<?php
/**
* @defgroup tripal_db_api DB Module API
* @ingroup tripal_api
* @ingroup tripal_db
* Provides an application programming interface (API) to manage references to external databases
*/
/**
* Purpose: To retrieve a chado database object
*
* @param $select_values
* An array meant to uniquely select a given database
*
* @return
* Chado database object
*
* The database is selected using tripal_core_chado select and as such the
* $select_values array parameter meant to uniquely identify the database to be
* returned follows the same form as when using tripal_core_chado_select directly.
*
* Example Usage:
* @code
$select_values = array(
'name' => 'SOFP'
);
$db_object = tripal_db_get_db($select_values);
* @endcode
* The above code selects the SOFP db and returns the following object:
* @code
$db_object = stdClass Object (
[db_id] => 49
[name] => SOFP
[description] =>
[urlprefix] =>
[url] =>
);
* @endcode
*
* @ingroup tripal_db_api
*/
function tripal_db_get_db ($select_values) {
$columns = array(
'db_id',
'name',
'description',
'urlprefix',
'url'
);
$results = tripal_core_chado_select('db', $columns, $select_values);
if (sizeof($results) == 1) {
return $results[0];
} elseif (empty($results)) {
watchdog('tripal_cdb',
'tripal_db_get_db: No db matches criteria values:%values',
array('%values' => print_r($select_values, TRUE)),
WATCHDOG_WARNING
);
return FALSE;
} else {
watchdog('tripal_db',
'tripal_db_get_db: 2+ dbs match criteria values:%values',
array('%values' => print_r($select_values, TRUE)),
WATCHDOG_WARNING
);
}
}
/**
* Purpose: To retrieve a chado db object
*
* @param $db_id
* db.db_id
* @return
* Chado db object with all fields from the chado db table
*
* @ingroup tripal_db_api
*/
function tripal_db_get_db_by_db_id ($db_id) {
$previous_db = tripal_db_set_active('chado');
$r = db_fetch_object(db_query(
"SELECT * FROM db WHERE db_id=%d", $db_id
));
tripal_db_set_active($previous_db);
return $r;
}
/**
* Purpose: To retrieve a chado db object
*
* @param $name
* db.name
* @return
* chado db object with all fields from the chado db table
*
* @ingroup tripal_db_api
*/
function tripal_db_get_db_by_name ($name) {
$previous_db = tripal_db_set_active('chado');
$r = db_fetch_object(db_query(
"SELECT * FROM db WHERE name='%s'", $name
));
tripal_db_set_active($previous_db);
return $r;
}
// Purpose: To retrieve a chado db object
//
// @params where_options: array(
// <column_name> => array(
// 'type' => <type of column: INT/**STRING>,
// 'value' => <the vlaue you want to filter on>,
// 'exact' => <if TRUE use =; if FALSE use ~>,
// )
// )
// @return chado db object with all fields from the chado db table
//
//function tripal_db_get_db ($where_options) {
/**
* Purpose: Create an options array to be used in a form element
* which provides a list of all chado dbs
*
* @return
* An array(db_id => name) for each db in the chado db table
*
* @ingroup tripal_db_api
*/
function tripal_db_get_db_options() {
$previous_db = tripal_db_set_active('chado');
$result = db_query(
"SELECT db_id, name FROM db"
);
tripal_db_set_active($previous_db);
$options = array();
while ( $r = db_fetch_object($result) ) {
$options[$r->db_id] = $r->name;
}
return $options;
}
// Purpose: To retrieve a chado dbxref object
//
// @param where_options: array(
// <column_name> => array(
// 'type' => <type of column: INT/**STRING>,
// 'value' => <the vlaue you want to filter on>,
// 'exact' => <if TRUE use =; if FALSE use ~>,
// )
// )
// @return chado dbxref object with all fields from the chado dbxref table
//
//function tripal_db_get_dbxref ($where_options) {
/**
* Purpose: To retrieve a chado database reference object
*
* @param $select_values
* An array meant to uniquely select a given database reference
*
* @return
* Chado database reference object
*
* The database reference is selected using tripal_core_chado select and as such the
* $select_values array parameter meant to uniquely identify the database reference to be
* returned follows the same form as when using tripal_core_chado_select directly.
*
* Example Usage:
* @code
$select_values = array(
'accession' => 'synonym',
'db_id' => array(
'name' => 'SOFP'
)
);
$dbxref_object = tripal_db_get_dbxref($select_values);
* @endcode
* The above code selects the synonym database reference and returns the following object:
* @code
$dbxref_object = stdClass Object (
[dbxref_id] => 2581
[accession] => synonym
[description] =>
[version] =>
[db_db_id] => 49
[db_name] => SOFP
[db_description] =>
[db_urlprefix] =>
[db_url] =>
);
* @endcode
*
* @ingroup tripal_db_api
*/
function tripal_db_get_dbxref ($select_values) {
$columns = array(
'dbxref_id',
'db_id',
'accession',
'description',
'version'
);
$results = tripal_core_chado_select('dbxref', $columns, $select_values);
if (sizeof($results) == 1) {
$dbxref = tripal_db_add_db_to_object(array('db_id' => $results[0]->db_id), $results[0], array());
unset($dbxref->db_id);
return $dbxref;
} elseif (empty($results)) {
watchdog('tripal_db',
'tripal_db_get_dbxref: No dbxref matches criteria values:%values',
array('%values' => print_r($select_values, TRUE)),
WATCHDOG_WARNING
);
return FALSE;
} else {
watchdog('tripal_db',
'tripal_db_get_dbxref: 2+ dbxrefs match criteria values:%values',
array('%values' => print_r($select_values, TRUE)),
WATCHDOG_WARNING
);
}
}
/**
* Purpose: To retrieve a chado dbxref object with a given accession
*
* @param $accession
* dbxref.accession
* @param $db_id
* dbxref.db_id
* @return
* chado dbxref object with all fields from the chado dbxref table
*
* @ingroup tripal_db_api
*/
function tripal_db_get_dbxref_by_accession ($accession, $db_id=0) {
if (!empty($db_id)) {
$previous_db = tripal_db_set_active('chado');
$r = db_fetch_object(db_query(
"SELECT * FROM dbxref WHERE accession='%s' AND db_id=%d",
$accession, $db_id
));
tripal_db_set_active($previous_db);
} else {
$previous_db = tripal_db_set_active('chado');
$r = db_fetch_object(db_query(
"SELECT * FROM dbxref WHERE accession='%s'",
$accession
));
tripal_db_set_active($previous_db);
}
return $r;
}
/**
* Implements hook_chado_dbxref_schema()
* Purpose: To add descriptions and foreign keys to default table description
* Note: This array will be merged with the array from all other implementations
*
* @return
* Array describing the dbxref table
*
* @ingroup tripal_schema_api
*/
function tripal_db_chado_dbxref_schema() {
$description = array();
$description['foreign keys']['db'] = array(
'table' => 'db',
'columns' => array(
'db_id' => 'db_id',
),
);
return $description;
}
/**
*
* @ingroup tripal_db_api
*/
function tripal_db_add_db($dbname){
$db_sql = "SELECT * FROM {db} WHERE name ='%s'";
$db = db_fetch_object(db_query($db_sql,$dbname));
if(!$db){
if(!db_query("INSERT INTO {db} (name) VALUES ('%s')",$dbname)){
watchdog('tripal_cv', "Cannot create '$dbname' db in Chado.",NULL,WATCHDOG_WARNING);
return 0;
}
$db = db_fetch_object(db_query($db_sql,$dbname));
}
return $db;
}
/**
*
* @ingroup tripal_db_api
*/
function tripal_db_add_dbxref($db_id,$accession,$version='',$description=''){
// check to see if the dbxref exists if not, add it
$dbxsql = "SELECT dbxref_id FROM {dbxref} WHERE db_id = %d and accession = '%s'";
$dbxref = db_fetch_object(db_query($dbxsql,$db_id,$accession));
if(!$dbxref){
$sql = "
INSERT INTO {dbxref} (db_id, accession, version, description)
VALUES (%d,'%s','%s','%s')
";
if(!db_query($sql,$db_id,$accession,$version,$description)){
watchdog('tripal_cv', "Failed to insert the dbxref record $accession",NULL,WATCHDOG_WARNING);
return 0;
}
print "Added Dbxref accession: $accession\n";
$dbxref = db_fetch_object(db_query($dbxsql,$db_id,$accession));
}
return $dbxref;
}