Start a python script from grails 3 - python

I created a web interface in Grails 3 where you can start different pipelines written in python via a web environment. I have created a simple form with a start button. The idea is now that when you press the start button the python pipeline is started. I can't figure it out I have tried several things a example is:
def cmd = "python amplicon_pipeline.py -i 'inputdir' -o 'outputdir' -a 'amplicon'"
def proc = cmd.execute()
proc.waitFor()
But nothing happens.
How can I get an external python script to start working when you press the start button?

Mention the full path to python and the script file.
Ex:
def cmd = ["/usr/bin/python", "/home/rm93/Documents/project_rivm/RIVM_amplicon_pipeline/amp‌​licon_pipeline.py", "-i", "/home/rm93/Documents/Git/BIGC_test_upload/amplicon_pipeline‌​/18/upload/", "-o", "/home/rm93/Documents/Git/BIGC_test_upload/amplicon_pipeline‌​/18/output/", "-a", "16sv4"]
def proc = cmd.execute()
proc.waitFor()
println proc.text

Related

Python script running installer.exe without user interaction

I am "translating" powershell scripts in to python, and I am having problems when it comes to run a installer.exe because it has to be automatic and with 0 interaction from the user. They just have to run the script and it installs both program and Microsoft Visual C++ versions. I mean, run, install and close on the background.
On powershell, it was so simple like doing this:
Start-Process -Wait -FilePath "$pwd\VC\vcredist2013_x64.exe" -ArgumentList "/passive /norestart" -PassThru | Out-Null
On python, i tried this and more:
import subprocess
def startProgram():
SW_HIDE = 0
info = subprocess.STARTUPINFO()
info.dwFlags = subprocess.STARTF_USESHOWWINDOW
info.wShowWindow = SW_HIDE
VC13=subprocess.Popen(r'vcredist2013_x64.exe', startupinfo=info)
VC13.wait()
startProgram()
But they are not working, the wizard still pops up.
You can try using the subprocess.run method instead, with the stdout and stderr parameters redirected to subprocess.DEVNULL. The /passive and /norestart arguments can be passed using the args parameter.
Here's an updated code snippet:
import subprocess
def startProgram():
subprocess.run(["vcredist2013_x64.exe", "/passive", "/norestart"], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
startProgram()

Execute a program with python, then send API commands to that program

I'm trying to write a python script that can launch DaVinci Resolve in headless mode, then send it some commands via its API, then close it.
What I'm looking for would look something like
Open resolve.exe with argument --nogui
Do stuff with the API here
Terminate this instance of Resolve
I've managed to launch an instance of Resolve in headless. But it always ends up being a subprocess of something else. While it's running as a subprocess, I can't get the API to communicate with it.
Here's the code of tried
import subprocess
args = ["C:\Program Files\Blackmagic Design\DaVinci Resolve\Resolve.exe", '--nogui']
resolve_headles = subprocess.Popen(args)
from python_get_resolve import GetResolve
resolve = GetResolve()
This should return an object of Resolve, but it always fails.
I believe this is because its running as a subprocess of my IDE
I've also tried this
from subprocess import call
dir = "C:\Program Files\Blackmagic Design\DaVinci Resolve"
cmdline = "Resolve.exe --nogui"
rc = call("start cmd /K " + cmdline, cwd=dir, shell=True)
This just has the same problem of Resolve running as a subprocess of Windows Command Processor.

How to resume a terminal with subprocess python

I am working with the subprocess module in Python. I am trying to run a series of terminals to automate a process.
To break it down:
I am suppose to have 3 terminals open to run a set of commands
like so:
Terminal 1: `cd src` -> `./run_script.sh`
Terminal 2: cd data -> `python prepare_data.py`
Terminal 3: `cd src` -> `./do_something.sh` #runs some docker container
Terminal 4: `cd src` -> `./do_another.sh`
Terminal 3: `./another_bash.sh`
To automate this the following:
class AutomateProcesses:
def run_terminal_1(self):
subprocess.call('./run_script.sh', shell=True, cwd='../src')
def run_terminal_2(self):
subprocess.call('python prepare_data.py', shell=True, cwd='../../data')
def run_terminal_3(self):
subprocess.call('./do_something.sh.sh', shell=True, cwd='../src')
def run_terminal_4(self):
subprocess.call('./do_another.sh', shell=True, cwd='../src')
How do I get back to terminal 3 to run the command?
It looks like you want to run several commands on a "terminal" (actually you don't see any terminal), it is just a sub-process that runs a shell.
I use the tool called pexpect (https://pexpect.readthedocs.io/en/latest/overview.html), it has the Windows-variant wexpect (https://pypi.org/project/wexpect/).
Below is the code sample, using the child variable, you can keep the "terminal" and send commands to it.
import pexpect
# log file to capture all the commands sent to the shell and their responses
output_file = open('log.txt','wb')
# create the bash shell sub-process
child = pexpect.spawn('/bin/bash', logfile=output_file)
child.stdout = output_file
child.expect(bytes('>', 'utf-8'))
# make sure you use the pair (sendline() and expect()) to wait until the command finishes
child.sendline(bytes('ls', 'utf-8'))
child.expect(bytes('>', 'utf-8'))
child.sendline(bytes('echo Hello World', 'utf-8'))
child.expect(bytes('>', 'utf-8'))
output_file.close()

Script to capture everything on screen

So I have this python3 script that does a lot of automated testing for me, it takes roughly 20 minutes to run, and some user interaction is required. It also uses paramiko to ssh to a remote host for a separate test.
Eventually, I would like to hand this script over to the rest of my team however, it has one feature missing: evidence collection!
I need to capture everything that appears on the terminal to a file. I have been experimenting with the Linux command 'script'. However, I cannot find an automated method of starting script, and executing the script.
I have a command in /usr/bin/
script log_name;python3.5 /home/centos/scripts/test.py
When I run my command, it just stalls. Any help would be greatly appreciated!
Thanks :)
Is a redirection of the output to a file what you need ?
python3.5 /home/centos/scripts/test.py > output.log 2>&1
Or if you want to keep the output on the terminal AND save it into a file:
python3.5 /home/centos/scripts/test.py 2>&1 | tee output.log
I needed to do this, and ended up with a solution that combined pexpect and ttyrec.
ttyrec produces output files that can be played back with a few different player applications - I use TermTV and IPBT.
If memory serves, I had to use pexpect to launch ttyrec (as well as my test's other commands) because I was using Jenkins to schedule the execution of my test, and pexpect seemed to be the easiest way to get a working interactive shell in a Jenkins job.
In your situation you might be able to get away with using just ttyrec, and skip the pexpect step - try running ttyrec -e command as mentioned in the ttyrec docs.
Finally, on the topic of interactive shells, there's an alternative to pexpect named "empty" that I've had some success with too - see http://empty.sourceforge.net/. If you're running Ubuntu or Debian you can install empty with apt-get install empty-expect
I actually managed to do it in python3, took a lot of work, but here is the python solution:
def record_log(output):
try:
with open(LOG_RUN_OUTPUT, 'a') as file:
file.write(output)
except:
with open(LOG_RUN_OUTPUT, 'w') as file:
file.write(output)
def execute(cmd, store=True):
proc = Popen(cmd.encode("utf8"), shell=True, stdout=PIPE, stderr=PIPE)
output = "\n".join((out.decode()for out in proc.communicate()))
template = '''Command:\n====================\n%s\nResult:\n====================\n%s'''
output = template % (cmd, output)
print(output)
if store:
record_log(output)
return output
# SSH function
def ssh_connect(start_message, host_id, user_name, key, stage_commands):
print(start_message)
try:
ssh.connect(hostname=host_id, username=user_name, key_filename=key, timeout=120)
except:
print("Failed to connect to " + host_id)
for command in stage_commands:
try:
ssh_stdin, ssh_stdout, ssh_stderr = ssh.exec_command(command)
except:
input("Paused, because " + command + " failed to run.\n Please verify and press enter to continue.")
else:
template = '''Command:\n====================\n%s\nResult:\n====================\n%s'''
output = ssh_stderr.read() + ssh_stdout.read()
output = template % (command, output)
record_log(output)
print(output)

How to run an AppleScript from within a Python script?

How to run an AppleScript from within a Python script?
The questions says it all..
(On a Mac obviously)
this nice article suggests the simple solution
cmd = """osascript -e 'tell app "Finder" to sleep'"""
def stupidtrick():
os.system(cmd)
though today you'd use the subprocess module instead of os.system, of course.
Be sure to also check page 2 of the article for many more info and options, including appscript.
A subprocess version which allows running an original apple script as-is, without having to escape quotes and other characters which can be tricky. It is a simplified version of the script found here which also does parametrization and proper escaping (Python 2.x).
import subprocess
script = '''tell application "System Events"
activate
display dialog "Hello Cocoa!" with title "Sample Cocoa Dialog" default button 2
end tell
'''
proc = subprocess.Popen(['osascript', '-'],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
stdout_output = proc.communicate(script)[0]
print stdout_output
NOTE: If you need to execute more than one script with the same Popen instance then you'll need to write explicitly with proc.stdin.write(script) and read with proc.stdout.read() because communicate() will close the input and output streams.
I got the Output folks... Here it's following:
import subprocess
import sys
for i in range(int(sys.argv[1])):
ip = str(sys.argv[2])
username = str(sys.argv[3])
pwd = str(sys.argv[4])
script = '''tell application "Terminal"
activate
do script with command "cd Desktop && python test_switch.py {ip} {username} {pwd}"
delay 15
end tell
'''
proc = subprocess.Popen(['osascript', '-'],
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
stdout_output = proc.communicate(script.format(ip=ip, username=username, pwd=pwd))[0]
I was pretty frustrated at the lack of detail in Apple's own documentation regarding how to do this AND to also pass in arguments. I had to send the desired arg (in this case a zoom id) as a string otherwise the argument didn't come through to the applescript app
Here's my code running from python:
f = script if os.path.exists(script) else _tempfile()
if not os.path.exists(script):
open(f,'w').write(script)
args = ["osascript", f, str(zoom_id)]
kwargs = {'stdout':open(os.devnull, 'wb'),'stderr':open(os.devnull, 'wb')}
#kwargs.update(params)
proc = subprocess.Popen(args,**kwargs)
and here is my applescript:
on run argv
set zoom_id to 0
zoom_id = item 1 in argv
tell application "zoom.us"
--do stuff
end tell
end run

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