annotate run_lastz_tarball.py @ 0:103538753e81 draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz commit 7b119b432f721e228a73396d4e8f0d54350b0481

#!/usr/bin/env python

import argparse
import concurrent.futures
import json
import multiprocessing
import os
import queue
import re
import shutil
import sys
import subprocess
import tarfile
import tempfile
import typing
import time


lastz_output_format_regex = re.compile(
    r"^(?:axt\+?|blastn|cigar|differences|general-?.+|lav|lav\+text|maf[-+]?|none|paf(?::wfmash)?|rdotplot|sam-?|softsam-?|text)$",
    re.IGNORECASE,
)


# Specifies the output format: lav, lav+text, axt, axt+, maf, maf+, maf-, sam, softsam, sam-, softsam-, cigar, BLASTN, PAF, PAF:wfmash, differences, rdotplot, text, general[:<fields>], or general-[:<fields>].
# ‑‑format=none can be used when no alignment output is desired.


def run_command(
    instance: int,
    input_queue: "queue.Queue[typing.Dict[str, typing.Any]]",
    output_queue: "queue.Queue[float]",
    debug: bool = False,
) -> None:
    os.chdir("galaxy/files")

    while True:
        command_dict = input_queue.get()

        if not command_dict:
            return

        args = ["lastz"]
        args.extend(command_dict["args"])

        stdin = command_dict["stdin"]
        if stdin is not None:
            stdin = open(stdin, "r")

        stdout = command_dict["stdout"]
        if stdout is not None:
            stdout = open(stdout, "w")

        stderr = command_dict["stderr"]
        if stderr is not None:
            stderr = open(stderr, "w")

        begin = time.perf_counter()
        p = subprocess.run(args, stdin=stdin, stdout=stdout, stderr=stderr)

        for var in [stdin, stdout, stderr]:
            if var is not None:
                var.close()

        if p.returncode != 0:
            sys.exit(f"command failed: {' '.join(args)}")
        else:
            stderr = command_dict["stderr"]
            if stderr is not None:
                try:
                    statinfo = os.stat(stderr, follow_symlinks=False)
                except:
                    statinfo = None

                if statinfo is None:
                    sys.exit(f"unable to stat stderr file: {' '.join(args)}")

                if statinfo.st_size != 0:
                    sys.exit(f"stderr file is not empty: {' '.join(args)}")

            elapsed = time.perf_counter() - begin
            output_queue.put(elapsed)

        if debug:
            print(f"runtime {elapsed}", file=sys.stderr, flush=True)


class BatchTar:
    def __init__(self, pathname: str, debug: bool = False) -> None:
        self.pathname = pathname
        self.debug = debug
        self.tarfile = None
        self.commands: typing.List[typing.Dict[str, typing.Any]] = []
        self._extract()
        self._load_commands()

    def batch_commands(self) -> typing.Iterator[typing.Dict[str, typing.Any]]:
        for command in self.commands:
            yield command

    def _load_commands(self) -> None:
        try:
            f = open("galaxy/commands.json")
        except FileNotFoundError:
            sys.exit(
                f"ERROR: input tarball missing galaxy/commands.json: {self.pathname}"
            )

        begin = time.perf_counter()
        for json_line in f:
            json_line = json_line.rstrip("\n")
            try:
                command_dict = json.loads(json_line)
            except json.JSONDecodeError:
                sys.exit(
                    f"ERROR: bad json line in galaxy/commands.json: {self.pathname}"
                )

            self._load_command(command_dict)

        f.close()
        elapsed = time.perf_counter() - begin

        if self.debug:
            print(
                f"loaded {len(self.commands)} commands in {elapsed} seconds ",
                file=sys.stderr,
                flush=True,
            )

    def _load_command(self, command_dict: typing.Dict[str, typing.Any]) -> None:
        # check command_dict structure
        field_types: typing.Dict[str, typing.List[typing.Any]] = {
            "executable": [str],
            "args": [list],
            "stdin": [str, "None"],
            "stdout": [str, "None"],
            "stderr": [str, "None"],
        }

        bad_format = False
        for field_name in field_types.keys():
            # missing field
            if field_name not in command_dict:
                bad_format = True
                break

            # incorrect field type
            good_type = False
            for field_type in field_types[field_name]:
                if isinstance(field_type, str) and field_type == "None":
                    if command_dict[field_name] is None:
                        good_type = True
                        break
                elif isinstance(command_dict[field_name], field_type):
                    good_type = True
                    break

            if good_type is False:
                bad_format = True

        if not bad_format:
            # all args must be strings
            for arg in command_dict["args"]:
                if not isinstance(arg, str):
                    bad_format = True
                    break

        if bad_format:
            sys.exit(
                f"ERROR: unexpected json format in line in galaxy/commands.json: {self.pathname}"
            )

        self.commands.append(command_dict)

    def _extract(self) -> None:
        try:
            self.tarball = tarfile.open(
                name=self.pathname, mode="r:*", format=tarfile.GNU_FORMAT
            )
        except FileNotFoundError:
            sys.exit(f"ERROR: unable to find input tarball: {self.pathname}")
        except tarfile.ReadError:
            sys.exit(f"ERROR: error reading input tarball: {self.pathname}")

        begin = time.perf_counter()
        self.tarball.extractall(filter="data")
        self.tarball.close()
        elapsed = time.perf_counter() - begin

        if self.debug:
            print(
                f"Extracted tarball in {elapsed} seconds", file=sys.stderr, flush=True
            )


class TarRunner:
    def __init__(
        self,
        input_pathname: str,
        output_pathname: str,
        parallel: int,
        debug: bool = False,
    ) -> None:
        self.input_pathname = input_pathname
        self.output_pathname = output_pathname
        self.parallel = parallel
        self.debug = debug
        self.batch_tar = BatchTar(self.input_pathname, debug=self.debug)
        self.output_file_format: typing.Dict[str, str] = {}
        self.output_files: typing.Dict[str, typing.List[str]] = {}
        self._set_output()
        self._set_target_query()

    def _set_output(self) -> None:
        for command_dict in self.batch_tar.batch_commands():
            output_file = None
            output_format = None

            for arg in command_dict["args"]:
                if arg.startswith("--format="):
                    output_format = arg[9:]
                elif arg.startswith("--output="):
                    output_file = arg[9:]

            if output_file is None:
                f = tempfile.NamedTemporaryFile(dir="galaxy/files", delete=False)
                output_file = os.path.basename(f.name)
                f.close()
                command_dict["args"].append(f"--output={output_file}")

            if output_format is None:
                output_format = "lav"
                command_dict["args"].append(f"--format={output_format}")

            if not lastz_output_format_regex.match(output_format):
                sys.exit(f"ERROR: invalid output format: {output_format}")

            self.output_file_format[output_file] = output_format

        for output_file, output_format in self.output_file_format.items():
            self.output_files.setdefault(output_format, [])
            self.output_files[output_format].append(output_file)

    def _set_target_query(self) -> None:
        for command_dict in self.batch_tar.batch_commands():
            new_args: typing.List[str] = []

            for arg in command_dict["args"]:
                if arg.startswith("--target="):
                    new_args.insert(0, arg[9:])
                elif arg.startswith("--query="):
                    new_args.insert(1, arg[8:])
                else:
                    new_args.append(arg)

            command_dict["args"] = new_args

    def run(self) -> None:
        run_times = []
        begin = time.perf_counter()

        with multiprocessing.Manager() as manager:
            input_queue: queue.Queue[typing.Dict[str, typing.Any]] = manager.Queue()
            output_queue: queue.Queue[float] = manager.Queue()

            for command_dict in self.batch_tar.batch_commands():
                input_queue.put(command_dict)

            # use the empty dict as a sentinel
            for _ in range(self.parallel):
                input_queue.put({})

            with concurrent.futures.ProcessPoolExecutor(
                max_workers=self.parallel
            ) as executor:
                futures = [
                    executor.submit(
                        run_command,
                        instance,
                        input_queue,
                        output_queue,
                        debug=self.debug,
                    )
                    for instance in range(self.parallel)
                ]

            for f in concurrent.futures.as_completed(futures):
                if not f.done() or f.cancelled() or f.exception() is not None:
                    sys.exit("lastz command failed")

            while not output_queue.empty():
                run_time = output_queue.get()
                run_times.append(run_time)

        elapsed = time.perf_counter() - begin

        if self.debug:
            print(f"elapsed {elapsed}", file=sys.stderr, flush=True)

        self._cleanup()

    def _cleanup(self) -> None:
        num_output_files = len(self.output_files.keys())

        for file_type, file_list in self.output_files.items():
            with open(f"output.{file_type}", "w") as ofh:
                for filename in file_list:
                    with open(f"galaxy/files/{filename}") as ifh:
                        for line in ifh:
                            ofh.write(line)

        if num_output_files == 1:
            file_type = list(self.output_files.keys())[0]
            src_filename = f"output.{file_type}"
            shutil.copy2(src_filename, self.output_pathname)


def main() -> None:
    if not hasattr(tarfile, "data_filter"):
        sys.exit("ERROR: extracting may be unsafe; consider updating Python")

    parser = argparse.ArgumentParser()
    parser.add_argument("--input", type=str, required=True)
    parser.add_argument("--output", type=str, required=True)
    parser.add_argument("--parallel", type=int, default=1, required=False)
    parser.add_argument("--debug", action="store_true", required=False)

    args = parser.parse_args()
    runner = TarRunner(args.input, args.output, args.parallel, args.debug)
    runner.run()


if __name__ == "__main__":
    main()