Can't get Crontab to work

Question

I've been trying to get crontab to work for a while but it doesnt seem to want to work. The python script I need to initialise every midnight works perfectly from the command terminal. The location of my python script is:

/home/rv/ncbi-blast-2.2.23+/database_backup/backup.py

My contab looks like this:

SHELL=/bin/bash
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/home/rv/ncbi-blast-2.2.23+/database_backup
MAILTO=root
HOME=/
# For details see man 4 crontabs

# Example of job definition:
# .---------------- minute (0 - 59)
# |  .------------- hour (0 - 23)
# |  |  .---------- day of month (1 - 31)
# |  |  |  .------- month (1 - 12) OR jan,feb,mar,apr ...
# |  |  |  |  .---- day of week (0 - 6) (Sunday=0 or 7) OR sun,mon,tue,wed,thu,fri,sat
# |  |  |  |  |
# *  *  *  *  *  command to be executed
0 0 * * * /usr/bin/python /home/rv/ncbi-blast-2.2.23+/database_backup/backup.py

My python script looks like the following:

#!/usr/bin/python

from subprocess import Popen
import datetime

today = datetime.date.today()

today = str(today)

#print today

f = open("/home/rv/ncbi-blast-2.2.23+/database_backup/%s.sql" % (today), "w")
x =  Popen(["mysqldump", "-u", "root", "-p*****", "normalisation"], stdout = f)
x.wait()
f.close()

Any idea where im going wrong?

---

Just looked at the cron logs and i got this for each time entry I tried

(root) BAD FILE MODE (/etc/crontab)

I got the same error when i tried with a shell script aswell

Answer 1

Perhaps instead of using Python, make a bash script:

mysql_backup.sh

#!/bin/bash
/PATH/TO/mysqldump -u root -p***** normalisation > /SOMEOTHER/PATH/TO/$(date '+%Y-%m-%d').sql

and place this in your crontab:

0 0 * * * /PATH/TO/mysql_backup.sh 

Answer 2

If it works from your user account but not from cron it's usually not cron. The cron daemon tries to start your application but since it doesn't set up the environment variables it will fail. Create a simple shell script to setup your environment variables and starts your python script. (You don't have a PATH so you must use full path names, etc.)

Looking at your script you can do all this pretty easily using just shell script commands. Shell scripting is vastly under-rated.

Answer 3

you can just check crontab cmd, and execute those cmd manually, e.g.

/usr/bin/scrond run-parts /etc/cron.daily

Answer 4

I don't have an idea as to where you are going wrong, but you can redirect stderr and stdout to a file in your crontab entry which might give you a hint. My syntax memory is rusty but it's something like <yourfile>.py &> errors.txt

Of course, this also introduces another failure point, which is that you don't have permission to write to wherever you are putting errors.txt. ;-)