I am writing a program to automate some qiime2 commands. I want to incorporate user input.
So far, I have:
# Items to import
import subprocess
from sys import argv
#Variables
format=argv[1]
# Import sequences for Phred33 format
if format=='Phred33':
cmnd = 'qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-path manifest.csv --output-path paired-end-demux.qza --source-format PairedEndFastqManifestPhred33'
print('executing {}'.format(cmnd))
res = subprocess.call(cmnd, shell=True)
print('command terminated with status', res)
# Import sequences for Phred64 format
if format=='Phred64':
cmnd = 'qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-path manifest.csv --output-path paired-end-demux.qza --source-format PairedEndFastqManifestPhred64'
print('executing {}'.format(cmnd))
res = subprocess.call(cmnd, shell=True)
print('command terminated with status', res)
This works fine since there's only two possible user inputs, but I'd rather not have the if statements down the line when there will be countless possible user inputs.
This would be better:
cmnd = 'qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-path manifest.csv --output-path paired-end-demux.qza --source-format PairedEndFastqManifest', format
But qiime2 gives me errors with this. Is there another way?
Thank you!
Don't use shell=True when the command you are executing is built from unsanitized user input. It can lead to the user being able to execute arbitrary commands, even if this is not wanted.
Also, pass the command as a list to subprocess.call to avoid issues with quoting.
cmnd = [
'qiime', 'tools', 'import',
'--type', 'SampleData[PairedEndSequencesWithQuality]',
'--input-path', 'manifest.csv',
'--output-path', 'paired-end-demux.qza',
'--source-format', 'PairedEndFastq{}'.format(format)
]
print('executing {}'.format(' '.join(cmnd)))
res = subprocess.call(cmnd)
References, related questions
subprocess.call using string vs using list
Actual meaning of 'shell=True' in subprocess
https://docs.python.org/2/library/subprocess.html#frequently-used-arguments
Related
im using an email lookup module, called holehe (more can be found on it here - https://github.com/megadose/holehe) and i want to make it so when you enter an email it will automatically with in your python console output what came out from the new CMD window, makes it easier for my and colleges to use. How can i go about this? My code it bellow
import holehe
import os
from os import system
import subprocess
email = input("Email:")
p = subprocess.Popen(["start", "cmd", "/k", "holehe", email], shell = True)
p.wait()
input()
Thank you for answers
I have the following program that wraps top in a pseudo terminal and prints it back to the real terminal.
import os
import pty
import subprocess
import sys
import time
import select
stdout_master_fd, stdout_slave_fd = pty.openpty()
stderr_master_fd, stderr_slave_fd = pty.openpty()
p = subprocess.Popen(
"top",
shell=True,
stdout=stdout_slave_fd,
stderr=stderr_slave_fd,
close_fds=True
)
stdout_parts = []
while p.poll() is None:
rlist, _, _ = select.select([stdout_master_fd, stderr_master_fd], [], [])
for f in rlist:
output = os.read(f, 1000) # This is used because it doesn't block
sys.stdout.write(output.decode("utf-8"))
sys.stdout.flush()
time.sleep(0.01)
This works well control sequences are handled as expected. However, the subprocess is not using the full dimensions of the real terminal.
For comparison, running the above program:
And running top directly:
I didn't find any api of the pty library to suggest dimensions could be provided.
The dimensions I get in practice for the pseudo terminal are height of 24 lines and width of 80 columns, I'm assuming it might be hardcoded somewhere.
Reading on Emulate a number of columns for a program in the terminal I found the following working solution, at least on my environment (OSX and xterm)
echo LINES=$LINES COLUMNS=$COLUMNS TERM=$TERM
which comes to LINES=40 COLUMNS=203 TERM=xterm-256color in my shell. Then setting the following in the script gives the expected output:
p = subprocess.Popen(
"top",
shell=True,
stdout=stdout_slave_fd,
stderr=stderr_slave_fd,
close_fds=True,
env={
"LINES": "40",
"COLUMNS": "203",
"TERM": "xterm-256color"
}
)
#Mugen's answer pointed me in the right direction but did not quite work, here is what worked for me personally :
import os
import subprocess
my_env = os.environ.copy()
my_env["LINES"] = "40"
my_env["COLUMNS"] = "203"
result = subprocess.Popen(
cmd,
stdout= subprocess.PIPE,
env=my_env
).communicate()[0]
So I had to first get my entire environment variable with os library and then add the elements I needed to it.
The solutions provided by #leas and #Mugen did not work for me, but I eventually stumbled upon ptyprocess Python module, which allows you to provide terminal dimensions when spawning a process.
For context, I am trying to use a Python script to run a PowerShell 7 script and capture the PowerShell script's output. The host OS is Ubuntu Linux 22.04.
My code looks something like this:
from ptyprocess import PtyProcessUnicode
# Run the PowerShell script
script_run_cmd = 'pwsh -file script.ps1 param1 param2'
p = PtyProcessUnicode.spawn(script_run_cmd.split(), dimensions=(24,130))
# Get all script output
script_output = []
while True:
try:
script_output.append(p.readline().rstrip())
except EOFError:
break
# Not sure if this is necessary
p.close()
I feel like there should be a class method to get all the output, but I couldn't find one and the above code works well for me.
I have some trouble to flash an stm32 over a python script. I'm using the ST-LINK_CLI.exe, provided by the ST Link Utility tool, to flash the uC and it works by using the CMD in Windows, but not over the python tool.
The error I get back from the subprocess.run(...) is "Unable to open file!" for the path I provide, but the same path works fine in the CMD from Windows.
import subprocess
path = 'C:/Users/U1/Desktop/test.hex'
path = path.encode('utf-8')
stlink_output=[]
try:
stlink_output = subprocess.run(
["ST-LINK_CLI.exe", "-c", "ID=0", "SWD", "-P", str(path), "-V", "-HardRST", "-Rst"],
check=False,
stdout=subprocess.PIPE).stdout.decode().splitlines()
except:
print("An error occured")
print(stlink_output)
Has anyone an idea, what can be wrong with the provided path? Should I use a different encoding?
You are not decoding your path, just casting your bytes as string, so you get a path like
"b'C:/Users/U1/Desktop/test.hex'"
Try to decode instead to get proper string
stlink_output = subprocess.run(
["ST-LINK_CLI.exe", "-c", "ID=0", "SWD", "-P", path.decode(), "-V", "-HardRST", "-Rst"],
check=False,
stdout=subprocess.PIPE).stdout.decode().splitlines()
If You're sure the output values are text please consider using run text=True parameter (and encoding if needed).
Just define path as string and use it (no need to encode/decode).
Also for python 3.4+ it is recommended to use pathlib module (allows neat checks and user expansion in Your code later).
So the code would look something like:
import subprocess
import pathlib
# `~` gets converted to current user home with expanduser()
# i.e. `C:/Users/U1` in Your case
path = pathlib.Path('~/Desktop/test.hex').expanduser()
if not path.exists():
raise FileNotFoundError(path)
stlink_output = subprocess.run(
["ST-LINK_CLI.exe", "-c", "ID=0", "SWD", "-P", path, "-V", "-HardRST", "-Rst"],
check=False,
# text option without decoding requires py3.7+...
# text=True,
# stdout=subprocess.PIPE).stdout.splitlines()
# ...so this is variant pre python3.7:
stdout=subprocess.PIPE).stdout.decode().splitlines()
print(stlink_output)
I have a script that I want to run from within Python (2.6.5) that follows the logic below:
Prompts the user for a password. It looks like ("Enter password: ") (*Note: Input does not echo to screen)
Output irrelevant information
Prompt the user for a response ("Blah Blah filename.txt blah blah (Y/N)?: ")
The last prompt line contains text which I need to parse (filename.txt). The response provided doesn't matter (the program could actually exit here without providing one, as long as I can parse the line).
My requirements are somewhat similar to Wrapping an interactive command line application in a Python script, but the responses there seem a bit confusing, and mine still hangs even when the OP mentions that it doesn't for him.
Through looking around, I've come to the conclusion that subprocess is the best way of doing this, but I'm having a few issues. Here is my Popen line:
p = subprocess.Popen("cmd", shell=True, stdout=subprocess.PIPE,
stderr=subprocess.STDOUT, stdin=subprocess.PIPE)
When I call a read() or readline() on stdout, the prompt is printer to the screen and it hangs.
If I call a write("password\n") for stdin, the prompt is written to the screen and it hangs. The text in write() is not written (I don't the cursor move the a new line).
If I call p.communicate("password\n"), same behavior as write()
I was looking for a few ideas here on the best way to input to stdin and possibly how to parse the last line in the output if your feeling generous, though I could probably figure that out eventually.
If you are communicating with a program that subprocess spawns, you should check out A non-blocking read on a subprocess.PIPE in Python. I had a similar problem with my application and found using queues to be the best way to do ongoing communication with a subprocess.
As for getting values from the user, you can always use the raw_input() builtin to get responses, and for passwords, try using the getpass module to get non-echoing passwords from your user. You can then parse those responses and write them to your subprocess' stdin.
I ended up doing something akin to the following:
import sys
import subprocess
from threading import Thread
try:
from Queue import Queue, Empty
except ImportError:
from queue import Queue, Empty # Python 3.x
def enqueue_output(out, queue):
for line in iter(out.readline, b''):
queue.put(line)
out.close()
def getOutput(outQueue):
outStr = ''
try:
while True: # Adds output from the Queue until it is empty
outStr+=outQueue.get_nowait()
except Empty:
return outStr
p = subprocess.Popen("cmd", stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=False, universal_newlines=True)
outQueue = Queue()
errQueue = Queue()
outThread = Thread(target=enqueue_output, args=(p.stdout, outQueue))
errThread = Thread(target=enqueue_output, args=(p.stderr, errQueue))
outThread.daemon = True
errThread.daemon = True
outThread.start()
errThread.start()
try:
someInput = raw_input("Input: ")
except NameError:
someInput = input("Input: ")
p.stdin.write(someInput)
errors = getOutput(errQueue)
output = getOutput(outQueue)
Once you have the queues made and the threads started, you can loop through getting input from the user, getting errors and output from the process, and processing and displaying them to the user.
Using threading it might be slightly overkill for simple tasks.
Instead os.spawnvpe can be used. It will spawn script shell as a process. You will be able to communicate interactively with the script.
In this example I passed password as an argument, obviously that is not a good idea.
import os
import sys
from getpass import unix_getpass
def cmd(cmd):
cmd = cmd.split()
code = os.spawnvpe(os.P_WAIT, cmd[0], cmd, os.environ)
if code == 127:
sys.stderr.write('{0}: command not found\n'.format(cmd[0]))
return code
password = unix_getpass('Password: ')
cmd_run = './run.sh --password {0}'.format(password)
cmd(cmd_run)
pattern = raw_input('Pattern: ')
lines = []
with open('filename.txt', 'r') as fd:
for line in fd:
if pattern in line:
lines.append(line)
# manipulate lines
If you just want a user to enter a password without it being echoed to the screen just use the standard library's getpass module:
import getpass
print("You entered:", getpass.getpass())
NOTE:The prompt for this function defaults to "Password: " also this will only work on command lines where echoing can be controlled. So if it doesn't work try running it from terminal.
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