Source code for shapepipe.pipeline.execute


This module defines methods for running the pipeline modules.

:Author: Samuel Farrens <>


import os
import subprocess as sp

[docs]def execute(command_line): """Execute. This method executes a given command line. Parameters ---------- command_line : str The command line to be executed Returns ------- tuple Stdout and stderr (both type str) Raises ------ TypeError For invalid input type """ if not isinstance(command_line, str): raise TypeError('Command line must be a string.') command = command_line.split() check_executable(command[0]) process = sp.Popen(command, stdout=sp.PIPE, stderr=sp.PIPE) stdout, stderr = process.communicate() return stdout.decode('utf-8'), stderr.decode('utf-8')
[docs]def check_executable(exe_name): """Check if Input is Executable. This methid checks if the input executable exists. Parameters ---------- exe_name : str Executable name Raises ------ TypeError For invalid input type OSError For non-existent executable """ if not isinstance(exe_name, str): raise TypeError('Executable name must be a string.') def is_exe(fpath): return os.path.isfile(fpath) and os.access(fpath, os.X_OK) fpath, fname = os.path.split(exe_name) if not fpath: res = any([ is_exe(os.path.join(path, exe_name)) for path in os.environ['PATH'].split(os.pathsep) ]) else: res = is_exe(exe_name) if not res: raise OSError( f'{exe_name} does not appear to be a valid executable on this ' + 'system.' )