Source Code for Module BioSQL.DBUtils

  1  # Copyright 2002 by Andrew Dalke.  All rights reserved. 
  2  # Revisions 2007-2008 by Peter Cock. 
  3  # This code is part of the Biopython distribution and governed by its 
  4  # license.  Please see the LICENSE file that should have been included 
  5  # as part of this package. 
  6  # 
  7  # Note that BioSQL (including the database schema and scripts) is 
  8  # available and licensed separately.  Please consult www.biosql.org 
  9   
 10  _dbutils = {} 
 11   
 12 -class Generic_dbutils: 
 13 -    def __init__(self): 
 14          pass 
 15   
 16 -    def tname(self, table): 
 17          if table != 'biosequence': return table 
 18          else: return 'bioentry' 
 19   
 20  # Disabled: better safe than sorry 
 21  ##    def next_id(self, cursor, table): 
 22  ##        # XXX brain-dead! Hopefully, the database will enforce PK unicity.. 
 23  ##        table = self.tname(table) 
 24  ##        sql = r"select 1+max(%s_id) from %s" % (table, table) 
 25  ##        cursor.execute(sql) 
 26  ##        rv = cursor.fetchone() 
 27  ##        return rv[0] 
 28           
 29 -    def last_id(self, cursor, table): 
 30          # XXX: Unsafe without transactions isolation 
 31          table = self.tname(table) 
 32          sql = r"select max(%s_id) from %s" % (table, table) 
 33          cursor.execute(sql) 
 34          rv = cursor.fetchone() 
 35          return rv[0] 
 36   
 37 -    def autocommit(self, conn, y = 1): 
 38          # Let's hope it was not really needed 
 39          pass 
 40   
 41 -class Mysql_dbutils(Generic_dbutils): 
 42 -    def last_id(self, cursor, table): 
 43          try : 
 44              #This worked on older versions of MySQL 
 45              return cursor.insert_id() 
 46          except AttributeError: 
 47              #See bug 2390 
 48              #Google suggests this is the new way, 
 49              #same fix also suggested by Eric Gibert: 
 50              return cursor.lastrowid 
 51           
 52  _dbutils["MySQLdb"] = Mysql_dbutils 
 53   
 54 -class Psycopg_dbutils(Generic_dbutils): 
 55 -    def next_id(self, cursor, table): 
 56          table = self.tname(table) 
 57          sql = r"select nextval('%s_pk_seq')" % table 
 58          cursor.execute(sql) 
 59          rv = cursor.fetchone() 
 60          return rv[0] 
 61           
 62 -    def last_id(self, cursor, table): 
 63          table = self.tname(table) 
 64          sql = r"select currval('%s_pk_seq')" % table 
 65          cursor.execute(sql) 
 66          rv = cursor.fetchone() 
 67          return rv[0] 
 68   
 69 -    def autocommit(self, conn, y = True): 
 70          conn.autocommit(y) 
 71  _dbutils["psycopg"] = Psycopg_dbutils 
 72   
 73 -class Pgdb_dbutils(Generic_dbutils): 
 74      """Add support for pgdb in the PyGreSQL database connectivity package. 
 75      """ 
 76 -    def next_id(self, cursor, table): 
 77          table = self.tname(table) 
 78          sql = r"select nextval('%s_pk_seq')" % table 
 79          cursor.execute(sql) 
 80          rv = cursor.fetchone() 
 81          return rv[0] 
 82   
 83 -    def last_id(self, cursor, table): 
 84          table = self.tname(table) 
 85          sql = r"select currval('%s_pk_seq')" % table 
 86          cursor.execute(sql) 
 87          rv = cursor.fetchone() 
 88          return rv[0] 
 89   
 90 -    def autocommit(self, conn, y = True): 
 91          raise NotImplementedError("pgdb does not support this!") 
 92   
 93  _dbutils["pgdb"] = Pgdb_dbutils 
 94   
 95 -def get_dbutils(module_name): 
 96      try: 
 97          return _dbutils[module_name]() 
 98      except: 
 99          return Generic_dbutils() 
100