Python Script working stand alone but not in crontab

Question

I have a python script which which calls bash script to get list of all new directories created in last hour. Python script is executable.

    #!/usr/bin/python
import subprocess
import os
import dicom
import time

dire = '.'
directories = subprocess.check_output(
        ['find', '/dicom', '-maxdepth', '1', '-type', 'd', '-mmin', '-120', '-type', 'd', '-mmin', '+5']
).splitlines()
number_of_directories = len(directories)
b_new = 0
for n in range(1,number_of_directories):
    dire_str = str(directories[n])
    #dire_str = str(dire_str)
    print(dire_str)
    for dirpath,dirnames,filenames in os.walk(dire_str,topdown=True):
        a =1
        for filename in filenames:
            print(dirpath)
            if filename[-4:] == '.dcm':
                firstfilename = os.path.join(dirpath, filename)
                dcm_info = dicom.read_file(firstfilename, force=True)
                if dcm_info[0x0019, 0x109c].value == 'epiRTme':
                    dirpath_nii = dirpath[:-4]
            a = dirpath[-3:]
            a = int(a)
            os.chdir(dirpath_nii)
                    subprocess.call('/home/sdcme/bin/nii_mdir_sdcme %s %s' % (a, a), shell=True)
                break
            break

Apparently if i call this python script standalone on command prompt, it works fine but when i set it to run after 60 min on crontab, the script throws following error:

Traceback (most recent call last):
  File "/home/sdcme/Final_concat_sdcme.py", line 9, in <module>
    ['find', '/dicom', '-maxdepth', '1', '-type', 'd', '-mmin', '-120', '-type', 'd', '-mmin', '+5']
  File "/usr/lib64/python2.7/subprocess.py", line 530, in check_output
    process = Popen(stdout=PIPE, *popenargs, **kwargs)
  File "/usr/lib64/python2.7/subprocess.py", line 672, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.7/subprocess.py", line 1201, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory
~

Crontab Script

*/59 * * * * Final_concat_sdcme.py &>~concatenation.log

can some one point out what is the problem here.. Appreciate help a lot.

EDIT:

Cron output LOG Error:

niidicom_sdcme: Command not found.
niidicom_sdcme: Command not found.
niidicom_sdcme: Command not found.
niidicom_sdcme: Command not found.
niidicom_sdcme: Command not found.
niidicom_sdcme: Command not found.

Actually my python script calls nii_mdir_sdcme script calls niidicom_sdcme. When i run above script independently on terminal there is no error but when cron job cals the above script->nii_mdir_sdcme->niidicom_sdcme then there seems to be problem .

Don't overwrite the PATH variable - it's required to find system and user binaries. Instead, use the full path to the script and output file in the crontab. e.g. /home/sdcme/Findal_concat_sdcme — arco444
– arco444, Commented Aug 3, 2015 at 13:29
@arco444 I have edited my question with error log. can you please tell me what mistake i am making... — learnningprogramming
– learnningprogramming, Commented Aug 19, 2015 at 15:02

Arkanosis · Accepted Answer · 2015-08-03 13:28:24Z

3

I'm afraid you're overriding $PATH with a path that doesn't contain the find command, don't you?

The following might work better:

directories = subprocess.check_output(
        ['/usr/bin/find', '/dicom', '-maxdepth', '1', '-type', 'd', '-mmin', '-120', '-type', 'd', '-mmin', '+5']
).splitlines()

answered Aug 3, 2015 at 13:28

Arkanosis

2,3341 gold badge15 silver badges18 bronze badges

Sign up to request clarification or add additional context in comments.

3 Comments

learnningprogramming Over a year ago

Can you please review my question agaian as i have added error log too. ? many thanks

Arkanosis Over a year ago

The fact you have overriden $PATH has an impact not only on commands you execute (such as find), but also on commands commands you execute execute (such as if nii_mdir_sdcme then executes niidicom_sdcme). So, you have to make sure any command executed, be it by you or by the other commands, is available in $PATH.

learnningprogramming Over a year ago

i changed my cron job script.. now instead of changing path i am giving path of the script like ~/script/nii_mdir_sdcme.. But still with these changes the error shown is same ..

Collectives™ on Stack Overflow

Python Script working stand alone but not in crontab

1 Answer 1

3 Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

3 Comments

Your Answer

Sign up or log in

Post as a guest

Related