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dbquery.py
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## CDS Invenio utility to run SQL queries. The core is taken from
## modpython FAQ and modified to suit our needs. The insert_id() is
## inspired by Erik Forsberg's mod_python slides.
## FIXME: note that this version of persistent connectivity to the
## database is not thread-safe; it works allright in the prefork model
## only (apache2-mpm-prefork). We should rather replace it with the
## connection pool technique when time permits. See:
## http://modpython.org/FAQ/faqw.py?req=show&file=faq03.003.htp
## This file is part of CDS Invenio.
## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007, 2008 CERN.
##
## CDS Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your option) any later version.
##
## CDS Invenio is distributed in the hope that it will be useful, but
## WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
## General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with CDS Invenio; if not, write to the Free Software Foundation, Inc.,
## 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
"""CDS Invenio utility to run SQL queries."""
__revision__ = "$Id$"
# dbquery clients can import these from here:
# pylint: disable-msg=W0611
from MySQLdb import escape_string
from MySQLdb import Warning, Error, InterfaceError, DataError, \
DatabaseError, OperationalError, IntegrityError, \
InternalError, NotSupportedError, \
ProgrammingError
import warnings
import string
import time
import marshal
import sys
from zlib import compress, decompress
from thread import get_ident
from invenio.config import CFG_ACCESS_CONTROL_LEVEL_SITE, \
CFG_MISCUTIL_SQL_MAX_CACHED_QUERIES, CFG_MISCUTIL_SQL_USE_SQLALCHEMY, \
CFG_MISCUTIL_SQL_RUN_SQL_MANY_LIMIT
from invenio.errorlib import register_exception
## Set the following flag to True in order to transform warning printed
## during run_sql usage into very verbose exception, useful for debugging
## purpouses.
CFG_RUN_SQL_WARNINGS_INTO_VERBOSE_EXCEPTIONS=False
if CFG_RUN_SQL_WARNINGS_INTO_VERBOSE_EXCEPTIONS:
warnings.filterwarnings('error', category=Warning, module='invenio\.dbquery')
if CFG_MISCUTIL_SQL_USE_SQLALCHEMY:
try:
import sqlalchemy.pool as pool
import MySQLdb as mysqldb
mysqldb = pool.manage(mysqldb, use_threadlocal=True)
connect = mysqldb.connect
except ImportError:
CFG_MISCUTIL_SQL_USE_SQLALCHEMY = False
from MySQLdb import connect
else:
from MySQLdb import connect
## DB config variables. These variables are to be set in invenio.conf
## by admins and then replaced in situ in this file by calling
## "inveniocfg --update-dbexec".
## Note that they are defined here and not in config.py in order to
## prevent them from being exported accidentally elsewhere, as no-one
## should know DB credentials but this file.
CFG_DATABASE_HOST = 'localhost'
CFG_DATABASE_PORT = '3306'
CFG_DATABASE_NAME = 'cdsinvenio'
CFG_DATABASE_USER = 'cdsinvenio'
CFG_DATABASE_PASS = 'my123p$ss'
_DB_CONN = {}
try:
_db_cache
except NameError:
_db_cache = {}
def _db_login(relogin = 0):
"""Login to the database."""
## Note: we are using "use_unicode=False", because we want to
## receive strings from MySQL as Python UTF-8 binary string
## objects, not as Python Unicode string objects, as of yet.
## Note: "charset='utf8'" is needed for recent MySQLdb versions
## (such as 1.2.1_p2 and above). For older MySQLdb versions such
## as 1.2.0, an explicit "init_command='SET NAMES utf8'" parameter
## would constitute an equivalent. But we are not bothering with
## older MySQLdb versions here, since we are recommending to
## upgrade to more recent versions anyway.
if CFG_MISCUTIL_SQL_USE_SQLALCHEMY:
return connect(host=CFG_DATABASE_HOST, port=int(CFG_DATABASE_PORT),
db=CFG_DATABASE_NAME, user=CFG_DATABASE_USER,
passwd=CFG_DATABASE_PASS,
use_unicode=False, charset='utf8')
else:
thread_ident = get_ident()
if relogin:
_DB_CONN[thread_ident] = connect(host=CFG_DATABASE_HOST,
port=int(CFG_DATABASE_PORT),
db=CFG_DATABASE_NAME,
user=CFG_DATABASE_USER,
passwd=CFG_DATABASE_PASS,
use_unicode=False, charset='utf8')
return _DB_CONN[thread_ident]
else:
if _DB_CONN.has_key(thread_ident):
return _DB_CONN[thread_ident]
else:
_DB_CONN[thread_ident] = connect(host=CFG_DATABASE_HOST,
port=int(CFG_DATABASE_PORT),
db=CFG_DATABASE_NAME,
user=CFG_DATABASE_USER,
passwd=CFG_DATABASE_PASS,
use_unicode=False, charset='utf8')
return _DB_CONN[thread_ident]
def _db_logout():
"""Close a connection."""
try:
del _DB_CONN[get_ident()]
except KeyError:
pass
def _db_cursor():
"""Retrieves the db cursor - reconnects in case of need"""
try:
db = _db_login()
cur = db.cursor()
return cur
except OperationalError: # unexpected disconnect, bad malloc error, etc
# FIXME: now reconnect is always forced, we may perhaps want to ping() first?
try:
db = _db_login(relogin = 1)
cur = db.cursor()
return cur
except OperationalError: # again an unexpected disconnect, bad malloc error, etc
raise
except Warning, wmsg:
msg = "Warning in executing query:\n%s\nwith parameters:\n%s\n%s" % (sql, param, wmsg)
print >> sys.stderr, msg
try:
raise Warning(msg)
except Warning:
register_exception()
raise
def run_sql_cached(sql, param=None, n=0, with_desc=0, affected_tables=['bibrec']):
"""
Run the SQL query and cache the SQL command for later reuse.
@param param: tuple of string params to insert in the query
(see notes below)
@param n: number of tuples in result (0 for unbounded)
@param with_desc: if true, will return a
DB API 7-tuple describing columns in query
@param affected_tables: is a list of tablenames of affected tables,
used to decide whether we should update the cache or whether we
can return cached result, depending on the last modification time
for corresponding tables. If empty, and if the cached result is
present in the cache, always return the cached result without
recomputing it. (This is useful to speed up queries that operate
on objects that virtually never change, e.g. list of defined
logical fields, that remain usually constant in between Apache
restarts. Note that this would be a dangerous default for any
query.)
@return: the result as provided by run_sql()
Note that it is pointless and even wrong to use this function with
SQL commands different from SELECT.
"""
global _db_cache
if CFG_ACCESS_CONTROL_LEVEL_SITE == 3:
# do not connect to the database as the site is closed for maintenance:
return []
key = repr((sql, param, n, with_desc))
# Garbage collecting needed?
if len(_db_cache) >= CFG_MISCUTIL_SQL_MAX_CACHED_QUERIES:
_db_cache = {}
# Query already in the cache?
if not _db_cache.has_key(key) or \
(affected_tables and _db_cache[key][1] <= max([get_table_update_time(table) for table in affected_tables])):
# Let's update the cache
result = run_sql(sql, param, n, with_desc)
_db_cache[key] = (result, time.strftime("%Y-%m-%d %H:%M:%S", time.localtime()))
### log_sql_query_cached(key, result, False) ### UNCOMMENT ONLY IF you REALLY want to log all queries
else:
result = _db_cache[key][0]
### log_sql_query_cached(key, result, True) ### UNCOMMENT ONLY IF you REALLY want to log all queries
return result
def run_sql(sql, param=None, n=0, with_desc=0):
"""Run SQL on the server with PARAM and return result.
@param param: tuple of string params to insert in the query
(see notes below)
@param n: number of tuples in result (0 for unbounded)
@param with_desc: if true, will return a
DB API 7-tuple describing columns in query
@return: if SELECT, SHOW, DESCRIBE statements: tuples of data, followed
by description if parameter
provided
if INSERT: last row id.
else: SQL result as provided by database
When the site is closed for maintenance (as governed by the
config variable CFG_ACCESS_CONTROL_LEVEL_SITE), do not attempt
to run any SQL queries but return empty list immediately.
Useful to be able to have the website up while MySQL database
is down for maintenance, hot copies, table repairs, etc.
In case of problems, exceptions are returned according to the
Python DB API 2.0. The client code can import them from this
file and catch them.
"""
if CFG_ACCESS_CONTROL_LEVEL_SITE == 3:
# do not connect to the database as the site is closed for maintenance:
return []
### log_sql_query(sql, param) ### UNCOMMENT ONLY IF you REALLY want to log all queries
if param:
param = tuple(param)
cur = _db_cursor()
rc = cur.execute(sql, param)
if string.upper(string.split(sql)[0]) in ("SELECT", "SHOW", "DESC", "DESCRIBE"):
if n:
recset = cur.fetchmany(n)
else:
recset = cur.fetchall()
if with_desc:
return recset, cur.description
else:
return recset
else:
if string.upper(string.split(sql)[0]) == "INSERT":
rc = cur.lastrowid
return rc
def run_sql_many(query, params, limit=CFG_MISCUTIL_SQL_RUN_SQL_MANY_LIMIT):
"""Run SQL on the server with PARAM.
This method does execute_many and is therefore more efficient than execute
but it has sense only with queries that affect state of a database
(INSERT, UPDATE). That is why the results just count number of affected rows
@param params: tuple of tuple of string params to insert in the query
(see notes below)
@param limit: query will be executed in a cycle for parameters >limit
(each iteration receive at most "limit" parameters)
@return: SQL result as provided by database
"""
cur = _db_cursor()
i = 0
r = None
while i < len(params):
if r is None:
r = cur.executemany(query, params[i:i+limit])
else:
r += cur.executemany(query, params[i:i+limit])
i += limit
return r
def blob_to_string(ablob):
"""Return string representation of ABLOB. Useful to treat MySQL
BLOBs in the same way for both recent and old MySQLdb versions.
"""
if ablob:
if type(ablob) is str:
# BLOB is already a string in MySQLdb 0.9.2
return ablob
else:
# BLOB is array.array in MySQLdb 1.0.0 and later
return ablob.tostring()
else:
return ablob
def log_sql_query_cached(key, result, hit_p):
"""Log SQL query cached into prefix/var/log/dbquery.log log file. In order
to enable logging of all SQL queries, please uncomment two lines
in run_sql_cached() above. Useful for fine-level debugging only!
"""
from invenio.config import CFG_LOGDIR
from invenio.dateutils import convert_datestruct_to_datetext
from invenio.textutils import indent_text
log_path = CFG_LOGDIR + '/dbquery.log'
date_of_log = convert_datestruct_to_datetext(time.localtime())
message = date_of_log + '-->\n'
message += indent_text('Key:\n' + indent_text(str(key), 2, wrap=True), 2)
message += indent_text('Result:\n' + indent_text(str(result) + (hit_p and ' HIT' or ' MISS'), 2, wrap=True), 2)
message += 'Cached queries: %i\n\n' % len(_db_cache)
try:
log_file = open(log_path, 'a+')
log_file.writelines(message)
log_file.close()
except:
pass
def log_sql_query(sql, param=None):
"""Log SQL query into prefix/var/log/dbquery.log log file. In order
to enable logging of all SQL queries, please uncomment one line
in run_sql() above. Useful for fine-level debugging only!
"""
from invenio.config import CFG_LOGDIR
from invenio.dateutils import convert_datestruct_to_datetext
from invenio.textutils import indent_text
log_path = CFG_LOGDIR + '/dbquery.log'
date_of_log = convert_datestruct_to_datetext(time.localtime())
message = date_of_log + '-->\n'
message += indent_text('Query:\n' + indent_text(str(sql), 2, wrap=True), 2)
message += indent_text('Params:\n' + indent_text(str(param), 2, wrap=True), 2)
message += '-----------------------------\n\n'
try:
log_file = open(log_path, 'a+')
log_file.writelines(message)
log_file.close()
except:
pass
def get_table_update_time(tablename):
"""Return update time of TABLENAME. TABLENAME can contain
wildcard `%' in which case we return the maximum update time
value.
"""
# Note: in order to work with all of MySQL 4.0, 4.1, 5.0, this
# function uses SHOW TABLE STATUS technique with a dirty column
# position lookup to return the correct value. (Making use of
# Index_Length column that is either of type long (when there are
# some indexes defined) or of type None (when there are no indexes
# defined, e.g. table is empty). When we shall use solely
# MySQL-5.0, we can employ a much cleaner technique of using
# SELECT UPDATE_TIME FROM INFORMATION_SCHEMA.TABLES WHERE
# table_name='collection'.
res = run_sql("SHOW TABLE STATUS LIKE %s", (tablename, ))
update_times = [] # store all update times
for row in res:
if type(row[10]) is long or \
row[10] is None:
# MySQL-4.1 and 5.0 have creation_time in 11th position,
# so return next column:
update_times.append(str(row[12]))
else:
# MySQL-4.0 has creation_time in 10th position, which is
# of type datetime.datetime or str (depending on the
# version of MySQLdb), so return next column:
update_times.append(str(row[11]))
return max(update_times)
def get_table_status_info(tablename):
"""Return table status information on TABLENAME. Returned is a
dict with keys like Name, Rows, Data_length, Max_data_length,
etc. If TABLENAME does not exist, return empty dict.
"""
# Note: again a hack so that it works on all MySQL 4.0, 4.1, 5.0
res = run_sql("SHOW TABLE STATUS LIKE %s", (tablename, ))
table_status_info = {} # store all update times
for row in res:
if type(row[10]) is long or \
row[10] is None:
# MySQL-4.1 and 5.0 have creation time in 11th position:
table_status_info['Name'] = row[0]
table_status_info['Rows'] = row[4]
table_status_info['Data_length'] = row[6]
table_status_info['Max_data_length'] = row[8]
table_status_info['Create_time'] = row[11]
table_status_info['Update_time'] = row[12]
else:
# MySQL-4.0 has creation_time in 10th position, which is
# of type datetime.datetime or str (depending on the
# version of MySQLdb):
table_status_info['Name'] = row[0]
table_status_info['Rows'] = row[3]
table_status_info['Data_length'] = row[5]
table_status_info['Max_data_length'] = row[7]
table_status_info['Create_time'] = row[10]
table_status_info['Update_time'] = row[11]
return table_status_info
def serialize_via_marshal(obj):
"""Serialize Python object via marshal into a compressed string."""
return compress(marshal.dumps(obj))
def deserialize_via_marshal(string):
"""Decompress and deserialize string into a Python object via marshal."""
return marshal.loads(decompress(string))
try:
import psyco
psyco.bind(serialize_via_marshal)
psyco.bind(deserialize_via_marshal)
except StandardError, e:
pass

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