Source code for gemseo.wrappers.disc_from_exe

# Copyright 2021 IRT Saint Exupéry,
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License version 3 as published by the Free Software Foundation.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# Lesser General Public License for more details.
# You should have received a copy of the GNU Lesser 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.
# Contributors:
#    INITIAL AUTHORS - initial API and implementation and/or
#                      initial documentation
#        :author:  Francois Gallard
"""Make a discipline from an executable."""
from __future__ import annotations

import logging
import re
import subprocess
from ast import literal_eval
from copy import deepcopy
from pathlib import Path
from typing import Callable
from typing import Mapping
from typing import MutableSequence
from typing import Sequence
from typing import Tuple
from typing import Union

from numpy import array
from numpy import ndarray
from strenum import StrEnum

from gemseo.core.data_processor import DataProcessor
from gemseo.core.data_processor import FloatDataProcessor
from gemseo.core.discipline import MDODiscipline
from gemseo.utils.run_folder_manager import FoldersIter
from gemseo.utils.run_folder_manager import RunFolderManager

LOGGER = logging.getLogger(__name__)

NUMERICS = [str(j) for j in range(10)]

[docs]class Parser(StrEnum): """Built-in parser types.""" KEY_VALUE = "KEY_VALUE" """The output file is expected to have a key-value structure for each line.""" TEMPLATE = "TEMPLATE" """The output is expected as a JSON file with the following format: .. code:: { "a": GEMSEO_OUTPUT{a::1.0}, "b": GEMSEO_OUTPUT{b::2.0}, "c": GEMSEO_OUTPUT{c::3.0} } """
OutputParser = Callable[ [Mapping[str, Tuple[int]], Sequence[str]], Mapping[str, Union[ndarray, float]] ] """Output parser type.""" InputWriter = Callable[ [ Union[str, Path], Mapping[str, ndarray], Mapping[str, Tuple[int, int, int]], MutableSequence[str], ], None, ] """Input writer type."""
[docs]class DiscFromExe(MDODiscipline): """Generic wrapper for executables. This :class:`.MDODiscipline` uses template files describing the input and output variables. The templates can be generated with a graphical user interface (GUI). by executing the module :mod:`~gemseo.wrappers.template_grammar_editor`. An input template file is a JSON file formatted as .. code:: { "a": GEMSEO_INPUT{a::1.0}, "b": GEMSEO_INPUT{b::2.0}, "c": GEMSEO_INPUT{c::3.0} } where ``"a"`` is the name of an input, and ``1.0`` is its default value. Similarly, an output template file is a JSON file formatted as .. code:: { "a": GEMSEO_OUTPUT{a::1.0}, "b": GEMSEO_OUTPUT{b::2.0}, "c": GEMSEO_OUTPUT{c::3.0} } where ``"a"`` is the name of an output, and ``1.0`` is its default value. The current limitations are - Only one input and one output template file, otherwise, inherit from this class and modify the parsers. Only limited input writing and output parser strategies are implemented. To change that, you can pass custom parsing and writing methods to the constructor. - The only limitation in the current file format is that it must be a plain text file and not a binary file. In this case, the way of interfacing it is to provide a specific parser to the :class:`.DiscFromExe`, with the :func:`.write_input_file_method` and :func:`.parse_outfile_method` arguments of the constructor. """ _run_folder_manager: RunFolderManager """The object generating unique names for run directories..""" input_template: str """The path to the input template file.""" output_template: str """The path to the output template file.""" input_filename: str """The name of the input file.""" output_filename: str """The name of the output file.""" executable_command: str """The executable command.""" parse_outfile: OutputParser """The function used to parse the output template file.""" write_input_file: InputWriter """The function used to write the input template file.""" data_processor: DataProcessor """A data processor to be used before the execution of the discipline.""" def __init__( self, input_template: str | Path, output_template: str | Path, output_folder_basepath: str | Path, executable_command: str, input_filename: str | Path, output_filename: str | Path, folders_iter: FoldersIter = FoldersIter.NUMBERED, name: str | None = None, parse_outfile_method: Parser | OutputParser = Parser.TEMPLATE, write_input_file_method: InputWriter | None = None, parse_out_separator: str = "=", use_shell: bool = True, ) -> None: """ Args: input_template: The path to the input template file. The input locations in the file are marked by ``GEMSEO_INPUT{input_name::1.0}``, where ``input_name`` is the name of the input variable, and ``1.0`` is its default value. output_template: The path to the output template file. The output locations in the file are marked by ``GEMSEO_OUTPUT{output_name::1.0}``, where ``output_name`` is the name of the output variable, and ``1.0`` is its default value. executable_command: The command to run the executable. E.g. ``python -i input.txt -o output.txt`` input_filename: The name of the input file to be generated in the output folder. E.g. ``"input.txt"``. output_filename: The name of the output file to be generated in the output folder. E.g. ``"output.txt"``. folders_iter: The type of unique identifiers for the output folders. If :attr:`~.FoldersIter.NUMBERED`, the generated output folders will be ``f"output_folder_basepath{i+1}"``, where ``i`` is the maximum value of the already existing ``f"output_folder_basepath{i}"`` folders. Otherwise, a unique number based on the UUID function is generated. This last option shall be used if multiple MDO processes are run in the same work folder. parse_outfile_method: The optional method that can be provided by the user to parse the output template file. If the :attr:`~.Parser.KEY_VALUE` is used as output parser, the user may specify the separator key. write_input_file_method: The method to write the input data file. If ``None``, use :func:`~.write_input_file`. parse_out_separator: The separator used for the :attr:`~.Parser.KEY_VALUE` output parser. use_shell: If ``True``, run the command using the default shell. Otherwise, run directly the command. output_folder_basepath: The base path of the execution directories. Raises: TypeError: If the provided ``parse_outfile_method`` is not callable. If the provided ``write_input_file_method`` is not callable. """ # noqa:D205 D212 D415 super().__init__(name=name) self._run_folder_manager = RunFolderManager( output_folder_basepath, folders_iter, use_shell ) self.input_template = input_template self.output_template = output_template self.input_filename = input_filename self.output_filename = output_filename self.executable_command = executable_command self.__use_shell = use_shell if parse_outfile_method == Parser.TEMPLATE: self.parse_outfile = parse_outfile elif parse_outfile_method == Parser.KEY_VALUE: self.parse_outfile = lambda a, b: parse_key_value_file( a, b, parse_out_separator ) else: self.parse_outfile = parse_outfile_method if not callable(self.parse_outfile): raise TypeError("The parse_outfile_method must be callable.") self.write_input_file = write_input_file_method or write_input_file if not callable(self.write_input_file): raise TypeError("The write_input_file_method must be callable.") self._out_pos = None self._input_data = None self._in_lines = None self._out_lines = None self.data_processor = FloatDataProcessor() self.__parse_templates_and_set_grammars() def __parse_templates_and_set_grammars(self) -> None: """Parse the templates and set the grammar of the discipline.""" with open(self.input_template) as infile: self._in_lines = infile.readlines() with open(self.output_template) as outfile: self._out_lines = outfile.readlines() self._input_data, self._in_pos = parse_template(self._in_lines, True) input_names = self._input_data.keys() self.input_grammar.update_from_names(input_names) names_to_values, self._out_pos = parse_template(self._out_lines, False) output_names = names_to_values.keys() self.output_grammar.update_from_names(output_names) LOGGER.debug( "Initialize discipline from template. Input grammar: %s", input_names ) LOGGER.debug( "Initialize discipline from template. Output grammar: %s", output_names ) self.default_inputs = { k: array([literal_eval(v)]) for k, v in self._input_data.items() } def _run(self) -> None: out_dir = self._run_folder_manager.get_unique_run_folder_path() out_dir.mkdir() self.write_input_file( out_dir / self.input_filename, self.local_data, self._in_pos, self._in_lines, ) if self.__use_shell: executable_command = self.executable_command else: executable_command = self.executable_command.split() err = executable_command, shell=self.__use_shell, stderr=subprocess.STDOUT, cwd=out_dir, ) if err != 0: raise RuntimeError(f"Execution failed and returned error code: {err}.") with open(out_dir / self.output_filename) as outfile: out_lines = outfile.readlines() if len(out_lines) != len(self._out_lines): raise ValueError( "The number of lines of the output file changed." "This is not supported yet" ) self.local_data.update(self.parse_outfile(self._out_pos, out_lines))
[docs]def parse_template( template_lines: Sequence[str], grammar_is_input: bool, ) -> tuple[dict[str, str], dict[str, tuple[int, int, int]]]: """Parse the input or output template. This function parses the input (or output) template. It returns the tuple (names_to_values, names_to_positions), where: - `names_to_values` is the `{name:value}` dict: - name is the data name - value is the parsed input or output value in the template - `names_to_positions` describes the template format {name:(start,end,line_number)}: - `name` is the name of the input data - `start` is the index of the starting point in the input file template. This index is a line index (character number on the line) - `end` is the index of the end character in the template - `line_number` is the index of the line in the file Args: template_lines: The lines of the template file. grammar_is_input: Whether the template file describes input variables. Returns: A data structure containing the parsed input or output template. """ regex = re.compile(INPUT_REGEX if grammar_is_input else OUTPUT_REGEX) # , re.MULTILINE names_to_values = {} names_to_positions = {} for line_index, line in enumerate(template_lines): for match in regex.finditer(line): name, value = match.groups()[0].split("::") names_to_values[name] = value if grammar_is_input: # If input mode: erase the template value. start, end = match.start(), match.end() else: # If output mode: catch all the output length and not more. start = match.start() end = start + len(value) names_to_positions[name] = (start, end, line_index) return names_to_values, names_to_positions
[docs]def write_input_file( input_file_path: str | Path, data: Mapping[str, ndarray], input_positions: Mapping[str, tuple[int, int, int]], input_lines: MutableSequence[str], float_format: str = "{:1.18g}", ) -> None: """Write the input file template from the input data. Args: input_file_path: The absolute path to the file to be written. data: The local data of the discipline. input_positions: The positions of the input variables, formatted as ``{"name": (start, end, line_number)}``, where ``"name"`` is the name of the input variable, ``start`` is the index of the starting point in the file, ``end`` is the index of the end character in the file, and ``line_number`` is the index of the line in the file. An index is a line index, i.e. a character number on the line. input_lines: The lines of the file. float_format: The format of the input data in the file. """ f_text = deepcopy(input_lines) for input_name, (start, end, line_number) in input_positions.items(): cline = f_text[line_number] f_text[line_number] = ( cline[:start] + float_format.format(data[input_name]) + cline[end:] ) with open(input_file_path, "w") as infile_o: infile_o.writelines(f_text)
[docs]def parse_key_value_file( _, out_lines: Sequence[str], separator: str = "=", ) -> dict[str, float]: """Parse the output file from the expected text positions. Args: out_lines: The lines of the output file template. separator: The separating characters of the key=value format. Returns: The output data in `.MDODiscipline` friendly data structure. Raises: ValueError: If the amount of separators in the lines are not consistent with the keys and values. If the float values cannot be parsed. """ data = {} for line in out_lines: if separator in line: key_and_value = line.strip().split(separator) if len(key_and_value) != 2: raise ValueError(f"unbalanced = in line {line}.") key, value = key_and_value try: data[key.strip()] = float(literal_eval(value.strip())) except Exception: raise ValueError(f"Failed to parse value as float {value}.") return data
[docs]def parse_outfile( output_positions: Mapping[str, tuple[int]], out_lines: Sequence[str], ) -> dict[str, ndarray]: """Parse the output template file from the expected text positions. Args: output_positions: The output position for each output variable, specified as ``{"name": (start, end, line_number)}``, where ``"name"`` is the name of the output variable, ``start`` is the index of the starting point in the file, ``end`` is the index of the end character in the file, and ``line_number`` is the index of the line in the file. An index is a line index, i.e. a character number on the line. out_lines: The lines of the file. Returns: The output data. """ values = {} for output_name, (start, _, line_number) in output_positions.items(): found_dot = False found_e = False # In case generated files has fewer lines if line_number > len(out_lines) - 1: break out_text = out_lines[line_number] i = start maxi = len(out_text) while True: # The problem is that the output file used for the template may be # using an output that is longer or shorter than the one generated # at runtime. We must find the proper end of the expression... i += 1 char = out_text[i] if char == ".": # We found the . in float notation if found_dot or found_e: break found_dot = True continue # We found the e in exp notation if char in ("E", "e"): if found_e: break found_e = True continue # Check that we have nout reached EOL or space or whatever if char not in NUMERICS: break if i == maxi - 1: break output_value = out_text[start:i]"Parsed %s got output %s", output_name, output_value) values[output_name] = array([float(output_value)]) return values