Python Not Running Shell Commands After Reboot Using Launch Agent - bash

Question

So, I'm starting a Python (2.7) script via a launch agent, on macOS 10.13. The script runs, and during execution, it triggers a restart of the computer. When the computer turns back on and logs in, the launch agent runs the script again. The script reads the logs, and does a switch:case to pick up where it left off.
The problem is, after the restart, the python script is unable to execute some shell commands. ls -l works fine. However, when I try to run something that isn't in /bin, it seems to just... skip over it. No errors, it simply doesn't do it.
Here's the related code. I've removed most of the specifics, as well as the switch control, because I've verified they are working, independently.
#!/usr/bin/python
import logging
import os
import subprocess
import time
#globals
path_to_plist = 'User/Me/Library/Preferences/PathTo.plist'
def spot_check():
#determine where we are in the test, verified it works
return loop_number
def func_that_checks_stuff():
results = subprocess.check_output(['System/Library/Path/To/tool','-toolarg'])
###process results
logging.info(results)
def restarts(power_on, power off):
#sets plist key values for the restart app
subprocess.Popen('defaults write {} plist_key1 {}'.format(path_to_plist, power_on), shell=True
subprocess.Popen('defaults write {} plist_key2 {}'.format(path_to_plist, power_off), shell=True
#run the restart app, which is a GUI application in /Applications
logging.info('Starting restart app')
subprocess.Popen('open -a RestartApp.app', shell=True)
time.sleep(power_on + 5)
def main():
###setup and config stuff, verified its working
#switch control stuff, verified its working
loop = spot_check()
if loop == 0:
#tool that shows text on the screen
subprocess.Popen('User/Me/Library/Scripts/Path/To/Text/tool -a -args', shell=True)
logging.info('I just ran that tool')
subprocess.check_output('ls -l', shell=True)
restarts(10, 0)
if loop == 1:
func_that_checks_stuff()
subprocess.Popen('User/Me/Library/Scripts/Path/To/Text/tool -a args', shell=True)
logging.info('Hey I ran that tool again, see?')
restarts(10, 0)
else:
func_that_checks_stuff()
subprocess.Popen('User/Me/Library/Scripts/Path/To/Text/tool -a args', shell=True)
print 'You finished!'
if __name__ == '__main__':
main()
So, if I start this using my launch agent, it will run through every sequence just fine.
On the first loop (prior to the restart), EVERYTHING works. All logging, all tools, everything.
After the restart, all the logging works, so I know it's following the switch control. The func_that_checks_stuff() works, and logs it's output correctly. The ls -l' call shows me exactly what I should see. But,Path/To/Text/tooldoesn't run, and when I callrestarts()`, it never opens the app.
No errors are produced, at least that I can find
What am I doing wrong? Is it something to do with the tool paths?

Answer 1

Update:
As it turns out, the solution was to add a ~20 second delay at the start of the script. It seems like it was trying to run the commands in question before Window Server had finished loading, and that freaked everything out. Not a particularly elegant solution, but it works for what I need in this project.