'''
Copyright (C) 2019 Vanessa Sochat.
This Source Code Form is subject to the terms of the
Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed
with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
'''
import os
import re
import semver
from freegenes.logger import bot, decodeUtf8String
import subprocess
import sys
import shlex
################################################################################
# Local commands and requests
################################################################################
def _process_sudo_cmd(cmd, sudo, sudo_options):
if sudo and sudo_options is not None:
if isinstance(sudo_options, str):
sudo_options = shlex.split(sudo_options)
cmd = ['sudo'] + sudo_options + cmd
elif sudo:
cmd = ['sudo'] + cmd
return cmd
[docs]def check_install(software, quiet=True):
'''check_install will attempt to run the singularity command, and
return True if installed. The command line utils will not run
without this check.
'''
cmd = [software, '--version']
found = False
try:
version = run_command(cmd, quiet=True)
except: # FileNotFoundError
return found
if version is not None:
if version['return_code'] == 0:
found = True
if not quiet:
version = version['message']
bot.info("Found %s version %s" % (software.upper(), version))
return found
[docs]def which(software):
'''which returns the full path to where software is installed.
'''
cmd = ['which', software]
result = run_command(cmd, quiet=True)['message'][0]
return result.strip('\n')
[docs]def get_installdir():
'''get_installdir returns the installation directory of the application
'''
return os.path.abspath(os.path.dirname(os.path.dirname(__file__)))
[docs]def stream_command(cmd, no_newline_regexp="Progess", sudo=False, sudo_options=None):
'''stream a command (yield) back to the user, as each line is available.
# Example usage:
results = []
for line in stream_command(cmd):
print(line, end="")
results.append(line)
Parameters
==========
cmd: the command to send, should be a list for subprocess
no_newline_regexp: the regular expression to determine skipping a
newline. Defaults to finding Progress
sudo_options: string or list of strings that will be passed as options to sudo
'''
cmd = _process_sudo_cmd(cmd, sudo, sudo_options)
process = subprocess.Popen(cmd,
stdout=subprocess.PIPE,
universal_newlines=True)
for line in iter(process.stdout.readline, ""):
if not re.search(no_newline_regexp, line):
yield line
process.stdout.close()
return_code = process.wait()
if return_code:
raise subprocess.CalledProcessError(return_code, cmd)
[docs]def run_command(cmd,
sudo=False,
capture=True,
no_newline_regexp="Progess",
quiet=False,
sudo_options=None):
'''run_command uses subprocess to send a command to the terminal. If
capture is True, we use the parent stdout, so the progress bar (and
other commands of interest) are piped to the user. This means we
don't return the output to parse.
Parameters
==========
cmd: the command to send, should be a list for subprocess
sudo: if needed, add to start of command
no_newline_regexp: the regular expression to determine skipping a
newline. Defaults to finding Progress
capture: if True, don't set stdout and have it go to console. This
option can print a progress bar, but won't return the lines
as output.
sudo_options: string or list of strings that will be passed as options to sudo
'''
cmd = _process_sudo_cmd(cmd, sudo, sudo_options)
stdout = None
if capture:
stdout = subprocess.PIPE
# Use the parent stdout and stderr
process = subprocess.Popen(cmd,
stderr=subprocess.PIPE,
stdout=stdout)
lines = []
found_match = False
for line in process.communicate():
if line:
line = decodeUtf8String(line)
lines.append(line)
if re.search(no_newline_regexp, line) and found_match:
if not quiet:
sys.stdout.write(line)
found_match = True
else:
if not quiet:
sys.stdout.write(line)
print(line.rstrip())
found_match = False
output = {'message': lines,
'return_code': process.returncode}
return output