connections.py

[Pedrissimo]

Does anyone know how to change the connections.py file in /usr/lib/python2.4/site-packages/MySQLdb/connections.py"
to a specific user?

The error I get is:

_mysql_exceptions.OperationalError: (1045, "Access denied for user 'root'@'localhost' (using password: NO)")

Attrched is the begiining of the file:

"""
 
This module implements connections for MySQLdb. Presently there is
only one class: Connection. Others are unlikely. However, you might
want to make your own subclasses. In most cases, you will probably
override Connection.default_cursor with a non-standard Cursor class.
 
"""
import cursors
from _mysql_exceptions import Warning, Error, InterfaceError, DataError, \
     DatabaseError, OperationalError, IntegrityError, InternalError, \
     NotSupportedError, ProgrammingError
import types, _mysql
 
 
def defaulterrorhandler(connection, cursor, errorclass, errorvalue):
    """
 
    If cursor is not None, (errorclass, errorvalue) is appended to
    cursor.messages; otherwise it is appended to
    connection.messages. Then errorclass is raised with errorvalue as
    the value.
 
    You can override this with your own error handler by assigning it
    to the instance.
 
    """
    error = errorclass, errorvalue
    if cursor:
        cursor.messages.append(error)
    else:
        connection.messages.append(error)
    del cursor
    del connection
    raise errorclass, errorvalue
 
 
class Connection(_mysql.connection):
 
    """MySQL Database Connection Object"""
 
    default_cursor = cursors.Cursor
 
    def __init__(self, *args, **kwargs):
        """
 
        Create a connection to the database. It is strongly recommended
        that you only use keyword parameters. Consult the MySQL C API
        documentation for more information.
 
        host
          string, host to connect
 
        user
          string, user to connect as
 
        passwd
          string, password to use

[bartonc]

Hello and welcome to the Python forum on TSDN.
The problem is not with /usr/lib/python2.4/site-packages/MySQLdb/connections.py

The error I get is:

_mysql_exceptions.OperationalError: (1045, "Access denied for user 'root'@'localhost' (using password: NO)")

The problem is that way you are calling it. Please post your code (not the library code). I'll dig up some examples that I have written which will help.

[bartonc]

Hello and welcome to the Python forum on TSDN.
The problem is not with /usr/lib/python2.4/site-packages/MySQLdb/connections.py"

The problem is that way you are calling it. Please post your code (not the library code). I'll dig up some examples that I have written which will help.

If this is a shared machine on "unix" you will most likely NOT have a root login and you will need the admin to create an account for you. If this is your own machine or you have an account already set up then you can get a connection like this:

from MySQLdb import *
# replace servername, username and password with your account info
dbconnect = connect(host=servername, user=username, passwd=password)
dbcursor = dbconnect.cursor()
# once you have a cursor, you can send SQL commands to the DB, like:
dbcursor.execute('SET autocommit=1')

Here are some useful classes and helper functions that I wrote.

[Pedrissimo]

Hi and thanks for getting back to me here is the code you asked for...

and the error again

_mysql_exceptions.OperationalError: (1045, "Access denied for user 'root'@'localhost' (using password: NO)")

import MySQLdb
import os
from splicegraph_jan06 import *
 
spliceCalcs={'hg17_JAN06':
             TableGroup(db='SPLICE_JAN06',suffix='hg17',clusters='cluster_hg17',
                        exons='isoform_exon_form_hg17',splices='splice_verificat
ion_hg17',
                        genomic='genomic_cluster_hg17',mrna='isoform_mrna_seq_hg
17',
                        protein='isoform_protein_seq_hg17'),
             'mm7_JAN06':
             TableGroup(db='SPLICE_JAN06',suffix='mm7',clusters='cluster_mm17',
                        exons='isoform_exon_form_mm7',splices='splice_verificati
on_mm7',
                        genomic='genomic_cluster_mm7',mrna='isoform_mrna_seq_mm7
',
                        protein='isoform_protein_seq_mm7')
             }
 
 
def getUserCursor(db):
    'get a cursor as the current user'
    db=MySQLdb.connect(db=db,read_default_file=os.environ['HOME']+'/.my.cnf',com
press=True)
    return db.cursor()
 
def getSpliceGraphFromDB(dbgroup,loadAll=False):
    """load data from MySQL using the designated database table group.
    If loadAll true, then load the entire splice graph into memory."""
    cursor=getUserCursor(dbgroup.db)
    import sys
    print >>sys.stderr,'Reading database schema...'
    idDict={}
    tables=describeDBTables(dbgroup.db,cursor,idDict)
    if hasattr(dbgroup,'suffix'):
        tables=suffixSubset(tables,dbgroup.suffix) # SET OF TABLES ENDING IN JUN
03
        idDict=indexIDs(tables) # CREATE AN INDEX OF THEIR PRIMARY KEYS
    for t in dbgroup.values():
        if t is not None and '.' in t and t not in tables: # THIS TABLE COMES FR
OM ANOTHER DATABASE...
            tables[t]=SQLTable(t,cursor) # SO GET IT FROM OTHER DATABASE
 
    # LOAD DATA & BUILD THE SPLICE GRAPH
    return loadSpliceGraph(tables,dbgroup.clusters,dbgroup.exons,dbgroup.splices
,
                           dbgroup.genomic,dbgroup.mrna,dbgroup.protein,loadAll)
 
def localCopy(localFile,cpCommand):
    'if not already present on local file location, run cpCommand'
    if not os.access(localFile,os.R_OK):
        cmd=cpCommand % localFile
        print 'copying data:',cmd
        exit_code=os.system(cmd)
        if exit_code!=0:
            raise OSError((exit_code,'command failed: %s' % cmd))
    return localFile

[bartonc]

Hi and thanks for getting back to me here is the code you asked for...

and the error again

_mysql_exceptions.OperationalError: (1045, "Access denied for user 'root'@'localhost' (using password: NO)")

import MySQLdb
import os
def getUserCursor(db):
    'get a cursor as the current user'
    db=MySQLdb.connect(db=db,read_default_file=os.environ['HOME']+'/.my.cnf',com
press=True)
    return db.cursor()

First I'd see if you can make this work

# replace servername, username and password with your account info
dbconnect = connect(host=servername, user=username, passwd=password)
dbcursor = dbconnect.cursor()
 

Then, if that works, check to see if your
my.cnf
is set up correctly. I should look like this:
You can specify connection parameters in the [client] section of an option file. The relevant section of the file might look like this:
[client]
host=host_name
user=user_name
password=your_pass
Section 4.3.2, “Using Option Files”, discusses option files further.
according to MySQL docs.
It also looks like you can specify other that "client" group using
read_default_group
configuration group to use from the default file
but mysqld docs are not very clear on that.

[Pedrissimo]

Hi again,

I enter the following lines you recommend

dbconnect = connect(host=hostname, user=root, passwd=*******)
dbcursor = dbconnect.cursor()

and get the following error?

File "/home/pedro/pygr/tests/lldb_jan06.py", line 22, in ?
dbconnect = connect(host=hostname, user=root, passwd=*******)
NameError: name 'connect' is not defined

First I'd see if you can make this work

# replace servername, username and password with your account info
dbconnect = connect(host=servername, user=username, passwd=password)
dbcursor = dbconnect.cursor()
 

Then, if that works, check to see if your
my.cnf
is set up correctly. I should look like this:
You can specify connection parameters in the [client] section of an option file. The relevant section of the file might look like this:
[client]
host=host_name
user=user_name
password=your_pass
Section 4.3.2, “Using Option Files”, discusses option files further.
according to MySQL docs.
It also looks like you can specify other that "client" group using
read_default_group
configuration group to use from the default file
but mysqld docs are not very clear on that.

[bartonc]

Hi again,

I enter the following lines you recommend

dbconnect = connect(host=hostname, user=root, passwd=*******)
dbcursor = dbconnect.cursor()

and get the following error?

File "/home/pedro/pygr/tests/lldb_jan06.py", line 22, in ?
dbconnect = connect(host=hostname, user=root, passwd=*******)
NameError: name 'connect' is not defined

Sorry, that was a snippet.. should be:

from MySQLdb import *
dbconnect = connect(host=hostname, user=root, passwd=*******)
dbcursor = dbconnect.cursor()
 

as in my reply #3 above.

[Pedrissimo]

Ok that worked but now I get another error from a second py program...

File "/home/pedro/pygr/tests/lldb_jan06.py", line 34, in getSpliceGraphFromDB
tables=describeDBTables(dbgroup.db,cursor,idDict)
File "/usr/lib/python2.4/site-packages/pygr/sqlgraph.py", line 212, in describeDBTables
cursor.execute('use %s' % name)
AttributeError: 'NoneType' object has no attribute 'execute'

Here is the portion of the script:

def describeDBTables(name,cursor,idDict):
    """
    Get table info about database <name> via <cursor>, and store primary keys
    in idDict, along with a list of the tables each key indexes.
    """
    cursor.execute('use %s' % name)
    cursor.execute('show tables')
    tables={}
    l=[c[0] for c in cursor.fetchall()]
    for t in l:

tname=name+'.'+t
o=SQLTable(tname,cursor)
[/code]

and the original change from the other py script


[code]
def getUserCursor(db):
'get a cursor as the current user'
#db=MySQLdb.connect(db=db,read_default_file=os.env iron['HOME']+'/.my.cnf',com
#press=True)
# return db.cursor()
from MySQLdb import *
dbconnect = connect(host='localhost', user='root', passwd='retep1er')
dbcursor = dbconnect.cursor()
[code]

Incidentally I changed my /etc/mysql/my.cnf file (my only my.cnf) file

[client]
[client]
user = 'root'
password = '********'
port = 3306
socket = /var/run/mysqld/mysqld.sock

with the original configuration of the py file

[code]
def getUserCursor(db):
'get a cursor as the current user'
db=MySQLdb.connect(db=db,read_default_file=os.envi ron['HOME']+'/.my.cnf',com
press=True)
return db.cursor()

[\CODE]

and this produced the original error?

[bartonc]

If this is a shared machine on "unix" you will most likely NOT have a root login and you will need the admin to create an account for you. If this is your own machine or you have an account already set up then you can get a connection like this:

from MySQLdb import *
# replace servername, username and password with your account info
dbconnect = connect(host=servername, user=username, passwd=password)
dbcursor = dbconnect.cursor()
# once you have a cursor, you can send SQL commands to the DB, like:
dbcursor.execute('SET autocommit=1')

Here are some useful classes and helper functions that I wrote.

Here for error handling example.