal_stock_add_ALL_property_page',
'page arguments' => array(1),
'access arguments' => array('create chado_stock content'),
'type' => MENU_CALLBACK
);
$items['node/%cs_node/db_references'] = array(
'title' => 'Add Database References',
'description' => 'Settings for Chado Stocks',
'page callback' => 'tripal_stock_add_ALL_dbreferences_page',
'page arguments' => array(1),
'access arguments' => array('create chado_stock content'),
'type' => MENU_CALLBACK
);
$items['node/%cs_node/relationships'] = array(
'title' => 'Add Relationships',
'description' => 'Settings for Chado Stocks',
'page callback' => 'tripal_stock_add_ALL_relationships_page',
'page arguments' => array(1),
'access arguments' => array('create chado_stock content'),
'type' => MENU_CALLBACK
);
//Edit/Deleting Secondary Properties-------------
$items['node/%cs_node/edit_properties'] = array(
'title' => 'Edit Properties',
'description' => 'Settings for Chado Stocks',
'page callback' => 'tripal_stock_edit_ALL_properties_page',
'page arguments' => array(1),
'access arguments' => array('edit chado_stock content'),
'type' => MENU_LOCAL_TASK,
'weight' => 8,
);
$items['node/%cs_node/edit_relationships'] = array(
'title' => 'Edit Relationships',
'description' => 'Settings for Chado Stocks',
'page callback' => 'tripal_stock_edit_ALL_relationships_page',
'page arguments' => array(1),
'access arguments' => array('edit chado_stock content'),
'type' => MENU_LOCAL_TASK,
'weight' => 9,
);
$items['node/%cs_node/edit_db_references'] = array(
'title' => 'Edit DB References',
'description' => 'Settings for Chado Stocks',
'page callback' => 'tripal_stock_edit_ALL_dbreferences_page',
'page arguments' => array(1),
'access arguments' => array('edit chado_stock content'),
'type' => MENU_LOCAL_TASK,
'weight' => 10,
);
return $items;
}
/**
* Implements Menu wildcard_load hook
*
* Purpose: Allows the node ID of a chado stock to be dynamically
* pulled from the path. The node is loaded from this node ID
* and supplied to the page as an arguement. This is an example
* of dynamic argument replacement using wildcards in the path.
*
* @param $nid
* The node ID passed in from the path
*
* @return
* The node object with the passed in nid
*
* @ingroup tripal_stock
*/
function cs_node_load($nid) {
if (is_numeric($nid)) {
$node = node_load($nid);
if ($node->type == 'chado_stock') {
return $node;
}
}
return FALSE;
}
/**
* Implementation of hook_perm().
*
* Purpose: Set the permission types that the chado stock module uses
*
* @return
* Listing of the possible permission catagories
*
* @ingroup tripal_stock
*/
function tripal_stock_perm() {
return array(
'access chado_stock content',
'create chado_stock content',
'edit chado_stock content',
'delete chado_stock content'
);
}
/**
* Implements hook_access(): Maps permission catagories to actions
*
* @param $op
* The operation current operation: one of create, update, delete
* @param $node
* The node object the current operation is being performed on
* @param $account
* A user object representing the user for whom the operation is to be performed
*
* @return
* TRUE grants access; FALSE denies it
*
* @ingroup tripal_stock
*/
function chado_stock_access($op, $node, $account) {
if ($op == 'create') {
if (!user_access('create chado_stock content', $account)) {
return FALSE;
}
}
if ($op == 'update') {
if (!user_access('edit chado_stock content', $account)) {
return FALSE;
}
}
if ($op == 'delete') {
if (!user_access('delete chado_stock content', $account)) {
return FALSE;
}
}
if ($op == 'view') {
if (!user_access('access chado_stock content', $account)) {
return FALSE;
}
}
return NULL;
}
/**
* Implements hook_views_api()
*
* Purpose: Essentially this hook tells drupal that there is views support for
* for this module which then includes tripal_stock.views.inc where all the
* views integration code is
*
* @return
* An array with fields important for views integration
*
* @ingroup tripal_stock
*/
function tripal_stock_views_api() {
return array(
'api' => 2.0,
);
}
/**
* Implements hook_theme(): Register themeing functions for this module
*
* @return
* An array of themeing functions to register
*
* @ingroup tripal_stock
*/
function tripal_stock_theme() {
return array(
// Property edit forms--------------------------
'tripal_stock_edit_ALL_properties_form' => array(
'arguments' => array('form'),
'function' => 'theme_tripal_stock_edit_ALL_properties_form',
),
'tripal_stock_edit_ALL_db_references_form' => array(
'arguments' => array('form'),
'function' => 'theme_tripal_stock_edit_ALL_db_references_form',
),
'tripal_stock_edit_ALL_relationships_form' => array(
'arguments' => array('form'),
'function' => 'theme_tripal_stock_edit_ALL_relationships_form',
),
// Block Templates------------------------------
'tripal_stock_base' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_stock_base',
),
'tripal_stock_properties' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_stock_properties',
),
'tripal_stock_references' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_stock_references',
),
'tripal_stock_relationships' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_stock_relationships',
),
'tripal_stock_synonyms' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_stock_synonyms',
),
'tripal_stock_collections' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_stock_collections',
),
'tripal_stock_collections' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_stock_collections',
),
'tripal_stock_phenotypes' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_stock_phenotypes',
),
'tripal_stock_genotypes' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_stock_genotypes',
),
'tripal_stock_locations' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_stock_locations',
),
'tripal_organism_stocks' => array(
'arguments' => array('node' => NULL),
'template' => 'tripal_organism_stocks',
),
);
}
/**
* Implements hook_node_info(): registers a stock node type
*
* @return
* An array describing various details of the node
*
* @ingroup tripal_stock
*/
function tripal_stock_node_info() {
return array(
'chado_stock' => array(
'name' => t('Stock'),
'module' => 'chado_stock',
'description' => t('A Chado Stock is a collection of material that can be sampled and have experiments performed on it.'),
'has_title' => TRUE,
'has_body' => FALSE,
),
);
}
/**
* Implements hook_load(): Prepares the chado_stock node
*
* @param $node
* The basic node containing all variables common to all nodes
*
* @return
* A stock node containing all the variables from the basic node and all stock specific variables
*
* @ingroup tripal_stock
*/
function chado_stock_load($node) {
// get the stock details from chado
$stock_id = chado_get_id_for_node('stock', $node);
// build the variable with all the stock details
$values = array('stock_id' => $stock_id);
$stock = tripal_core_generate_chado_var('stock', $values);
// add this to the node
$additions = new stdClass();
$additions->stock = $stock;
return $additions;
}
/**
* Implements hook_form(): Creates the main Add/Edit/Delete Form for chado stocks
*
* Parts to be added by this form
* name,
* uniquename,
* description,
* type => select from cvterm with key cvterm_id,
* organism => select from available with key organism_id
* main_db_reference => accession, version, description, db_name(select from dropdown)
*
* @param $node
* An empty node object on insert OR the current stock node object on update
* @param $form_state
* The current state of the form
*
* @return
* A description of the form to be rendered by drupal_get_form()
*
* @ingroup tripal_stock
*/
function chado_stock_form($node, $form_state) {
// Expand all fields needed
$fields_needed = array('stock.uniquename', 'stock.name', 'stock.stock_id', 'stock.type_id', 'stock.organism_id', 'stock.description', 'stock.dbxref_id', 'dbxref.accession', 'dbxref.description', 'dbxref.db_id', 'db.db_id');
foreach ($fields_needed as $field_name) {
// Check to see if it's excluded and expand it if so
if ($node->expandable_fields) {
if (in_array($field_name, $node->expandable_fields)) {
$node = tripal_core_expand_chado_vars($node, 'field', $field_name);
}
}
}
// This defines the path for the next step in a simulated multipart form
// NOTE: The %node gets replaced with the nid in insert
$form['next_step_path'] = array(
'#type' => 'hidden',
'#value' => 'node/%node/properties'
);
// If you don't want a multipart form set this to false
// Will then do default redirect (to new node) on submit
$form['simulate_multipart'] = array(
'#type' => 'textfield',
'#attributes' => array('style' => "display:none"),
'#default_value' => TRUE
);
if (!isset($node->stock->uniquename)) {
$form['progress'] = array(
'#type' => 'item',
'#value' => tripal_stock_add_chado_properties_progress('main')
);
}
$form['names'] = array(
'#type' => 'fieldset',
'#title' => t('Stock Name')
);
$form['names']['title'] = array(
'#type' => 'textfield',
'#title' => t('Name'),
'#default_value' => $node->stock->name,
'#required' => TRUE
);
$form['names']['uniquename'] = array(
'#type' => 'textfield',
'#title' => t('Unique Name'),
'#default_value' => $node->stock->uniquename,
'#required' => TRUE
);
$form['names']['stock_id'] = array(
'#type' => 'hidden',
'#value' => $node->stock->stock_id
);
$form['details'] = array(
'#type' => 'fieldset',
'#title' => t('Stock Details')
);
$type_options = tripal_cv_get_cvterm_options( variable_get('chado_stock_types_cv', 'NULL') );
$type_options[0] = 'Select a Type';
if ($node->nid == '') {
$type_default = 0; }
else { $type_default = $node->stock->type_id->cvterm_id; }
$form['details']['type_id'] = array(
'#type' => 'select',
'#title' => t('Type of Stock'),
'#options' => $type_options,
'#default_value' => $type_default,
'#required' => TRUE,
);
$stock_oganism_options = tripal_organism_get_organism_options();
$stock_oganism_options[0] = 'Select An Organism';
if ($node->nid == '') {
$organism_default = 0; }
else { $organism_default = $node->stock->organism_id->organism_id; }
$form['details']['organism_id'] = array(
'#type' => 'select',
'#title' => t('Source Organism for stock'),
'#default_value' => $organism_default,
'#options' => $stock_oganism_options,
'#required' => TRUE
);
$form['details']['stock_description'] = array(
'#type' => 'textarea',
'#title' => t('Notes'),
'#default_value' => $node->stock->description,
'#description' => t('Briefly enter any notes on the above stock. This should not include phenotypes or genotypes.'),
);
$form['database_reference'] = array(
'#type' => 'fieldset',
'#title' => t('Stock Database Reference')
);
$form['database_reference']['accession'] = array(
'#type' => 'textfield',
'#title' => t('Accession'),
'#default_value' => $node->stock->dbxref_id->accession
);
$form['database_reference']['db_description'] = array(
'#type' => 'textarea',
'#title' => t('Description of Database Reference'),
'#default_value' => $node->stock->dbxref_id->description,
'#description' => t('Optionally enter a description about the database accession.')
);
$db_options = tripal_db_get_db_options();
$db_options[0] = 'Select a Database';
if ($node->nid == '') {
$db_default = 0; }
else { $db_default = $node->stock->dbxref_id->db_id->db_id; }
$form['database_reference']['database'] = array(
'#type' => 'select',
'#title' => t('Database'),
'#options' => $db_options,
'#default_value' => $db_default
);
return $form;
}
/**
* Implements hook_validate(): Validate the input from the chado_stock node form
*
* @param $node
* The current node including fields with the form element names and submitted values
* @param $form
* A description of the form to be rendered by drupal_get_form()
*
* @ingroup tripal_stock
*/
function chado_stock_validate($node, &$form) {
$int_in_chado_sql = "SELECT count(*) as count FROM %s WHERE %s=%d";
$string_in_chado_sql = "SELECT count(*) as count FROM %s WHERE %s='%s'";
// Validate Uniquename only if add
if (empty($node->stock_id)) {
$previous_db = tripal_db_set_active('chado');
$chado_row = db_fetch_object(db_query("SELECT * FROM {stock} WHERE uniquename='" . $node->uniquename . "'"));
tripal_db_set_active($previous_db);
if (!empty($chado_row->stock_id)) {
$drupal_row = db_fetch_object(db_query("SELECT * FROM {chado_stock} WHERE stock_id=" . $chado_row->stock_id));
if (!empty($drupal_row->nid)) {
$link = l('node/' . $drupal_row->nid, $node->uniquename);
form_set_error('uniquename', "There is already a stock with that uniquename $link. Please enter another uniquename.");
}
else {
form_set_error('uniquename', "There is already a stock with that uniquename (although it's not sync'd with drupal). Please enter another uniquename.");
}
}
}
// Check Type of Stock is valid cvterm_id in chado ( $form['values']['details']['type_id'] )
if ( $node->type_id == 0) {
form_set_error('type_id', 'Please select a type of stock.');
}
else {
$previous_db = tripal_db_set_active('chado');
$num_rows = db_fetch_object(db_query($int_in_chado_sql, 'cvterm', 'cvterm_id', $node->type_id));
tripal_db_set_active($previous_db);
if ( $num_rows->count != 1) {
form_set_error('type_id', "The type you selected is not valid. Please choose another one. (CODE:$num_rows)"); }
}
// Check Source Organism is valid organism_id in chado ( $form['values']['details']['organism_id'] )
if ( $node->organism_id == 0) {
form_set_error('organism_id', 'Please select a source organism for this stock');
}
else {
$previous_db = tripal_db_set_active('chado');
$num_rows = db_fetch_object(db_query($int_in_chado_sql, 'organism', 'organism_id', $node->organism_id));
tripal_db_set_active($previous_db);
if ( $num_rows->count != 1 ) {
form_set_error('organism_id', "The organism you selected is not valid. Please choose another one. (CODE:$num_rows)"); }
}
// Check if Accession also database
if ($node->accession != '') {
if ($node->database == 0) {
// there is an accession but no database selected
form_set_error('database', 'You need to enter both a database and an accession for that database in order to add a database reference.');
}
}
else {
if ($node->database > 0) {
// there is a database selected but no accession
form_set_error('accession', 'You need to enter both a database and an accession for that database in order to add a database reference.');
}
}
// Check database is valid db_id in chado ( $form['values']['database_reference']['database'] )
if ( $node->database > 0) {
$previous_db = tripal_db_set_active('chado');
$num_rows = db_fetch_object(db_query($int_in_chado_sql, 'db', 'db_id', $node->database));
tripal_db_set_active($previous_db);
if ($num_rows->count != 1) {
form_set_error('database', 'The database you selected is not valid. Please choose another one.'); }
}
}
/**
* Implements hook_insert(): Inserts data from chado_stock_form() into drupal and chado
*
* @param $node
* The current node including fields with the form element names and submitted values
*
* @return
* TRUE if the node was successfully inserted into drupal/chado; FALSE otherwise
*
* @ingroup tripal_stock
*/
function chado_stock_insert($node) {
//If the chado stock exists
// then don't create but simply link to node
if ($node->chado_stock_exists) {
if (!empty($node->stock_id)) {
db_query(
"INSERT INTO {chado_stock} (nid, vid, stock_id) "
."VALUES (%d, %d, %d)",
$node->nid,
$node->vid,
$node->stock_id
);
}
return $node;
}
// create dbxref
if ( !empty($node->accession) ) {
if ( !empty($node->database) ) {
$values = array(
'db_id' => $node->database,
'accession' => $node->accession,
);
if (!tripal_core_chado_select('dbxref', array(dbxref_id), $values)) {
$values['description'] = $node->db_description;
$values['version'] = '1';
$dbxref_status = tripal_core_chado_insert('dbxref', $values);
if (!$dbxref_status) {
drupal_set_message(t('Unable to add database reference to this stock.'), 'warning');
watchdog('tripal_stock',
'Insert Stock: Unable to create dbxref where values:%values',
array('%values' => print_r($values, TRUE)),
WATCHDOG_WARNING
);
}
}
else { $dbxref_status = 1; }
}
}
// create stock
if ($dbxref_status) {
$values = array(
'dbxref_id' => array(
'db_id' => $node->database,
'accession' => $node->accession
),
'organism_id' => $node->organism_id,
'name' => $node->title,
'uniquename' => $node->uniquename,
'description' => $node->stock_description,
'type_id' => $node->type_id
);
$stock_status = tripal_core_chado_insert('stock', $values);
}
else {
$values = array(
'organism_id' => $node->organism_id,
'name' => $node->title,
'uniquename' => $node->uniquename,
'description' => $node->stock_description,
'type_id' => $node->type_id
);
$stock_status = tripal_core_chado_insert('stock', $values);
}
// create drupal chado_stock entry
if ($stock_status) {
$values = array(
'organism_id' => $node->organism_id,
'uniquename' => $node->uniquename,
'type_id' => $node->type_id
);
$chado_stock = tripal_core_chado_select('stock', array('stock_id'), $values);
if (!empty($chado_stock[0]->stock_id)) {
db_query(
"INSERT INTO {chado_stock} (nid, vid, stock_id) "
."VALUES (%d, %d, %d)",
$node->nid,
$node->vid,
$chado_stock[0]->stock_id
);
//Move on to next stage of Stock Creation based on next_stage_path field
if ($node->simulate_multipart) {
$next_stage_path = preg_replace('/%node/', $node->nid, $node->next_step_path);
$_REQUEST['destination'] = $next_stage_path;
}
}
else {
drupal_set_message(t('Error during stock creation.'), 'error');
watchdog('tripal_stock',
'Insert Stock: Unable to find newly created stock where values:%values',
array('%values' => print_r($values, TRUE)),
WATCHDOG_ERROR
);
return FALSE;
}
}
else {
drupal_set_message(t('Error during stock creation.'), 'error');
watchdog('tripal_stock',
'Insert Stock: Unable to create stock where values:%values',
array('%values' => print_r($values, TRUE)),
WATCHDOG_WARNING
);
return FALSE;
}
}
/**
* Implements hook_update(): Handles Editing/Updating of main stock info
*
* NOTE: Currently just writes over all old data
*
* @param $node
* The current node including fields with the form element names and submitted values
*
* @return
* TRUE if the node was successfully updated in drupal/chado; FALSE otherwise
*
* @ingroup tripal_stock
*/
function chado_stock_update($node) {
if ($node->revision) {
chado_stock_insert($node);
}
else {
//update dbxref
if ($node->database) {
if ($node->accession) {
$dbxref_mode = '';
$stock = tripal_core_chado_select(
'stock',
array('dbxref_id', 'type_id'),
array('stock_id' => $node->stock_id)
);
if ($stock[0]->dbxref_id) {
$values = array(
'db_id' => $node->database,
'accession' => $node->accession,
'description' => $node->db_description
);
$dbxref_status = tripal_core_chado_update(
'dbxref',
array('dbxref_id' => $stock[0]->dbxref_id),
$values
);
$dbxref_mode = 'Update';
}
else {
if ($stock[0]->type_id) {
//create the dbxref
//used the type_id as a control to check we have a stock but not a dbxref
$values = array(
'db_id' => $node->database,
'accession' => $node->accession,
'description' => $node->db_description,
'version' => '1',
);
$dbxref_status = tripal_core_chado_insert(
'dbxref',
$values
);
$dbxref_mode = 'Create';
}
else {
drupal_set_message(t('Unable to find stock to Update'), 'error');
watchdog(
'tripal_stock',
'Stock Update: Unable to find stock to update using values: %values',
array('%values', print_r($values, TRUE)),
WATCHDOG_ERROR
);
return FALSE;
}
}
}
}
if (!$dbxref_status) {
watchdog(
'tripal_stock',
'Stock Update: Unable to %mode main stock dbxref with values: %values',
array('%values' => print_r($values, TRUE), '%mode' => $dbxref_mode),
WATCHDOG_WARNING
);
}
//can't change stock id which is all thats stored in drupal thus only update chado
$update_values = array(
'organism_id' => $node->organism_id,
'name' => $node->title,
'uniquename' => $node->uniquename,
'description' => $node->stock_description,
'type_id' => $node->type_id,
);
if ($dbxref_status) {
$update_values['dbxref_id'] = array(
'db_id' => $node->database,
'accession' => $node->accession
);
}
$status = tripal_core_chado_update(
'stock',
array('stock_id' => $node->stock_id),
$update_values
);
if (!$status) {
drupal_set_message(t('Unable to update stock'), 'error');
watchdog(
'tripal_stock',
'Stock Update: Unable to update stock using match values: %mvalues and update values: %uvalues',
array('%mvalues' => print_r(array('stock_id' => $node->stock_id), TRUE), '%uvalues' => print_r($update_values, TRUE)),
WATCHDOG_ERROR
);
}
}
}
/**
* Implements hook_delete(): Handles deleting of chado_stocks
*
* NOTE: Currently deletes data -no undo or record-keeping functionality
*
* @param $node
* The current node including fields with the form element names and submitted values
*
* @return
* TRUE if the node was successfully deleted from drupal/chado; FALSE otherwise
*
* @ingroup tripal_stock
*/
function chado_stock_delete($node) {
// Set stock in chado: is_obsolete = TRUE
$previous_db = tripal_db_set_active('chado');
db_query(
"DELETE FROM {stock} WHERE stock_id=%d",
$node->stock->stock_id
);
tripal_db_set_active($previous_db);
//remove drupal node and all revisions
db_query(
"DELETE FROM {chado_stock} WHERE nid=%d",
$node->nid
);
}
/**
* Purpose: Implement Blocks relating to stock content
*
* @param $op
* What kind of information to retrieve about the block or blocks.
* Possible values include list, configure, save, view.
* @param $delta
* Which block to return (not applicable if $op is 'list').
* @param $edit
* If $op is 'save', the submitted form data from the configuration form.
*
* @return
* One of the following depending on $op: An array of block descriptions (list), the configuration
* form (configure), nothing (save), an array defining subject and content for the block indexed
* by $delta (view)
*
* @ingroup tripal_stock
*/
function tripal_stock_block($op = 'list', $delta = 0, $edit=array()) {
switch ($op) {
case 'list':
$blocks['base']['info'] = t('Tripal Stock Details');
$blocks['base']['cache'] = BLOCK_NO_CACHE;
$blocks['properties']['info'] = t('Tripal Stock Properties');
$blocks['properties']['cache'] = BLOCK_NO_CACHE;
$blocks['references']['info'] = t('Tripal Stock References');
$blocks['references']['cache'] = BLOCK_NO_CACHE;
$blocks['relationships_as_object']['info'] = t('Tripal Stock Relationships');
$blocks['relationships_as_object']['cache'] = BLOCK_NO_CACHE;
$blocks['synonyms']['info'] = t('Tripal Stock Synonyms');
$blocks['synonyms']['cache'] = BLOCK_NO_CACHE;
$blocks['collections']['info'] = t('Tripal Stock Collections');
$blocks['collections']['cache'] = BLOCK_NO_CACHE;
$blocks['phenotypes']['info'] = t('Tripal Stock Phenotypes');
$blocks['phenotypes']['cache'] = BLOCK_NO_CACHE;
$blocks['genotypes']['info'] = t('Tripal Stock Genotypes');
$blocks['genotypes']['cache'] = BLOCK_NO_CACHE;
$blocks['locations']['info'] = t('Tripal Stock Locations');
$blocks['locations']['cache'] = BLOCK_NO_CACHE;
$blocks['orgstocks']['info'] = t('Tripal Organism Stocks');
$blocks['orgstocks']['cache'] = BLOCK_NO_CACHE;
return $blocks;
case 'view':
if (user_access('access chado_stock content') and arg(0) == 'node' and is_numeric(arg(1))) {
$nid = arg(1);
$node = node_load($nid);
$block = array();
switch ($delta) {
case 'base':
$block['subject'] = t('Stock Details');
$block['content'] = theme('tripal_stock_base', $node);
break;
case 'properties':
$block['subject'] = t('Properties');
$block['content'] = theme('tripal_stock_properties', $node);
break;
case 'references':
$block['subject'] = t('References');
$block['content'] = theme('tripal_stock_references', $node);
break;
case 'relationships':
$block['subject'] = t('Relationships');
$block['content'] = theme('tripal_stock_relationships', $node);
break;
case 'synonyms':
$block['subject'] = t('Synonyms');
$block['content'] = theme('tripal_stock_synonyms', $node);
break;
case 'collections':
$block['subject'] = t('Stock Collections');
$block['content'] = theme('tripal_stock_collections', $node);
break;
case 'phenotypes':
$block['subject'] = t('Stock Phenotypes');
$block['content'] = theme('tripal_stock_phenotypes', $node);
break;
case 'genotypes':
$block['subject'] = t('Stock Genotypes');
$block['content'] = theme('tripal_stock_genotypes', $node);
break;
case 'locations':
$block['subject'] = t('Stock Locations');
$block['content'] = theme('tripal_stock_locations', $node);
break;
case 'orgstocks':
$block['subject'] = t('Organism Stocks');
$block['content'] = theme('tripal_organism_stocks', $node);
break;
}
return $block;
}
}
}
/**
*
*
* @ingroup tripal_stock
*/
function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
// we want to provide a new variable that contains the matched stocks.
$stock = $variables['node']->stock;
// 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 S.name, S.uniquename, S.stock_id, CS.nid, CVT.name as rel_type, CVTs.name as obj_type
FROM stock_relationship SR
INNER JOIN stock S on SR.object_id = S.stock_id
INNER JOIN cvterm CVT on SR.type_id = CVT.cvterm_id
INNER JOIN cvterm CVTs on S.type_id = CVTs.cvterm_id
LEFT JOIN chado_stock CS on S.stock_id = CS.stock_id
WHERE SR.subject_id = %d
";
$as_subject = chado_query($sql, $stock->stock_id);
$sql = "
SELECT S.name, S.uniquename, S.stock_id, CS.nid, CVT.name as rel_type, CVTs.name as sub_type
FROM stock_relationship SR
INNER JOIN stock S on SR.subject_id = S.stock_id
INNER JOIN cvterm CVT on SR.type_id = CVT.cvterm_id
INNER JOIN cvterm CVTs on S.type_id = CVTs.cvterm_id
LEFT JOIN chado_stock CS on S.stock_id = CS.stock_id
WHERE SR.object_id = %d
";
$as_object = chado_query($sql, $stock->stock_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;
}
$stock->all_relationships = $relationships;
}
/**
* Implementation of hook_nodeapi().
* Display stock information for associated organisms
* This function also provides contents for indexing
*
* @ingroup tripal_stock
*/
function tripal_stock_nodeapi(&$node, $op, $teaser, $page) {
switch ($op) {
// Note that this function only adds stock view to an organism/feature
// node.
case 'view':
// add the stock to the organism/feature search indexing
if ($node->build_mode == NODE_BUILD_SEARCH_INDEX) {
}
elseif ($node->build_mode == NODE_BUILD_SEARCH_RESULT) {
}
else {
switch ($node->type) {
case 'chado_organism':
// Show stock if the organism/feature is not at teaser view
$node->content['tripal_organism_stocks'] = array(
'#value' => theme('tripal_organism_stocks', $node),
);
break;
}
}
break;
}
}
/**
*
*
* @ingroup tripal_stock
*/
function tripal_stock_preprocess_tripal_organism_stocks(&$variables) {
$organism = $variables['node']->organism;
if (!$organism) {
return;
}
// get the stocks for this organism
$sql = "SELECT S.name, S.stock_id, S.uniquename, CVT.name as cvname ".
"FROM {stock} S ".
" INNER JOIN {cvterm} CVT on S.type_id = CVT.cvterm_id ".
"WHERE organism_id = %s".
"ORDER BY stock_id ASC";
// the counting SQL
$csql = "SELECT count(*) ".
"FROM {stock} S".
" INNER JOIN {cvterm} CVT on S.type_id = CVT.cvterm_id ".
"WHERE organism_id = %s ".
"GROUP BY organism_id ";
$previous_db = tripal_db_set_active('chado'); // use chado database
$org_stocks = pager_query($sql, 25, 0, $csql, $organism->organism_id);
tripal_db_set_active($previous_db); // now use drupal database
// get the pager and reformat so it shows the right block
$pager = theme('pager');
// prepare the query that will lookup node ids
$sql = "SELECT nid FROM {chado_stock} ".
"WHERE stock_id = %d";
$i=0;
$stocks = array();
while ($stock = db_fetch_object($org_stocks)) {
$node = db_fetch_object(db_query($sql, $stock->stock_id));
$stock->nid = $node->nid;
$stocks[$i++] = $stock;
}
$organism->stock_browser = array('stocks' => $stocks, 'pager' => $pager, 'enabled' => TRUE );
}
/**
*
*
* @ingroup tripal_stock
*/
function tripal_stock_preprocess_tripal_stock_base(&$variables) {
$stock = $variables['node']->stock;
$num_seq = db_result(chado_query("SELECT count(*) FROM feature_stock WHERE stock_id = %d", $stock->stock_id));
$stock->num_seq = $num_seq;
}