Python: Running external executables in your test

There are some helper functions for running external programs. You can use these instead of any of the half-dozen or so variants of popen that are in the standard library. This interface is simpler, it will not be deprecated as often as the other popen variants, and it is easier to be compatible with python testing packages.

Do not use subprocess

You most likely want to capture the stdout and stderr of the external program in your test log. By default, this will not work in subprocess – it will go to the stdout/stderr of pdkrun. If you want to use subprocess, you have to take special actions to capture the stdout/stderr and repeat it into Python’s stdout/stderr.

Instead, use the run_process function:

# NO
import subprocess [ 'ls', '-l' ] )

import pandokia.helpers.process as process

# run the program, capturing output into a file
status = process.run_process( [ 'ls', '-l' ], output_file='myfile.tmp' )

# read the file and print it to the stdout being used by the test [ "myfile.tmp" ] )

Since Pandokia will only run one test at a time in any working directory, it is not necessary to guarantee a unique name for the temp file. Since the output file will be created, it is not necessary to delete it before using it.

Running an external process

run_process executes a command with stdout/stderr redirected into a file:

import pandokia.helpers.process as pr
import os

arg = [ 'ls', '-ld', '.' ]

# run the process with arg list, using default environment and output file
status = pr.run_process( arg )

# explicitly read the output
out = open('output_file','r').read()
print "output was:"
print out
print "exit code is %d" % status

# run the process, explicitly specify everything
status = pr.run_process( arg, env=os.environ, output_file='myfile.tmp' )
out = open('myfile.tmp','r').read()

# just repeat the output to our own stdout
print "output was:" [ 'myfile.tmp' ] )
print "exit code is %d" % status

cat reads each file in a list and writes the content to stdout:

import pandokia.helpers.process as pr [ 'myfile.tmp' ] )

This is much like os.system("cat myfile.tmp") with one significant difference: os.system will write stdout to the same stdout that pandokia is writing to, so the output will not appear in your test report; will write the output into the sys.stdout that the test is using, which means that the file content will appear in the test report.

IRAF tasks

If you have Pyraf installed, you can run IRAF tasks:

import pandokia.helpers.filecomp as filecomp
import pandokia.helpers.process as process

tda = { }

f = open('parfile','w')
input,s,a,"dev$pix",,,Input images
output,s,a,"foo.fits",,,Output images or directory
verbose,b,h,no,,,Print operations performed?


process.run_pyraf_task('imcopy', 'parfile', output_file='foo.txt', tda=tda )

The tda dict is optional. If you supply it, task parameters will be entered as TDAs.

This is a simplified interface for pyraf tasks. You can also use the full capabilities of pyraf directly.

If the task returns an error, it will raise pr.RunPyrafTaskException which contains the values task and err:

except process.RunPyrafTaskException as e :
    print "task ",e.task
    print "err  ",e.err

The call may also raise any of the pyraf-related exceptions.