"""
# Copyright (C) 2017-2022 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 pwd
import re
import shlex
import subprocess
import sys
from spython.logger import bot, decodeUtf8String
def _process_sudo_cmd(cmd, sudo, sudo_options):
"""
Process the sudo command and honor adding environment (or not)
"""
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 [x for x in cmd if x]
def check_install(software="singularity", 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 Exception: # 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
def get_singularity_version():
"""
get the full singularity client version as reported by
singularity --version [...]. For Singularity 3.x, this means:
"singularity version 3.0.1-1"
"""
version = os.environ.get("SPYTHON_SINGULARITY_VERSION", "")
if version == "":
try:
version = run_command(["singularity", "--version"], quiet=True)
except Exception: # FileNotFoundError
return version
if version["return_code"] == 0:
if version["message"]:
version = version["message"][0].strip("\n")
return version
def get_userhome():
"""
Get the user home based on the effective uid
"""
return pwd.getpwuid(os.getuid())[5]
def get_username():
"""
Get the user name based on the effective uid
"""
return pwd.getpwuid(os.getuid())[0]
def get_installdir():
"""
Get_installdir returns the installation directory of the application
"""
return os.path.abspath(os.path.dirname(os.path.dirname(__file__)))
def stream_command(
cmd,
no_newline_regexp="Progess",
sudo=False,
sudo_options=None,
output_type="stdout",
):
"""
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
"""
if output_type not in ["stdout", "stderr", "both"]:
bot.exit(
"Invalid output type %s. Must be stderr, stdout or both." % output_type
)
cmd = _process_sudo_cmd(cmd, sudo, sudo_options)
stderr_pipe = subprocess.STDOUT if output_type == "both" else subprocess.PIPE
process = subprocess.Popen(
cmd, stdout=subprocess.PIPE, stderr=stderr_pipe, universal_newlines=True
)
# Allow the runner to choose streaming output or error
stream = process.stdout.readline
if output_type == "stderr":
stream = process.stderr.readline
# Stream lines back to the caller
for line in iter(stream, ""):
if not re.search(no_newline_regexp, line):
yield line
# If there is an error, raise.
process.stdout.close()
return_code = process.wait()
if return_code:
# Some situations may return process without an attached stderr object
# to read from
if process.stderr:
print(process.stderr.read(), file=sys.stderr)
raise subprocess.CalledProcessError(return_code, cmd)
def run_command(
cmd,
sudo=False,
capture=True,
no_newline_regexp="Progess",
quiet=False,
sudo_options=None,
environ=None,
background=False,
):
"""
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
background: run in background and don't try to get output.
"""
cmd = _process_sudo_cmd(cmd, sudo, sudo_options)
stdout = None
if capture:
stdout = subprocess.PIPE
# Use the parent stdout and stderr
if background:
subprocess.Popen(cmd, env=environ)
return
process = subprocess.Popen(cmd, stderr=subprocess.PIPE, stdout=stdout, env=environ)
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
def format_container_name(name, special_characters=None):
"""
format_container_name will take a name supplied by the user,
remove all special characters (except for those defined by "special-characters"
and return the new image name.
"""
if special_characters is None:
special_characters = []
return "".join(e.lower() for e in name if e.isalnum() or e in special_characters)
def split_uri(container):
"""
Split the uri of a container into the protocol and image part
An empty protocol is returned if none found.
A trailing slash is removed from the image part.
"""
parts = container.split("://", 1)
if len(parts) == 2:
protocol, image = parts
else:
protocol = ""
image = parts[0]
return protocol, image.rstrip("/")
def remove_uri(container):
"""
remove_uri will remove docker:// or shub:// or library:// from the uri
"""
return split_uri(container)[1]