=> array( * 'type' => , * 'value' => , * 'exact' => , * ) * ) * @return chado db object with all fields from the chado db table */ function tripal_db_get_db ($where_options) { $previous_db = tripal_db_set_active('chado'); $where= array(); //generate the where clause from supplied options // the key is the column name foreach ($where_options as $key => $val_array) { if (preg_match('/INT/', $val_array['type'])) { $where[] = $key."=".$val_array['value']; } else { if ($val_array['exact']) { $operator='='; } else { $operator='~'; } $where[] = $key.$operator."'".$val_array['value']."'"; } } $r = db_fetch_object(db_query( "SELECT * FROM db WHERE ".implode(' AND ',$where) )); tripal_db_set_active($previous_db); return $r; } /************************************************************************* * 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 */ 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 $options; } /************************************************************************* * Purpose: To retrieve a chado dbxref object * * @params where_options: array( * => array( * 'type' => , * 'value' => , * 'exact' => , * ) * ) * @return chado dbxref object with all fields from the chado dbxref table */ function tripal_db_get_dbxref ($where_options) { $previous_db = tripal_db_set_active('chado'); $where= array(); //generate the where clause from supplied options // the key is the column name foreach ($where_options as $key => $val_array) { if (preg_match('/INT/', $val_array['type'])) { $where[] = $key."=".$val_array['value']; } else { if ($val_array['exact']) { $operator='='; } else { $operator='~'; } $where[] = $key.$operator."'".$val_array['value']."'"; } } $r = db_fetch_object(db_query( "SELECT * FROM dbxref WHERE ".implode(' AND ',$where) )); tripal_db_set_active($previous_db); return $r; } /************************************************************************* * Purpose: To retrieve a chado dbxref object with a given accession * * @params dbxref.accession * @params dbxref.db_id * @return chado dbxref object with all fields from the chado dbxref table */ function tripal_db_get_dbxref_by_accession ($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; } /**************************************************************************** * @section Chado Table Descriptions ****************************************************************************/ /**************************************************************************** * 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 */ function tripal_stock_chado_dbxref_schema() { $description = array(); $description['foreign keys']['db'] = array( 'table' => 'db', 'columns' => array( 'cv_id' => 'db_id', ), ); return $description; }