Single quotes in the expanded args should be escaped #31
Description
Hello,
thank you for this library.
I noticed a small bug when using single quotes in arguments.
I believe that single quotes in the expanded args (
Line 615 in 665d5b5
In my case I'm running
bash, "-c", "source /tmp/init.sh ; /bin/sort '-s' '-k' '3' '-t' '\t'"
(note I use , to separate the arguments, in total two arguments are passed to bash)
which will then be translated into
d #15300 [ 0.06] * # Script:
d #15300 [ 0.06] | #!/bin/bash
d #15300 [ 0.06] | bash '-c' 'source /tmp/init.sh ; /bin/sort '-s' '-k' '3' '-t' ' ''
However this fails with:
/bin/sort: option requires an argument -- 't'
Try '/bin/sort --help' for more information.
I believe what happens internally is that bash -c treats source /tmp/init.sh ; /bin/sort as the first string and as per documentation everything after becomes an argument:
If the -c option is present, then commands are read from string. If there are arguments after the string, they are assigned to the positional parameters, starting with $0.
To solve this I believe that the single quotes within the expanded args should be escaped (e.g. via https://creativeandcritical.net/str-replace-c)
=======
consider this minimal example:
#!/usr/bin/env python
import drmaa
import os
def main():
error_log = os.path.join(os.getcwd(), 'error.log')
with drmaa.Session() as s:
print('Creating job template')
jt = s.createJobTemplate()
jt.remoteCommand = "/bin/bash"
jt.args = [ '-c', "/bin/sort '-s' '-k' '3' '-t' '\t'" ]
jt.errorPath = ":" + error_log
jobid = s.runJob(jt)
print('Your job has been submitted with ID {0}'.format(jobid))
retval = s.wait(jobid, drmaa.Session.TIMEOUT_WAIT_FOREVER)
print('Job: {0} finished with status {1}'.format(retval.jobId, retval.exitStatus))
with open(error_log, 'r') as fin:
print(fin.read())
print('Cleaning up')
s.deleteJobTemplate(jt)
os.remove(error_log)
if __name__=='__main__':
main()results in
$ python foo.py
Creating job template
Your job has been submitted with ID 7990
Job: 7990 finished with status 2
/bin/sort: option requires an argument -- 't'
Try '/bin/sort --help' for more information.
Cleaning up