Source code for pycbc.workflow.configuration

# Copyright (C) 2013,2017 Ian Harry, Duncan Brown
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# Public License for more details.
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.

# =============================================================================
#                                   Preamble
# =============================================================================
This module provides a wrapper to the ConfigParser utilities for pycbc
workflow construction. This module is described in the page here:

import os
import logging
import stat
import shutil
import subprocess
from shutil import which
import urllib.parse
from urllib.parse import urlparse

from pycbc.types.config import InterpolatingConfigParser

logger = logging.getLogger('pycbc.workflow.configuration')

# NOTE urllib is weird. For some reason it only allows known schemes and will
# give *wrong* results, rather then failing, if you use something like gsiftp
# We can add schemes explicitly, as below, but be careful with this!

[docs]def resolve_url(url, directory=None, permissions=None, copy_to_cwd=True): """Resolves a URL to a local file, and returns the path to that file. If a URL is given, the file will be copied to the current working directory. If a local file path is given, the file will only be copied to the current working directory if ``copy_to_cwd`` is ``True`` (the default). """ u = urlparse(url) # determine whether the file exists locally islocal = u.scheme == "" or u.scheme == "file" if not islocal or copy_to_cwd: # create the name of the destination file if directory is None: directory = os.getcwd() filename = os.path.join(directory, os.path.basename(u.path)) else: filename = u.path if islocal: # check that the file exists if not os.path.isfile(u.path): errmsg = "Cannot open file %s from URL %s" % (u.path, url) raise ValueError(errmsg) # for regular files, make a direct copy if requested elif copy_to_cwd: if os.path.isfile(filename): # check to see if src and dest are the same file src_inode = os.stat(u.path)[stat.ST_INO] dst_inode = os.stat(filename)[stat.ST_INO] if src_inode != dst_inode: shutil.copy(u.path, filename) else: shutil.copy(u.path, filename) elif u.scheme == "http" or u.scheme == "https": # Would like to move ciecplib import to top using import_optional, but # it needs to be available when documentation runs in the CI, and I # can't get it to install in the GitHub CI import ciecplib # Make the scitokens logger a little quieter # (it is called through ciecpclib) logging.getLogger('scitokens').setLevel(logger.level + 10) with ciecplib.Session() as s: if u.netloc in ("", ""): # authenticate with using callback s.get("") r = s.get(url, allow_redirects=True) r.raise_for_status() output_fp = open(filename, "wb") output_fp.write(r.content) output_fp.close() elif u.scheme == "osdf": # OSDF will require a scitoken to be present and stashcp to be # available. Thanks Dunky for the code here! cmd = [ which("stashcp") or "stashcp", u.path, filename, ] try:, check=True, capture_output=True) except subprocess.CalledProcessError as err: # Print information about the failure print(err.cmd, "failed with") print(err.stderr.decode()) print(err.stdout.decode()) raise return filename else: # TODO: We could support other schemes as needed errmsg = "Unknown URL scheme: %s\n" % (u.scheme) errmsg += "Currently supported are: file, http, and https." raise ValueError(errmsg) if not os.path.isfile(filename): errmsg = "Error trying to create file %s from %s" % (filename, url) raise ValueError(errmsg) if permissions: if os.access(filename, os.W_OK): os.chmod(filename, permissions) else: # check that the file has at least the permissions requested s = os.stat(filename)[stat.ST_MODE] if (s & permissions) != permissions: errmsg = "Could not change permissions on %s (read-only)" % url raise ValueError(errmsg) return filename
[docs]def add_workflow_command_line_group(parser): """ The standard way of initializing a ConfigParser object in workflow will be to do it from the command line. This is done by giving a --local-config-files filea.ini fileb.ini filec.ini command. You can also set config file override commands on the command line. This will be most useful when setting (for example) start and end times, or active ifos. This is done by --config-overrides section1:option1:value1 section2:option2:value2 ... This can also be given as --config-overrides section1:option1 where the value will be left as ''. To remove a configuration option, use the command line argument --config-delete section1:option1 which will delete option1 from [section1] or --config-delete section1 to delete all of the options in [section1] Deletes are implemented before overrides. This function returns an argparse OptionGroup to ensure these options are parsed correctly and can then be sent directly to initialize an WorkflowConfigParser. Parameters ----------- parser : argparse.ArgumentParser instance The initialized argparse instance to add the workflow option group to. """ workflowArgs = parser.add_argument_group( "Configuration", "Options needed for parsing " "config file(s)." ) workflowArgs.add_argument( "--config-files", nargs="+", action="store", metavar="CONFIGFILE", help="List of config files to be used in " "analysis.", ) workflowArgs.add_argument( "--config-overrides", nargs="*", action="store", metavar="SECTION:OPTION:VALUE", help="List of section,option,value combinations to " "add into the configuration file. Normally the gps " "start and end times might be provided this way, " "and user specific locations (ie. output directories). " "This can also be provided as SECTION:OPTION or " "SECTION:OPTION: both of which indicate that the " "corresponding value is left blank.", ) workflowArgs.add_argument( "--config-delete", nargs="*", action="store", metavar="SECTION:OPTION", help="List of section,option combinations to delete " "from the configuration file. This can also be " "provided as SECTION which deletes the enture section" " from the configuration file or SECTION:OPTION " "which deletes a specific option from a given " "section.", )
[docs]class WorkflowConfigParser(InterpolatingConfigParser): """ This is a sub-class of InterpolatingConfigParser, which lets us add a few additional helper features that are useful in workflows. """ def __init__( self, configFiles=None, overrideTuples=None, parsedFilePath=None, deleteTuples=None, copy_to_cwd=False, ): """ Initialize an WorkflowConfigParser. This reads the input configuration files, overrides values if necessary and performs the interpolation. See Parameters ----------- configFiles : Path to .ini file, or list of paths The file(s) to be read in and parsed. overrideTuples : List of (section, option, value) tuples Add the (section, option, value) triplets provided in this list to the provided .ini file(s). If the section, option pair is already present, it will be overwritten. parsedFilePath : Path, optional (default=None) If given, write the parsed .ini file back to disk at this location. deleteTuples : List of (section, option) tuples Delete the (section, option) pairs provided in this list from provided .ini file(s). If the section only is provided, the entire section will be deleted. copy_to_cwd : bool, optional Copy the configuration files to the current working directory if they are not already there, even if they already exist locally. If False, files will only be copied to the current working directory if they are remote. Default is False. Returns -------- WorkflowConfigParser Initialized WorkflowConfigParser instance. """ if configFiles is not None: configFiles = [ resolve_url(cFile, copy_to_cwd=copy_to_cwd) for cFile in configFiles ] InterpolatingConfigParser.__init__( self, configFiles, overrideTuples, parsedFilePath, deleteTuples, skip_extended=True, ) # expand executable which statements self.perform_exe_expansion() # Resolve any URLs needing resolving self.curr_resolved_files = {} self.resolve_urls() # Check for any substitutions that can be made self.perform_extended_interpolation()
[docs] def perform_exe_expansion(self): """ This function will look through the executables section of the ConfigParser object and replace any values using macros with full paths. For any values that look like ${which:lalapps_tmpltbank} will be replaced with the equivalent of which(lalapps_tmpltbank) Otherwise values will be unchanged. """ # Only works on executables section if self.has_section("executables"): for option, value in self.items("executables"): # Check the value newStr = self.interpolate_exe(value) if newStr != value: self.set("executables", option, newStr)
[docs] def interpolate_exe(self, testString): """ Replace testString with a path to an executable based on the format. If this looks like ${which:lalapps_tmpltbank} it will return the equivalent of which(lalapps_tmpltbank) Otherwise it will return an unchanged string. Parameters ----------- testString : string The input string Returns -------- newString : string The output string. """ # First check if any interpolation is needed and abort if not testString = testString.strip() if not (testString.startswith("${") and testString.endswith("}")): return testString # This may not be an exe interpolation, so even if it has ${ ... } form # I may not have to do anything newString = testString # Strip the ${ and } testString = testString[2:-1] testList = testString.split(":") # Maybe we can add a few different possibilities for substitution if len(testList) == 2: if testList[0] == "which": newString = which(testList[1]) if not newString: errmsg = "Cannot find exe %s in your path " % (testList[1]) errmsg += "and you specified ${which:%s}." % (testList[1]) raise ValueError(errmsg) return newString
[docs] def section_to_cli(self, section, skip_opts=None): """Converts a section into a command-line string. For example: .. code:: [section_name] foo = bar = 10 yields: `'--foo --bar 10'`. Parameters ---------- section : str The name of the section to convert. skip_opts : list, optional List of options to skip. Default (None) results in all options in the section being converted. Returns ------- str : The options as a command-line string. """ if skip_opts is None: skip_opts = [] read_opts = [ opt for opt in self.options(section) if opt not in skip_opts ] opts = [] for opt in read_opts: opts.append("--{}".format(opt)) val = self.get(section, opt) if val != "": opts.append(val) return " ".join(opts)
[docs] def get_cli_option(self, section, option_name, **kwds): """Return option using CLI action parsing Parameters ---------- section: str Section to find option to parse option_name: str Name of the option to parse from the config file kwds: keywords Additional keywords are passed directly to the argument parser. Returns ------- value: The parsed value for this option """ import argparse optstr = self.section_to_cli(section) parser = argparse.ArgumentParser() name = "--" + option_name.replace("_", "-") parser.add_argument(name, **kwds) args, _ = parser.parse_known_args(optstr.split()) return getattr(args, option_name)
[docs] def resolve_urls(self): """ This function will look through all sections of the ConfigParser object and replace any URLs that are given the resolve magic flag with a path on the local drive. Specifically for any values that look like ${resolve:} the file will be replaced with the output of resolve_url(URL) Otherwise values will be unchanged. """ # Only works on executables section for section in self.sections(): for option, value in self.items(section): # Check the value value_l = value.split(' ') new_str_l = [self.resolve_file_url(val) for val in value_l] new_str = ' '.join(new_str_l) if new_str is not None and new_str != value: self.set(section, option, new_str)
[docs] def resolve_file_url(self, test_string): """ Replace test_string with a path to an executable based on the format. If this looks like ${which:lalapps_tmpltbank} it will return the equivalent of which(lalapps_tmpltbank) Otherwise it will return an unchanged string. Parameters ----------- test_string : string The input string Returns -------- new_string : string The output string. """ # First check if any interpolation is needed and abort if not test_string = test_string.strip() if not (test_string.startswith("${") and test_string.endswith("}")): return test_string # This may not be a "resolve" interpolation, so even if it has # ${ ... } form I may not have to do anything # Strip the ${ and } test_string_strip = test_string[2:-1] test_list = test_string_strip.split(":", 1) if len(test_list) == 2: if test_list[0] == "resolve": curr_lfn = os.path.basename(test_list[1]) if curr_lfn in self.curr_resolved_files: return self.curr_resolved_files[curr_lfn] local_url = resolve_url(test_list[1]) self.curr_resolved_files[curr_lfn] = local_url return local_url return test_string