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# Copyright 2002 by Andrew Dalke. All rights reserved.
# Revisions 2007-2010 copyright by Peter Cock. All rights reserved.
# Revisions 2009 copyright by Brad Chapman. All rights reserved.
# Revisions 2013 copyright by Tiago Antao. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
#
# Note that BioSQL (including the database schema and scripts) is
# available and licensed separately. Please consult www.biosql.org
"""Helper code for Biopython's BioSQL code (for internal use)."""
import os
_dbutils = {}
class Generic_dbutils:
"""Default database utilities."""
def __init__(self):
"""Create a Generic_dbutils object."""
pass
def tname(self, table):
"""Return the name of the table."""
if table != "biosequence":
return table
else:
return "bioentry"
def last_id(self, cursor, table):
"""Return the last used id for a table."""
# XXX: Unsafe without transactions isolation
table = self.tname(table)
sql = f"select max({table}_id) from {table}"
cursor.execute(sql)
rv = cursor.fetchone()
return rv[0]
def execute(self, cursor, sql, args=None):
"""Just execute an sql command."""
cursor.execute(sql, args or ())
def executemany(self, cursor, sql, seq):
"""Execute many sql commands."""
cursor.executemany(sql, seq)
def autocommit(self, conn, y=1):
"""Set autocommit on the database connection."""
# Let's hope it was not really needed
pass
class Sqlite_dbutils(Generic_dbutils):
"""Custom database utilities for SQLite."""
def _sub_placeholder(self, sql):
"""Format the argument placeholders for sqlite (PRIVATE)."""
return sql.replace("%s", "?")
def execute(self, cursor, sql, args=None):
"""Execute SQL command.
Replaces %s with ? for variable substitution in sqlite3.
"""
sql = self._sub_placeholder(sql)
cursor.execute(sql, args or ())
def executemany(self, cursor, sql, seq):
"""Execute many sql statements."""
sql = self._sub_placeholder(sql)
cursor.executemany(sql, seq)
_dbutils["sqlite3"] = Sqlite_dbutils
class Mysql_dbutils(Generic_dbutils):
"""Custom database utilities for MySQL."""
def last_id(self, cursor, table):
"""Return the last used id for a table."""
if os.name == "java":
return Generic_dbutils.last_id(self, cursor, table)
try:
# This worked on older versions of MySQL
return cursor.insert_id()
except AttributeError:
# See bug 2390
# Google suggests this is the new way,
# same fix also suggested by Eric Gibert:
return cursor.lastrowid
_dbutils["MySQLdb"] = Mysql_dbutils
class _PostgreSQL_dbutils(Generic_dbutils):
"""Base class for any PostgreSQL adaptor."""
def next_id(self, cursor, table):
table = self.tname(table)
sql = f"SELECT nextval('{table}_pk_seq')"
cursor.execute(sql)
rv = cursor.fetchone()
return rv[0]
def last_id(self, cursor, table):
table = self.tname(table)
sql = f"SELECT currval('{table}_pk_seq')"
cursor.execute(sql)
rv = cursor.fetchone()
return rv[0]
class Psycopg2_dbutils(_PostgreSQL_dbutils):
"""Custom database utilities for Psycopg2 (PostgreSQL)."""
def autocommit(self, conn, y=True):
"""Set autocommit on the database connection."""
if y:
if os.name == "java":
conn.autocommit = 1
else:
conn.set_isolation_level(0)
else:
if os.name == "java":
conn.autocommit = 0
else:
conn.set_isolation_level(1)
_dbutils["psycopg2"] = Psycopg2_dbutils
class Pgdb_dbutils(_PostgreSQL_dbutils):
"""Custom database utilities for Pgdb (aka PyGreSQL, for PostgreSQL)."""
def autocommit(self, conn, y=True):
"""Set autocommit on the database connection. Currently not implemented."""
raise NotImplementedError("pgdb does not support this!")
_dbutils["pgdb"] = Pgdb_dbutils
def get_dbutils(module_name):
"""Return the correct dbutils object for the database driver."""
try:
return _dbutils[module_name]()
except KeyError:
return Generic_dbutils()
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