Apple Script to execute terminal command and display results - applescript

I am totally newbie with Apple script (and scripts in general).
I have a Terminal command which uses cfgutil to display informations about a lot of iPad.
The command is as follows:
./cfgutil -f --format JSON get-property name firmwareVersion batteryCurrentCapacity passcodeProtected configurationProfiles installedApps
cfgutil is inside Apple Configurator 2 app
/Applications/Apple\\ Configurator\\ 2.app/Contents/MacOS/cfgutil
I made an Apple Script to generate a text file from a Python script.
on run {input, parameters}
tell application "Terminal"
activate
do script with command "/Applications/Apple\\ Configurator\\ 2.app/Contents/MacOS/cfgutil -f --format JSON get-property name firmwareVersion batteryCurrentCapacity passcodeProtected configurationProfiles installedApps | python3  /Users/admin/Desktop/jsonpy3.py > /Users/admin/Desktop/Check.txt | top; exit"
end tell
end run
The Python script (thx to flaf):
#!/usr/bin/env python3
import sys
import json
human_readable_fields = {
'name': 'Nom',
'firmwareVersion': 'Firmware',
'batteryCurrentCapacity': 'Charge',
'passcodeProtected': 'Passcode',
'configurationProfiles': 'Profils',
'installedApps': 'Applications',
}
template = ' '.join(
['{name:<25.25}', # name will be truncated to 25 characters.
'{firmwareVersion:>10}',
'{batteryCurrentCapacity:>10}',
'{passcodeProtected:>15}',
'{configurationProfiles:>10}',
'{installedApps:>15}']
)
data = json.loads(''.join(sys.stdin.readlines()))
device_ids = data['Devices']
devices = []
for device_id in device_ids:
d = data['Output'][device_id]
device = {'id': device_id,
'name': d['name'],
'firmwareVersion': d['firmwareVersion'],
'batteryCurrentCapacity': d['batteryCurrentCapacity'],
'passcodeProtected': d['passcodeProtected'],
'configurationProfiles': len(d['configurationProfiles']),
'installedApps': len(d['installedApps'])}
devices.append(device)
# The header.
print(template.format(**human_readable_fields))
for device in devices:
if device['passcodeProtected']:
device['passcodeProtected'] = 'activé'
else:
device['passcodeProtected'] = 'désactivé'
# A device.
print(template.format(**device))
But I would prefer an only Apple Script that display results in a popup window.
Is there a good person to help me ? :)

Related

Bash Script - Not collateral after echo due to new line [duplicate]

I want to write a function that will execute a shell command and return its output as a string, no matter, is it an error or success message. I just want to get the same result that I would have gotten with the command line.
What would be a code example that would do such a thing?
For example:
def run_command(cmd):
# ??????
print run_command('mysqladmin create test -uroot -pmysqladmin12')
# Should output something like:
# mysqladmin: CREATE DATABASE failed; error: 'Can't create database 'test'; database exists'
In all officially maintained versions of Python, the simplest approach is to use the subprocess.check_output function:
>>> subprocess.check_output(['ls', '-l'])
b'total 0\n-rw-r--r-- 1 memyself staff 0 Mar 14 11:04 files\n'
check_output runs a single program that takes only arguments as input.1 It returns the result exactly as printed to stdout. If you need to write input to stdin, skip ahead to the run or Popen sections. If you want to execute complex shell commands, see the note on shell=True at the end of this answer.
The check_output function works in all officially maintained versions of Python. But for more recent versions, a more flexible approach is available.
Modern versions of Python (3.5 or higher): run
If you're using Python 3.5+, and do not need backwards compatibility, the new run function is recommended by the official documentation for most tasks. It provides a very general, high-level API for the subprocess module. To capture the output of a program, pass the subprocess.PIPE flag to the stdout keyword argument. Then access the stdout attribute of the returned CompletedProcess object:
>>> import subprocess
>>> result = subprocess.run(['ls', '-l'], stdout=subprocess.PIPE)
>>> result.stdout
b'total 0\n-rw-r--r-- 1 memyself staff 0 Mar 14 11:04 files\n'
The return value is a bytes object, so if you want a proper string, you'll need to decode it. Assuming the called process returns a UTF-8-encoded string:
>>> result.stdout.decode('utf-8')
'total 0\n-rw-r--r-- 1 memyself staff 0 Mar 14 11:04 files\n'
This can all be compressed to a one-liner if desired:
>>> subprocess.run(['ls', '-l'], stdout=subprocess.PIPE).stdout.decode('utf-8')
'total 0\n-rw-r--r-- 1 memyself staff 0 Mar 14 11:04 files\n'
If you want to pass input to the process's stdin, you can pass a bytes object to the input keyword argument:
>>> cmd = ['awk', 'length($0) > 5']
>>> ip = 'foo\nfoofoo\n'.encode('utf-8')
>>> result = subprocess.run(cmd, stdout=subprocess.PIPE, input=ip)
>>> result.stdout.decode('utf-8')
'foofoo\n'
You can capture errors by passing stderr=subprocess.PIPE (capture to result.stderr) or stderr=subprocess.STDOUT (capture to result.stdout along with regular output). If you want run to throw an exception when the process returns a nonzero exit code, you can pass check=True. (Or you can check the returncode attribute of result above.) When security is not a concern, you can also run more complex shell commands by passing shell=True as described at the end of this answer.
Later versions of Python streamline the above further. In Python 3.7+, the above one-liner can be spelled like this:
>>> subprocess.run(['ls', '-l'], capture_output=True, text=True).stdout
'total 0\n-rw-r--r-- 1 memyself staff 0 Mar 14 11:04 files\n'
Using run this way adds just a bit of complexity, compared to the old way of doing things. But now you can do almost anything you need to do with the run function alone.
Older versions of Python (3-3.4): more about check_output
If you are using an older version of Python, or need modest backwards compatibility, you can use the check_output function as briefly described above. It has been available since Python 2.7.
subprocess.check_output(*popenargs, **kwargs)
It takes takes the same arguments as Popen (see below), and returns a string containing the program's output. The beginning of this answer has a more detailed usage example. In Python 3.5+, check_output is equivalent to executing run with check=True and stdout=PIPE, and returning just the stdout attribute.
You can pass stderr=subprocess.STDOUT to ensure that error messages are included in the returned output. When security is not a concern, you can also run more complex shell commands by passing shell=True as described at the end of this answer.
If you need to pipe from stderr or pass input to the process, check_output won't be up to the task. See the Popen examples below in that case.
Complex applications and legacy versions of Python (2.6 and below): Popen
If you need deep backwards compatibility, or if you need more sophisticated functionality than check_output or run provide, you'll have to work directly with Popen objects, which encapsulate the low-level API for subprocesses.
The Popen constructor accepts either a single command without arguments, or a list containing a command as its first item, followed by any number of arguments, each as a separate item in the list. shlex.split can help parse strings into appropriately formatted lists. Popen objects also accept a host of different arguments for process IO management and low-level configuration.
To send input and capture output, communicate is almost always the preferred method. As in:
output = subprocess.Popen(["mycmd", "myarg"],
stdout=subprocess.PIPE).communicate()[0]
Or
>>> import subprocess
>>> p = subprocess.Popen(['ls', '-a'], stdout=subprocess.PIPE,
... stderr=subprocess.PIPE)
>>> out, err = p.communicate()
>>> print out
.
..
foo
If you set stdin=PIPE, communicate also allows you to pass data to the process via stdin:
>>> cmd = ['awk', 'length($0) > 5']
>>> p = subprocess.Popen(cmd, stdout=subprocess.PIPE,
... stderr=subprocess.PIPE,
... stdin=subprocess.PIPE)
>>> out, err = p.communicate('foo\nfoofoo\n')
>>> print out
foofoo
Note Aaron Hall's answer, which indicates that on some systems, you may need to set stdout, stderr, and stdin all to PIPE (or DEVNULL) to get communicate to work at all.
In some rare cases, you may need complex, real-time output capturing. Vartec's answer suggests a way forward, but methods other than communicate are prone to deadlocks if not used carefully.
As with all the above functions, when security is not a concern, you can run more complex shell commands by passing shell=True.
Notes
1. Running shell commands: the shell=True argument
Normally, each call to run, check_output, or the Popen constructor executes a single program. That means no fancy bash-style pipes. If you want to run complex shell commands, you can pass shell=True, which all three functions support. For example:
>>> subprocess.check_output('cat books/* | wc', shell=True, text=True)
' 1299377 17005208 101299376\n'
However, doing this raises security concerns. If you're doing anything more than light scripting, you might be better off calling each process separately, and passing the output from each as an input to the next, via
run(cmd, [stdout=etc...], input=other_output)
Or
Popen(cmd, [stdout=etc...]).communicate(other_output)
The temptation to directly connect pipes is strong; resist it. Otherwise, you'll likely see deadlocks or have to do hacky things like this.
This is way easier, but only works on Unix (including Cygwin) and Python2.7.
import commands
print commands.getstatusoutput('wc -l file')
It returns a tuple with the (return_value, output).
For a solution that works in both Python2 and Python3, use the subprocess module instead:
from subprocess import Popen, PIPE
output = Popen(["date"],stdout=PIPE)
response = output.communicate()
print response
I had the same problem but figured out a very simple way of doing this:
import subprocess
output = subprocess.getoutput("ls -l")
print(output)
Note: This solution is Python3 specific as subprocess.getoutput() doesn't work in Python2
Something like that:
def runProcess(exe):
p = subprocess.Popen(exe, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
while(True):
# returns None while subprocess is running
retcode = p.poll()
line = p.stdout.readline()
yield line
if retcode is not None:
break
Note, that I'm redirecting stderr to stdout, it might not be exactly what you want, but I want error messages also.
This function yields line by line as they come (normally you'd have to wait for subprocess to finish to get the output as a whole).
For your case the usage would be:
for line in runProcess('mysqladmin create test -uroot -pmysqladmin12'.split()):
print line,
This is a tricky but super simple solution which works in many situations:
import os
os.system('sample_cmd > tmp')
print(open('tmp', 'r').read())
A temporary file(here is tmp) is created with the output of the command and you can read from it your desired output.
Extra note from the comments:
You can remove the tmp file in the case of one-time job. If you need to do this several times, there is no need to delete the tmp.
os.remove('tmp')
Vartec's answer doesn't read all lines, so I made a version that did:
def run_command(command):
p = subprocess.Popen(command,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
return iter(p.stdout.readline, b'')
Usage is the same as the accepted answer:
command = 'mysqladmin create test -uroot -pmysqladmin12'.split()
for line in run_command(command):
print(line)
You can use following commands to run any shell command. I have used them on ubuntu.
import os
os.popen('your command here').read()
Note: This is deprecated since python 2.6. Now you must use subprocess.Popen. Below is the example
import subprocess
p = subprocess.Popen("Your command", shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()[0]
print p.split("\n")
I had a slightly different flavor of the same problem with the following requirements:
Capture and return STDOUT messages as they accumulate in the STDOUT buffer (i.e. in realtime).
#vartec solved this Pythonically with his use of generators and the 'yield'
keyword above
Print all STDOUT lines (even if process exits before STDOUT buffer can be fully read)
Don't waste CPU cycles polling the process at high-frequency
Check the return code of the subprocess
Print STDERR (separate from STDOUT) if we get a non-zero error return code.
I've combined and tweaked previous answers to come up with the following:
import subprocess
from time import sleep
def run_command(command):
p = subprocess.Popen(command,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
# Read stdout from subprocess until the buffer is empty !
for line in iter(p.stdout.readline, b''):
if line: # Don't print blank lines
yield line
# This ensures the process has completed, AND sets the 'returncode' attr
while p.poll() is None:
sleep(.1) #Don't waste CPU-cycles
# Empty STDERR buffer
err = p.stderr.read()
if p.returncode != 0:
# The run_command() function is responsible for logging STDERR
print("Error: " + str(err))
This code would be executed the same as previous answers:
for line in run_command(cmd):
print(line)
Your Mileage May Vary, I attempted #senderle's spin on Vartec's solution in Windows on Python 2.6.5, but I was getting errors, and no other solutions worked. My error was: WindowsError: [Error 6] The handle is invalid.
I found that I had to assign PIPE to every handle to get it to return the output I expected - the following worked for me.
import subprocess
def run_command(cmd):
"""given shell command, returns communication tuple of stdout and stderr"""
return subprocess.Popen(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
stdin=subprocess.PIPE).communicate()
and call like this, ([0] gets the first element of the tuple, stdout):
run_command('tracert 11.1.0.1')[0]
After learning more, I believe I need these pipe arguments because I'm working on a custom system that uses different handles, so I had to directly control all the std's.
To stop console popups (with Windows), do this:
def run_command(cmd):
"""given shell command, returns communication tuple of stdout and stderr"""
# instantiate a startupinfo obj:
startupinfo = subprocess.STARTUPINFO()
# set the use show window flag, might make conditional on being in Windows:
startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
# pass as the startupinfo keyword argument:
return subprocess.Popen(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
stdin=subprocess.PIPE,
startupinfo=startupinfo).communicate()
run_command('tracert 11.1.0.1')
On Python 3.7+, use subprocess.run and pass capture_output=True:
import subprocess
result = subprocess.run(['echo', 'hello', 'world'], capture_output=True)
print(repr(result.stdout))
This will return bytes:
b'hello world\n'
If you want it to convert the bytes to a string, add text=True:
result = subprocess.run(['echo', 'hello', 'world'], capture_output=True, text=True)
print(repr(result.stdout))
This will read the bytes using your default encoding:
'hello world\n'
If you need to manually specify a different encoding, use encoding="your encoding" instead of text=True:
result = subprocess.run(['echo', 'hello', 'world'], capture_output=True, encoding="utf8")
print(repr(result.stdout))
Splitting the initial command for the subprocess might be tricky and cumbersome.
Use shlex.split() to help yourself out.
Sample command
git log -n 5 --since "5 years ago" --until "2 year ago"
The code
from subprocess import check_output
from shlex import split
res = check_output(split('git log -n 5 --since "5 years ago" --until "2 year ago"'))
print(res)
>>> b'commit 7696ab087a163e084d6870bb4e5e4d4198bdc61a\nAuthor: Artur Barseghyan...'
Without shlex.split() the code would look as follows
res = check_output([
'git',
'log',
'-n',
'5',
'--since',
'5 years ago',
'--until',
'2 year ago'
])
print(res)
>>> b'commit 7696ab087a163e084d6870bb4e5e4d4198bdc61a\nAuthor: Artur Barseghyan...'
Here a solution, working if you want to print output while process is running or not.
I added the current working directory also, it was useful to me more than once.
Hoping the solution will help someone :).
import subprocess
def run_command(cmd_and_args, print_constantly=False, cwd=None):
"""Runs a system command.
:param cmd_and_args: the command to run with or without a Pipe (|).
:param print_constantly: If True then the output is logged in continuous until the command ended.
:param cwd: the current working directory (the directory from which you will like to execute the command)
:return: - a tuple containing the return code, the stdout and the stderr of the command
"""
output = []
process = subprocess.Popen(cmd_and_args, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=cwd)
while True:
next_line = process.stdout.readline()
if next_line:
output.append(str(next_line))
if print_constantly:
print(next_line)
elif not process.poll():
break
error = process.communicate()[1]
return process.returncode, '\n'.join(output), error
For some reason, this one works on Python 2.7 and you only need to import os!
import os
def bash(command):
output = os.popen(command).read()
return output
print_me = bash('ls -l')
print(print_me)
If you need to run a shell command on multiple files, this did the trick for me.
import os
import subprocess
# Define a function for running commands and capturing stdout line by line
# (Modified from Vartec's solution because it wasn't printing all lines)
def runProcess(exe):
p = subprocess.Popen(exe, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
return iter(p.stdout.readline, b'')
# Get all filenames in working directory
for filename in os.listdir('./'):
# This command will be run on each file
cmd = 'nm ' + filename
# Run the command and capture the output line by line.
for line in runProcess(cmd.split()):
# Eliminate leading and trailing whitespace
line.strip()
# Split the output
output = line.split()
# Filter the output and print relevant lines
if len(output) > 2:
if ((output[2] == 'set_program_name')):
print filename
print line
Edit: Just saw Max Persson's solution with J.F. Sebastian's suggestion. Went ahead and incorporated that.
According to #senderle, if you use python3.6 like me:
def sh(cmd, input=""):
rst = subprocess.run(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, input=input.encode("utf-8"))
assert rst.returncode == 0, rst.stderr.decode("utf-8")
return rst.stdout.decode("utf-8")
sh("ls -a")
Will act exactly like you run the command in bash
Improvement for better logging.
For better output you can use iterator.
From below, we get better
from subprocess import Popen, getstatusoutput, PIPE
def shell_command(cmd):
result = Popen(cmd, shell=True, stdout=PIPE, stderr=PIPE)
output = iter(result.stdout.readline, b'')
error = iter(result.stderr.readline, b'')
print("##### OutPut ###")
for line in output:
print(line.decode("utf-8"))
print("###### Error ########")
for line in error:
print(error.decode("utf-8")) # Convert bytes to str
status, terminal_output = run_command(cmd)
print(terminal_output)
shell_command("ls") # this will display all the files & folders in directory
Other method using getstatusoutput ( Easy to understand)
from subprocess import Popen, getstatusoutput, PIPE
status_Code, output = getstausoutput(command)
print(output) # this will give the terminal output
# status_code, output = getstatusoutput("ls") # this will print the all files & folder available in the directory
If you use the subprocess python module, you are able to handle the STDOUT, STDERR and return code of command separately. You can see an example for the complete command caller implementation. Of course you can extend it with try..except if you want.
The below function returns the STDOUT, STDERR and Return code so you can handle them in the other script.
import subprocess
def command_caller(command=None)
sp = subprocess.Popen(command, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=False)
out, err = sp.communicate()
if sp.returncode:
print(
"Return code: %(ret_code)s Error message: %(err_msg)s"
% {"ret_code": sp.returncode, "err_msg": err}
)
return sp.returncode, out, err
I would like to suggest simppl as an option for consideration. It is a module that is available via pypi: pip install simppl and was runs on python3.
simppl allows the user to run shell commands and read the output from the screen.
The developers suggest three types of use cases:
The simplest usage will look like this:
from simppl.simple_pipeline import SimplePipeline
sp = SimplePipeline(start=0, end=100):
sp.print_and_run('<YOUR_FIRST_OS_COMMAND>')
sp.print_and_run('<YOUR_SECOND_OS_COMMAND>') ```
To run multiple commands concurrently use:
commands = ['<YOUR_FIRST_OS_COMMAND>', '<YOUR_SECOND_OS_COMMAND>']
max_number_of_processes = 4
sp.run_parallel(commands, max_number_of_processes) ```
Finally, if your project uses the cli module, you can run directly another command_line_tool as part of a pipeline. The other tool will
be run from the same process, but it will appear from the logs as
another command in the pipeline. This enables smoother debugging and
refactoring of tools calling other tools.
from example_module import example_tool
sp.print_and_run_clt(example_tool.run, ['first_number', 'second_nmber'],
{'-key1': 'val1', '-key2': 'val2'},
{'--flag'}) ```
Note that the printing to STDOUT/STDERR is via python's logging module.
Here is a complete code to show how simppl works:
import logging
from logging.config import dictConfig
logging_config = dict(
version = 1,
formatters = {
'f': {'format':
'%(asctime)s %(name)-12s %(levelname)-8s %(message)s'}
},
handlers = {
'h': {'class': 'logging.StreamHandler',
'formatter': 'f',
'level': logging.DEBUG}
},
root = {
'handlers': ['h'],
'level': logging.DEBUG,
},
)
dictConfig(logging_config)
from simppl.simple_pipeline import SimplePipeline
sp = SimplePipeline(0, 100)
sp.print_and_run('ls')
Here is a simple and flexible solution that works on a variety of OS versions, and both Python 2 and 3, using IPython in shell mode:
from IPython.terminal.embed import InteractiveShellEmbed
my_shell = InteractiveShellEmbed()
result = my_shell.getoutput("echo hello world")
print(result)
Out: ['hello world']
It has a couple of advantages
It only requires an IPython install, so you don't really need to worry about your specific Python or OS version when using it, it comes with Jupyter - which has a wide range of support
It takes a simple string by default - so no need to use shell mode arg or string splitting, making it slightly cleaner IMO
It also makes it cleaner to easily substitute variables or even entire Python commands in the string itself
To demonstrate:
var = "hello world "
result = my_shell.getoutput("echo {var*2}")
print(result)
Out: ['hello world hello world']
Just wanted to give you an extra option, especially if you already have Jupyter installed
Naturally, if you are in an actual Jupyter notebook as opposed to a .py script you can also always do:
result = !echo hello world
print(result)
To accomplish the same.
The output can be redirected to a text file and then read it back.
import subprocess
import os
import tempfile
def execute_to_file(command):
"""
This function execute the command
and pass its output to a tempfile then read it back
It is usefull for process that deploy child process
"""
temp_file = tempfile.NamedTemporaryFile(delete=False)
temp_file.close()
path = temp_file.name
command = command + " > " + path
proc = subprocess.run(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
if proc.stderr:
# if command failed return
os.unlink(path)
return
with open(path, 'r') as f:
data = f.read()
os.unlink(path)
return data
if __name__ == "__main__":
path = "Somepath"
command = 'ecls.exe /files ' + path
print(execute(command))
eg, execute('ls -ahl')
differentiated three/four possible returns and OS platforms:
no output, but run successfully
output empty line, run successfully
run failed
output something, run successfully
function below
def execute(cmd, output=True, DEBUG_MODE=False):
"""Executes a bash command.
(cmd, output=True)
output: whether print shell output to screen, only affects screen display, does not affect returned values
return: ...regardless of output=True/False...
returns shell output as a list with each elment is a line of string (whitespace stripped both sides) from output
could be
[], ie, len()=0 --> no output;
[''] --> output empty line;
None --> error occured, see below
if error ocurs, returns None (ie, is None), print out the error message to screen
"""
if not DEBUG_MODE:
print "Command: " + cmd
# https://stackoverflow.com/a/40139101/2292993
def _execute_cmd(cmd):
if os.name == 'nt' or platform.system() == 'Windows':
# set stdin, out, err all to PIPE to get results (other than None) after run the Popen() instance
p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
else:
# Use bash; the default is sh
p = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True, executable="/bin/bash")
# the Popen() instance starts running once instantiated (??)
# additionally, communicate(), or poll() and wait process to terminate
# communicate() accepts optional input as stdin to the pipe (requires setting stdin=subprocess.PIPE above), return out, err as tuple
# if communicate(), the results are buffered in memory
# Read stdout from subprocess until the buffer is empty !
# if error occurs, the stdout is '', which means the below loop is essentially skipped
# A prefix of 'b' or 'B' is ignored in Python 2;
# it indicates that the literal should become a bytes literal in Python 3
# (e.g. when code is automatically converted with 2to3).
# return iter(p.stdout.readline, b'')
for line in iter(p.stdout.readline, b''):
# # Windows has \r\n, Unix has \n, Old mac has \r
# if line not in ['','\n','\r','\r\n']: # Don't print blank lines
yield line
while p.poll() is None:
sleep(.1) #Don't waste CPU-cycles
# Empty STDERR buffer
err = p.stderr.read()
if p.returncode != 0:
# responsible for logging STDERR
print("Error: " + str(err))
yield None
out = []
for line in _execute_cmd(cmd):
# error did not occur earlier
if line is not None:
# trailing comma to avoid a newline (by print itself) being printed
if output: print line,
out.append(line.strip())
else:
# error occured earlier
out = None
return out
else:
print "Simulation! The command is " + cmd
print ""

How do you pass output from one Nextflow Channel to another and run an .Rmd file?

I have a Nextflow pipeline that has two channels.
The first channel runs and outputs 6 .tsv files to a folder called 'results'.
The second channel is supposed to use all of these 6 .tsv files and create a .pdf report using knitr in R in a process called 'createReport'.
My workflow code looks like this:
workflow {
inputFileChannel = Channel.fromPath(params.pathOfInputFile, type: 'file') // | collect | createReport // creating channel to pass in input file
findNumOfProteins(inputFileChannel) // passing in the channel to the process
findAminoAcidFrequency(inputFileChannel)
getProteinDescriptions(inputFileChannel)
getNumberOfLines(inputFileChannel)
getNumberOfLinesWithoutSpaces(inputFileChannel)
getLengthFreq(inputFileChannel)
outputFileChannel = Channel.fromPath("$params.outdir.main/*.tsv", type: 'file').buffer(size:6)
createReport(outputFileChannel)
My 'createReport' process currently looks like this:
process createReport {
module 'R/4.2.2'
publishDir params.outdir.output, mode: 'copy'
output:
path 'report.pdf'
script:
"""
R -e "rmarkdown::render('./createReport.Rmd')"
"""
}
And my 'createReport.Rmd' looks like this (tested in Rstudio and gives the correct .pdf output:
---
title: "R Markdown Practice"
author: "-"
date: "2022-12-08"
output: pdf_document
---
{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(readr)
dataSet <- list.files(path="/Users/-/Desktop/code/nextflow_practice/results/", pattern="*.tsv")
print(dataSet)
for (data in dataSet) {
print(paste("Showing the table for:", data))
targetData <- read.table(file=paste("/Users/-/Desktop/code/nextflow_practice/results/", data, sep=""),
head=TRUE,
nrows=5,
sep="\t")
print(targetData)
if (data == "length_data.tsv") {
data_to_graph <- read_tsv(paste("/Users/-/Desktop/code/nextflow_practice/results/", data, sep=""), show_col_types = FALSE)
plot(x = data_to_graph$LENGTH,y = data_to_graph$FREQ, xlab = "x-axis", ylab = "y-axis", main = "P")
}
writeLines("-----------------------------------------------------------------")
}
What would be the correct way to write the createReport process and the workflow sections so as to be able to pass the 6 .tsv outputs from the first channel into the second channel to create the report?
Sorry I am very new to Nextflow and the documentation doesn't help me as much as I would like it to!
Your outputFileChannel looks like it is trying to access files in the publishDir. The problem with accessing files in this directory (i.e. 'results') is that:
Files are copied into the specified directory in an asynchronous
manner, thus they may not be immediately available in the published
directory at the end of the process execution. For this reason files
published by a process must not be accessed by other downstream
processes.
Assuming your inputFileChannel is intended to be a value channel, you could use the following. This requires the outputs of the six process to be declared in their output blocks (using the path qualifier). We could then just mix and collect these files. Your Rmd file and list of TSV files could then be passed to your createReport process. Note that if you move your Rmd into the base directory of your pipeline project (i.e. in the same directory as your main.nf script), you can distribute it with your workflow. By providing the Rmd over a channel, this approach ensures it is staged into the process working directory when the job is run. For example:
workflow {
inputFile = file( params.pathOfInputFile )
findNumOfProteins( inputFile )
findAminoAcidFrequency( inputFile )
getProteinDescriptions( inputFile )
getNumberOfLines( inputFile )
getNumberOfLinesWithoutSpaces( inputFile )
getLengthFreq( inputFile )
Channel.empty() \
| mix( findNumOfProteins.out ) \
| mix( findAminoAcidFrequency.out ) \
| mix( getProteinDescriptions.out ) \
| mix( getNumberOfLines.out ) \
| mix( getNumberOfLinesWithoutSpaces.out ) \
| mix( getLengthFreq.out ) \
| collect \
| set { outputs }
rmd = file("${baseDir}/createReport.Rmd")
createReport( outputs, rmd )
}
process createReport {
module 'R/4.2.2'
publishDir "${params.outdir}/report", mode: 'copy'
input:
path 'input_dir/*'
path rmd
output:
path 'report.pdf'
"""
Rscript -e "rmarkdown::render('${rmd}')"
"""
}
Note that the createReport process above will stage the input TSV files under a folder called 'input_dir' in the process working directory. You could change this if you want to, but I think this keeps the working directory neat and tidy. Just be sure to modify your Rmd script to point to this folder. For example, you might choose to use something like:
dataSet <- list.files(path="./input_dir", pattern="*.tsv")
Or perhaps even:
dataSet <- list.files(pattern="*.tsv", recursive=TRUE)

TextFSM Template for Netmiko for "inc" phrase

I am trying to create a textfsm template with the Netmiko library. While it works for most of the commands, it does not work when I try performing "inc" operation in the network device. The textfsm index file seems like it is not recognizing the same command for 2 different templates; for instance:
If I am giving the command - show running | inc syscontact
And give another command - show running | inc syslocation
in textfsm index; the textfsm template seems like it is recognizing only the first command; and not the second command.
I understand that I can get the necessary data by the regex expression for syscontact and syslocation for the commands( via the template ), however I want to achieve this by the "inc" command from the device itself. Is there a way this can be done?
you need to escape the pipe in the index file. e.g. sh[[ow]] ru[[nning]] \| inc syslocation
There is a different way to parse that you want all datas which is called TTP module. You can take the code I wrote below as an example. You can create your own templates.
from pprint import pprint
from ttp import ttp
import json
import time
with open("showSystemInformation.txt") as f:
data_to_parse = f.read()
ttp_template = """
<group name="Show_System_Information">
System Name : {{System_Name}}
System Type : {{System_Type}} {{System_Type_2}}
System Version : {{Version}}
System Up Time : {{System_Uptime_Days}} days, {{System_Uptime_HR_MIN_SEC}} (hr:min:sec)
Last Saved Config : {{Last_Saved_Config}}
Time Last Saved : {{Last_Time_Saved_Date}} {{Last_Time_Saved_HR_MIN_SEC}}
Time Last Modified : {{Last_Time_Modified_Date}} {{Last_Time_Modifed_HR_MIN_SEC}}
</group>
"""
parser = ttp(data=data_to_parse, template=ttp_template)
parser.parse()
# print result in JSON format
results = parser.result(format='json')[0]
print(results)
Example run:
[appadmin#ryugbz01 Nokia]$ python3 showSystemInformation.py
[
{
"Show_System_Information": {
"Last_Saved_Config": "cf3:\\config.cfg",
"Last_Time_Modifed_HR_MIN_SEC": "11:46:57",
"Last_Time_Modified_Date": "2022/02/09",
"Last_Time_Saved_Date": "2022/02/07",
"Last_Time_Saved_HR_MIN_SEC": "15:55:39",
"System_Name": "SR7-2",
"System_Type": "7750",
"System_Type_2": "SR-7",
"System_Uptime_Days": "17",
"System_Uptime_HR_MIN_SEC": "05:24:44.72",
"Version": "C-16.0.R9"
}
}
]

GPG not working with python 3.8 but ok with 3.6

I have just started dabbling with Python and I’m stuck with my first project
I need help in trying to make some sense out gpg. I have been struggle with trying to get gpg to work with python 3.8.1. If run the code in Thonny Python 3.6.9 in run just fine.
The version is gpg (GnuPG) 2.2.4 libgcrypt 1.8.1
Home directory : /home/bob/.gnupg
gnupg : /usr/local/lib/python3.8/site-packages/gnupg
using Python 3.6.9 works just fine
#!/usr/bin/python3
from pathlib import Path
import gnupg
# My gpg keys home directory.
#gpg = gnupg.GPG(homedir='/home/bob/.gnupg')
gpg = gnupg.GPG(gnupghome='/home/bob/.gnupg')
local_path = Path("/home/bob")
src_dir = ("/home/bob/Tbox/Channels2.csv")
with open(src_dir, 'rb') as afile:
# text = afile.read()
status = gpg.encrypt_file(afile,
['bobh#gunas.co.uk'],
output='/home/bob/Tbox/Channels2.csv.gpg')
print('ok: ', status.ok)
print('status: ', status.status)
print('stderr: ', status.stderr)
SHELL OUTPUT
ok: True
status: encryption ok
stderr: [GNUPG:] KEY_CONSIDERED 4678A2C439E752DA3DAE2EBA7357BB95381CD73 0
[GNUPG:] KEY_CONSIDERED 4678A2C439E752DA3DAE2EBA7357BB95381CD73 0
[GNUPG:] ENCRYPTION_COMPLIANCE_MODE 23
[GNUPG:] BEGIN_ENCRYPTION 2 9
[GNUPG:] END_ENCRYPTION
however if I run the code in Thonny Python 3.8.1 I not working withy error message in Shell
#!/usr/bin/python3
from pathlib import Path
import gnupg
# My gpg keys home directory.
gpg = gnupg.GPG(homedir='/home/bob/.gnupg')
#gpg = gnupg.GPG(gnupghome='/home/bob/.gnupg')
local_path = Path("/home/bob")
backup_dir = Path("/home/bob/Tbox/tbackup-test")
src_dir = ("/home/bob/Tbox/Channels2.csv")
with open(src_dir, 'rb') as afile:
text = afile.read()
# status = gpg.encrypt_file(text,
status = gpg.encrypt(afile,
['bobh#gunas.co.uk'],
output='/home/bob/Tbox/Channels2.csv.gpg')
print('ok: ', status.ok)
print('status: ', status.status)
print('stderr: ', status.stderr)
SHELL OUTPUT
ok: False
status: None
stderr: gpg: Sorry, no terminal at all requested - can't get input
I have tried add the line no-tty to the gpg.conf file but this did not help.
I have tried with some example of the net but with on joy, one problem I have found is to do with gpg and the word Context like c = gpg.core.Context(armor=True) error AttributeError: 'GPG' object has no attribute 'core'.
In the second example, instead of:
status = gpg.encrypt(afile,
you probably need:
status = gpg.encrypt(text,
Basically you need to decide if you are encrypting a file, or the contents of a file (that you're reading in variable 'text'), and then you either use gpg.encrypt or gpg.encrypt_file accordingly.

Best Way of redirecting output to a VTE terminal

Which is the best way of redirect the output of a command to a VTE terminal?
i came with this idea:
On the VTE execute:
tty > /usr/tmp/terminal_number
then read the file from the python program:
with open('/usr/tmp/terminal_number', 'r') as f:
self.VTE_redirect_path=f.readline()
then execute the bash commands, for exemple:
os.system('''echo "foo" > {0}'''.format(self.VTE_redirect_path))
The problem of this method is that the file terminal_number containing /dev/pts/# needs to be refreshed. Also i don't really like the idea of having to create files to communicate. Is there any direct solution?
#Quentin The solution that you gave me prints the console output really bad (it doesn't indents) so i had to use my solution. Here is a clear example:
from gi.repository import Gtk, GObject, Vte, GLib
import os, time, threading
def command_on_VTE(self,command):
length=len(command)
self.terminal.feed_child(command, length)
class TheWindow(Gtk.Window):
def __init__(self):
Gtk.Window.__init__(self, title="inherited cell renderer")
self.set_default_size(600, 300)
self.terminal=Vte.Terminal()
self.terminal.fork_command_full(
Vte.PtyFlags.DEFAULT, #default is fine
os.environ['HOME'], #where to start the command?
["/bin/bash"], #where is the emulator?
[], #it's ok to leave this list empty
GLib.SpawnFlags.DO_NOT_REAP_CHILD,
None, #at least None is required
None,
)
#set up the interface
box = Gtk.Box(orientation=Gtk.Orientation.VERTICAL)
#a scroll window is required for the terminal
scroller = Gtk.ScrolledWindow()
scroller.set_hexpand(True)
scroller.set_vexpand(True)
scroller.add(self.terminal)
box.pack_start(scroller, False, True, 2)
self.add(box)
#To get the command to automatically run
#a newline(\n) character is used at the end of the
#command string.
command_on_VTE(self,'''tty > /tmp/terminal_number\n''') # Get the terminal ID
# read the terminal ID
while not os.path.exists("/tmp/terminal_number"):
time.sleep(0.1)
with open('/tmp/terminal_number', 'r') as f:
self.VTE_redirect_path=f.readline()
os.remove('/tmp/terminal_number')
# this cleans the vte
os.system('''printf "\\033c" > {0}'''.format(self.VTE_redirect_path))
# this calls the exemple
threading.Thread(target=self.make_a_test).start()
def make_a_test(self):
os.system('''ls -laR /home/ > {rdc}
echo "-------- The listing ended -------
Note that the input of the commands are not printed
" > {rdc}'''.format(rdc=self.VTE_redirect_path))
win = TheWindow()
win.connect("delete-event", Gtk.main_quit)
win.show_all()
Gtk.main()
I haven't found a way of getting the Terminal ID with out passing for the creation of a temporary file. This could be skipped if there is some way to pass a variable from the VTE to the python script. Any help on this would be great!
In VTE you use terminal.feed("string")
See vte_terminal_feed.
With python Popen is the suggested method to execute commands.
If you are wanting to use commands then you should do this.
#Uncomment the next line to get the print() function of python 3
#from __future__ import print_function
import os
import subprocess
from subprocess import Popen
command = "echo \"something\""
env = os.environ.copy()
try:
po = Popen(command, shell=True, stdout=subprocess.PIPE, stdin=subprocess.PIPE,
universal_newlines=True, env=env)
po.wait()
output, error_output = po.communicate()
if po.returncode:
print(error_output)
else:
print(output)
except OSError as e:
print('Execution failed:', e, file=sys.stderr)
If you want to use gtk with gtk vte then do this instead.
#place the following in a method of a vte instance
env = os.environ.copy()
try:
po = Popen(command, shell=True, stdout=subprocess.PIPE, stdin=subprocess.PIPE,
universal_newlines=True, env=env)
po.wait()
output, error_output = po.communicate()
if po.returncode:
print(error_output)
else:
self.feed(output) #here you're printing to your terminal.
except OSError as e:
print('Execution failed:', e, file=sys.stderr)
For the finest control in a regular terminal you can try the cmd module. This will require that you produce your own prompt so it is a more specific option to get what you want.

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