How to read a database created with python with R - python

I've created a database with the python package sqlite3.
import sqlite3
conn=sqlite3.connect('foo.sqlite')
c=conn.cursor()
c.execute('CREATE TABLE foo (bar1 int, bar2 int)')
conn.commit()
conn.close
Then for statistical purposes I try to read this database with R (I use the R package RSQLite)
library('RSQLite')
drv=dbDriver('SQLite')
foo=dbConnect(drv,'foo.sqlite')
If I want to list the table I've just created with Python
dbListTables(foo)
R says that the database is empty :
character(0)
Am I doing something wrong or does R cannot read a Python database ?
Thanks for your help

Try closing your database connection in python, rather than just instantiating the close method:
conn.close()
Spot the difference? Then it all works for me.
> dbListTables(foo)
[1] "foo"
although it all works for me even if I don't close the connection, and even if I've not quit python after the commit. So, umm...

Related

How to make python modules based sqlite3 print raw sqlite3 commands as debug messages? [duplicate]

I'm using Sqlite3 database in my Python application and query it using parameters substitution.
For example:
cursor.execute('SELECT * FROM table WHERE id > ?', (10,))
Some queries do not return results properly and I would like to log them and try to query sqlite manually.
How can I log these queries with parameters instead of question marks?
Python 3.3 has sqlite3.Connection.set_trace_callback:
import sqlite3
connection = sqlite3.connect(':memory:')
connection.set_trace_callback(print)
The function you provide as argument gets called for every SQL statement that is executed through that particular Connection object. Instead of print, you may want to use a function from the logging module.
Assuming that you have a log function, you could call it first :
query, param = 'SELECT * FROM table WHERE id > ?', (10,)
log(query.replace('?', '%s') % param)
cursor.execute(query, param)
So you don't modify your query at all.
Moreover, this is not Sqlite specific.

Python mysql doesn't see data change in database

i need some help with python an mysql.
I have the following code, which is executing in infinite loop:
db = MySQLdb.connect("127.0.0.1","user","password","dbname" )
while True:
cursor = db.cursor()
cursor.execute("SELECT * FROM requests WHERE status <> 'Finished'")
all_pending_requests = cursor.fetchall()
cursor.close()
And that works fine the first time i run it. But when i go to a tool like mysql workbench or i type it myself in in terminal, i update some rows and set their status to something that is not "Finished". So by doing that the next time the loop executes i should get those rows as a result but i get nothing. Do you guys now why this is happening maybe?
Thanks for help.
I am not certain but would assume that you are using InnoDB storage engine in MySQL and MySQLdb version >=1.2.0. You need to commit before the changes are being reflected. As of version 1.2.0, MySQLdb disables auto-commit by default. Confirmation of the same is here. Try adding db.commit() as the last line in the loop.

UPDATE statement on Access database fails silently under pyodbc

I have a problem with a simple UPDATE statement. I wrote a Python tool which creates a lot of UPDATE statements and after creating them I want to execute them on my Access database but it doesn't work This is one statement for example:
UPDATE FCL_B_COVERSHEET_A SET BRANCH = 0 WHERE OBJ_ID = '1220140910132011062005';
The statement syntax is not the problem. I tested it and it works.
This next code snippet shows the initialization for the connect object.
strInputPathMDB = "C:\\Test.mdb"
DRV = '{Microsoft Access Driver (*.mdb)}';
con = pyodbc.connect('Driver={0};Dbq={1};Uid={2};Pwd={3};'.format(DRV,strInputPathMDB,"administrator",""))
After that I wrote a method which execute one SQL statement
def executeSQLStatement(conConnection, strSQL):
arcpy.AddMessage(strSQL)
cursor = conConnection.cursor()
cursor.execute(strSQL)
conConnection.commit()
and if I execute this code everything seems to work - no error message or anything like that - but also the data is not updated and I don't know what I'm doing wrong ...
for strSQL in sqlStateArray:
executeSQLStatement(con, strSQL)
con.close()
I hope you understand what my problem is. Thanks for your help.
Chris
The issue here was that the .mdb file was in the root folder of the C: drive. Root folders often restrict normal users to read-only access so the database file was being opened as read-only. Moving the .mdb file to a public folder solved the problem.

SQLite Insert command in Python script Doesn't work on web

I'm trying to use an SQLite insert operation in a python script, it works when I execute it manually on the command line but when I try to access it on the web it won't insert it in the database. Here is my function:
def insertdb(unique_id,number_of_days):
conn = sqlite3.connect('database.db')
print "Opened database successfully";
conn.execute("INSERT INTO IDENT (ID_NUM,DAYS_LEFT) VALUES (?,?)",(unique_id,number_of_days));
conn.commit()
print "Records created successfully";
conn.close()
When it is executed on the web, it only shows the output "Opened database successfully" but does not seem to insert the value into the database. What am I missing? Is this a server configuration issue? I have checked the database permissions on writing and they are correctly set.
The problem is almost certainly that you're trying to create or open a database named database.db in whatever happens to be the current working directory, and one of the following is true:
The database exists and you don't have permission to write to it. So, everything works until you try to do something that requires write access (like commiting an INSERT).
The database exists, and you have permission to write to it, but you don't have permission to create new files in the directory. So, everything works until sqlite needs to create a temporary file (which it almost always will for execute-ing an INSERT).
Meanwhile, you don't mention what web server/container/etc. you're using, but apparently you have it configured to just swallow all errors silently, which is a really, really bad idea for any debugging. Configure it to report the errors in some way. Otherwise, you will never figure out what's going on with anything that goes wrong.
If you don't have control over the server configuration, you can at least wrap all your code in a try/except and manually log exceptions to some file you have write access to (ideally via the logging module, or just open and write if worst comes to worst).
Or, you can just do that with dumb print statements, as you're already doing:
def insertdb(unique_id,number_of_days):
conn = sqlite3.connect('database.db')
print "Opened database successfully";
try:
conn.execute("INSERT INTO IDENT (ID_NUM,DAYS_LEFT) VALUES (?,?)",(unique_id,number_of_days));
conn.commit()
print "Records created successfully";
except Exception as e:
print e # or, better, traceback.print_exc()
conn.close()

Print the actual query MySQLdb runs?

I'm looking for a way to debug queries as they are executed and I was wondering if there is a way to have MySQLdb print out the actual query that it runs, after it has finished inserting the parameters and all that? From the documentation, it seems as if there is supposed to be a Cursor.info() call that will give information about the last query run, but this does not exist on my version (1.2.2).
This seems like an obvious question, but for all my searching I haven't been able to find the answer.
We found an attribute on the cursor object called cursor._last_executed that holds the last query string to run even when an exception occurs. This was easier and better for us in production than using profiling all the time or MySQL query logging as both of those have a performance impact and involve more code or more correlating separate log files, etc.
Hate to answer my own question but this is working better for us.
You can print the last executed query with the cursor attribute _last_executed:
try:
cursor.execute(sql, (arg1, arg2))
connection.commit()
except:
print(cursor._last_executed)
raise
Currently, there is a discussion how to get this as a real feature in pymysql (see pymysql issue #330: Add mogrify to Cursor, which returns the exact string to be executed; pymysql should be used instead of MySQLdb)
edit: I didn't test it by now, but this commit indicates that the following code might work:
cursor.mogrify(sql, (arg1, arg2))
For me / for now _last_executed doesn't work anymore. In the current version you want to access
cursor.statement.
see: https://dev.mysql.com/doc/connector-python/en/connector-python-api-mysqlcursor-statement.html
For mysql.connector:
cursor.statement
https://dev.mysql.com/doc/connector-python/en/connector-python-api-mysqlcursor-statement.html
cursor.statement and cursor._last_executed raised AttributeError exception
cursor._executed
worked for me!
One way to do it is to turn on profiling:
cursor.execute('set profiling = 1')
try:
cursor.execute('SELECT * FROM blah where foo = %s',[11])
except Exception:
cursor.execute('show profiles')
for row in cursor:
print(row)
cursor.execute('set profiling = 0')
yields
(1L, 0.000154, 'SELECT * FROM blah where foo = 11')
Notice the argument(s) were inserted into the query, and that the query was logged even though the query failed.
Another way is to start the server with logging turned on:
sudo invoke-rc.d mysql stop
sudo mysqld --log=/tmp/myquery.log
Then you have to sift through /tmp/myquery.log to find out what the server received.
I've had luck with cursor._last_executed generally speaking, but it doesn't work correctly when used with cursor.executemany(). That drops all but the last statement. Here's basically what I use now in that instance instead (based on tweaks from the actual MySQLDb cursor source):
def toSqlResolvedList( cursor, sql, dynamicValues ):
sqlList=[]
try:
db = cursor._get_db()
if isinstance( sql, unicode ):
sql = sql.encode( db.character_set_name() )
for values in dynamicValues :
sqlList.append( sql % db.literal( values ) )
except: pass
return sqlList
This read-only property returns the last executed statement as a string. The statement property can be useful for debugging and displaying what was sent to the MySQL server.
The string can contain multiple statements if a multiple-statement string was executed. This occurs for execute() with multi=True. In this case, the statement property contains the entire statement string and the execute() call returns an iterator that can be used to process results from the individual statements. The statement property for this iterator shows statement strings for the individual statements.
str = cursor.statement
source: https://dev.mysql.com/doc/connector-python/en/connector-python-api-mysqlcursor-statement.html
I can't say I've ever seen
Cursor.info()
In the documentation, and I can't find it after a few minutes searching. Maybe you saw some old documentation?
In the mean time you can always turn on MySQL Query Logging and have a look at the server's log files.
assume that your sql is like select * from table1 where 'name' = %s
from _mysql import escape
from MySQLdb.converters import conversions
actual_query = sql % tuple((escape(item, conversions) for item in parameters))

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