Source code for spython.utils.terminal

"""

# 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 semver
from spython.logger import bot
from spython.logger import 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="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: # 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="singularity"): """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_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: # FileNotFoundError return version if version["return_code"] == 0: if version["message"]: version = version["message"][0].strip("\n") return version
[docs]def get_userhome(): """get the user home based on the effective uid""" return pwd.getpwuid(os.getuid())[5]
[docs]def get_username(): """get the user name based on the effective uid""" return pwd.getpwuid(os.getuid())[0]
[docs]def get_singularity_version_info(): """get the full singularity client version as a semantic version" """ version_string = get_singularity_version() prefix = "singularity version " if version_string.startswith(prefix): version_string = version_string[len(prefix) :] elif "/" in version_string: # Handle old stuff like "x.y.z-pull/123-0a5d" version_string = version_string.replace("/", "+", 1) return semver.VersionInfo.parse(version_string)
[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, 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"]: bot.exit("Invalid output type %s. Must be stderr or stdout." % output_type) cmd = _process_sudo_cmd(cmd, sudo, sudo_options) process = subprocess.Popen( cmd, stdout=subprocess.PIPE, stderr=subprocess.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: print(process.stderr.read(), file=sys.stderr) raise subprocess.CalledProcessError(return_code, cmd)
[docs]def run_command( cmd, sudo=False, capture=True, no_newline_regexp="Progess", quiet=False, sudo_options=None, environ=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, 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
################################################################################ # Parsing and Formatting ################################################################################
[docs]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)
[docs]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("/")
[docs]def remove_uri(container): """remove_uri will remove docker:// or shub:// or library:// from the uri""" return split_uri(container)[1]