'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 $r; } // Purpose: To retrieve a chado db object // // @params where_options: array( // => array( // 'type' => , // 'value' => , // 'exact' => , // ) // ) // @return chado db object with all fields from the chado db table // //function tripal_db_get_db ($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 $options; } // Purpose: To retrieve a chado dbxref object // // @param where_options: array( // => array( // 'type' => , // 'value' => , // 'exact' => , // ) // ) // @return chado dbxref object with all fields from the chado dbxref table // //function tripal_db_get_dbxref ($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; }