Source Code for Module BioSQL.DBUtils

  1  # Copyright 2002 by Andrew Dalke.  All rights reserved. 
  2  # Revisions 2007-2010 copyright by Peter Cock.  All rights reserved. 
  3  # Revisions 2009 copyright by Brad Chapman.  All rights reserved. 
  4  # This code is part of the Biopython distribution and governed by its 
  5  # license.  Please see the LICENSE file that should have been included 
  6  # as part of this package. 
  7  # 
  8  # Note that BioSQL (including the database schema and scripts) is 
  9  # available and licensed separately.  Please consult www.biosql.org 
 10   
 11  _dbutils = {} 
 12   
 13   
 14 -class Generic_dbutils: 
 15      """Default database utilities.""" 
 16 -    def __init__(self): 
 17          pass 
 18   
 19 -    def tname(self, table): 
 20          if table != 'biosequence': 
 21              return table 
 22          else: 
 23              return 'bioentry' 
 24   
 25 -    def last_id(self, cursor, table): 
 26          # XXX: Unsafe without transactions isolation 
 27          table = self.tname(table) 
 28          sql = r"select max(%s_id) from %s" % (table, table) 
 29          cursor.execute(sql) 
 30          rv = cursor.fetchone() 
 31          return rv[0] 
 32   
 33 -    def execute(self, cursor, sql, args=None): 
 34          """Just execute an sql command. 
 35          """ 
 36          cursor.execute(sql, args or ()) 
 37   
 38 -    def autocommit(self, conn, y=1): 
 39          # Let's hope it was not really needed 
 40          pass 
 41   
 42   
 43 -class Sqlite_dbutils(Generic_dbutils): 
 44      """Custom database utilities for SQLite.""" 
 45 -    def execute(self, cursor, sql, args=None): 
 46          """Execute SQL command, replacing %s with ? for variable substitution in sqlite3. 
 47          """ 
 48          cursor.execute(sql.replace("%s", "?"), args or ()) 
 49   
 50  _dbutils["sqlite3"] = Sqlite_dbutils 
 51   
 52   
 53 -class Mysql_dbutils(Generic_dbutils): 
 54      """Custom database utilities for MySQL.""" 
 55 -    def last_id(self, cursor, table): 
 56          try: 
 57              #This worked on older versions of MySQL 
 58              return cursor.insert_id() 
 59          except AttributeError: 
 60              #See bug 2390 
 61              #Google suggests this is the new way, 
 62              #same fix also suggested by Eric Gibert: 
 63              return cursor.lastrowid 
 64   
 65  _dbutils["MySQLdb"] = Mysql_dbutils 
 66   
 67   
 68 -class _PostgreSQL_dbutils(Generic_dbutils): 
 69      """Base class for any PostgreSQL adaptor.""" 
 70 -    def next_id(self, cursor, table): 
 71          table = self.tname(table) 
 72          sql = r"select nextval('%s_pk_seq')" % table 
 73          cursor.execute(sql) 
 74          rv = cursor.fetchone() 
 75          return rv[0] 
 76   
 77 -    def last_id(self, cursor, table): 
 78          table = self.tname(table) 
 79          sql = r"select currval('%s_pk_seq')" % table 
 80          cursor.execute(sql) 
 81          rv = cursor.fetchone() 
 82          return rv[0] 
 83   
 84   
 85 -class Psycopg2_dbutils(_PostgreSQL_dbutils): 
 86      """Custom database utilities for Psycopg2 (PostgreSQL).""" 
 87 -    def autocommit(self, conn, y=True): 
 88          if y: 
 89              conn.set_isolation_level(0) 
 90          else: 
 91              conn.set_isolation_level(1) 
 92   
 93  _dbutils["psycopg2"] = Psycopg2_dbutils 
 94   
 95   
 96 -class Pgdb_dbutils(_PostgreSQL_dbutils): 
 97      """Custom database utilities for Pgdb (aka PyGreSQL, for PostgreSQL).""" 
 98 -    def autocommit(self, conn, y=True): 
 99          raise NotImplementedError("pgdb does not support this!") 
100   
101  _dbutils["pgdb"] = Pgdb_dbutils 
102   
103   
104 -def get_dbutils(module_name): 
105      try: 
106          return _dbutils[module_name]() 
107      except KeyError: 
108          return Generic_dbutils() 
109