From 536e9df528ce8a61647626d1820836f9e4c61348 Mon Sep 17 00:00:00 2001 From: Florian Rupprecht Date: Sun, 16 Jun 2024 19:18:35 -0400 Subject: [PATCH] Restructure --- poetry.lock | 198 +++++++++++++++++-------------------- src/styxdocker/__init__.py | 116 +++++++++++++++------- 2 files changed, 169 insertions(+), 145 deletions(-) diff --git a/poetry.lock b/poetry.lock index 4705d83..76de8dd 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. 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"typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"}, + {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"}, + {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, ] [[package]] diff --git a/src/styxdocker/__init__.py b/src/styxdocker/__init__.py index 56b99a0..5ca9ff5 100644 --- a/src/styxdocker/__init__.py +++ b/src/styxdocker/__init__.py @@ -1,14 +1,17 @@ """.. include:: ../../README.md""" # noqa: D415 +import logging +import os +import pathlib import pathlib as pl import re +import shlex from collections import deque from concurrent.futures import ThreadPoolExecutor from functools import partial -from subprocess import PIPE, CalledProcessError, Popen -from typing import Callable +from subprocess import PIPE, Popen -from styxdefs import Execution, Metadata, Runner +from styxdefs import Execution, InputPathType, Metadata, OutputPathType, Runner def _docker_mount(host_path: str, container_path: str, readonly: bool) -> str: @@ -21,19 +24,46 @@ def _docker_mount(host_path: str, container_path: str, readonly: bool) -> str: return f"type=bind,source={host_path},target={container_path}{readonly_str}" -class DockerExecution(Execution): +class StyxDockerError(Exception): + """Styx Docker error.""" + + def __init__( + self, + return_code: int | None = None, + docker_args: list[str] | None = None, + command_args: list[str] | None = None, + ) -> None: + """Create StyxDockerError.""" + message = "Command failed." + + if return_code is not None: + message += f"\n- Return code: {return_code}" + + if docker_args is not None: + message += f"\n- Docker args: {shlex.join(docker_args)}" + + if command_args is not None: + message += f"\n- Command args: {shlex.join(command_args)}" + + super().__init__(message) + + +class _DockerExecution(Execution): """Docker execution.""" - def __init__(self, metadata: Metadata, output_dir: pl.Path) -> None: + def __init__( + self, logger: logging.Logger, output_dir: pathlib.Path, metadata: Metadata + ) -> None: """Create DockerExecution.""" - self.metadata = metadata + self.logger: logging.Logger = logger self.input_files: list[tuple[pl.Path, str]] = [] self.input_file_next_id = 0 self.output_files: list[tuple[pl.Path, str]] = [] self.output_file_next_id = 0 self.output_dir = output_dir + self.metadata = metadata - def input_file(self, host_file: pl.Path | str) -> str: + def input_file(self, host_file: InputPathType) -> str: """Resolve input file.""" _host_file = pl.Path(host_file) local_file = f"/styx_input/{self.input_file_next_id}/{_host_file.name}" @@ -41,7 +71,7 @@ def input_file(self, host_file: pl.Path | str) -> str: self.input_files.append((_host_file, local_file)) return local_file - def output_file(self, local_file: str, optional: bool = False) -> pl.Path: + def output_file(self, local_file: str, optional: bool = False) -> OutputPathType: """Resolve output file.""" return self.output_dir / local_file @@ -60,6 +90,13 @@ def run(self, cargs: list[str]) -> None: # Output directory self.output_dir.mkdir(parents=True, exist_ok=True) + # Create run script + run_script = self.output_dir / "run.sh" + # Ensure utf-8 encoding and unix newlines + run_script.write_text( + f"#!/bin/bash\n{shlex.join(cargs)}\n", encoding="utf-8", newline="\n" + ) + mounts.append("--mount") mounts.append( _docker_mount( @@ -84,27 +121,26 @@ def run(self, cargs: list[str]) -> None: "/bin/bash", *docker_extra_args, container, - "-l", - "-c", - " ".join(cargs), + "./run.sh", ] - print(f"Executing docker command: '{docker_command}'") + self.logger.debug(f"Running docker: {shlex.join(docker_command)}") + self.logger.debug(f"Running command: {shlex.join(cargs)}") - def stdout_handler(line: str) -> None: - print(line) + def _stdout_handler(line: str) -> None: + self.logger.info(line) - def stderr_handler(line: str) -> None: - print(line) + def _stderr_handler(line: str) -> None: + self.logger.error(line) with Popen(docker_command, text=True, stdout=PIPE, stderr=PIPE) as process: with ThreadPoolExecutor(2) as pool: # two threads to handle the streams exhaust = partial(pool.submit, partial(deque, maxlen=0)) - exhaust(stdout_handler(line[:-1]) for line in process.stdout) # type: ignore - exhaust(stderr_handler(line[:-1]) for line in process.stderr) # type: ignore + exhaust(_stdout_handler(line[:-1]) for line in process.stdout) # type: ignore + exhaust(_stderr_handler(line[:-1]) for line in process.stderr) # type: ignore return_code = process.poll() if return_code: - raise CalledProcessError(return_code, process.args) + raise StyxDockerError(return_code, docker_command, cargs) def _default_execution_output_dir(metadata: Metadata) -> pl.Path: @@ -116,24 +152,30 @@ def _default_execution_output_dir(metadata: Metadata) -> pl.Path: class DockerRunner(Runner): """Docker runner.""" - def __init__( - self, execution_output_dir: Callable[[Metadata], pl.Path] | None = None - ) -> None: - """Create a new DockerRunner. - - Args: - execution_output_dir: A function that returns the output - directory for a given Metadata. - If None, a folder named 'output_' will be used. - This function is called once before every execution. - """ - self.execution_output_dir: Callable[[Metadata], pl.Path] = ( - _default_execution_output_dir - if execution_output_dir is None - else execution_output_dir - ) + logger_name = "styx_docker_runner" + + def __init__(self, data_dir: InputPathType | None = None) -> None: + """Create a new DockerRunner.""" + self.data_dir = pathlib.Path(data_dir or "styx_tmp") + self.uid = os.urandom(8).hex() + self.execution_counter = 0 + + # Configure logger + self.logger = logging.getLogger(self.logger_name) + if not self.logger.hasHandlers(): + self.logger.setLevel(logging.DEBUG) + ch = logging.StreamHandler() + ch.setLevel(logging.DEBUG) + formatter = logging.Formatter("[%(levelname).1s] %(message)s") + ch.setFormatter(formatter) + self.logger.addHandler(ch) def start_execution(self, metadata: Metadata) -> Execution: """Start execution.""" - output_dir = self.execution_output_dir(metadata) - return DockerExecution(metadata, output_dir) + self.execution_counter += 1 + return _DockerExecution( + logger=self.logger, + output_dir=self.data_dir + / f"{self.uid}_{self.execution_counter - 1}_{metadata.name}", + metadata=metadata, + )