comparison run_lastz_tarball.py @ 11:aa5586d83ae3 draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/batched_lastz commit e93d50e4ea6522b591e24c3b0ddbe8f9d322a93a

10:d10e7502aba8

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")

    # These are not considered errors even though
    # we will end up with a segmented alignment
    truncation_regex = re.compile(

    while True:
        command_dict = input_queue.get()

        if not command_dict:
            return

        args = ["lastz", "--allocate:traceback=1.99G"]
        args.extend(command_dict["args"])

        stdin = command_dict["stdin"]

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

        if p.returncode == 0:
            stderr = command_dict["stderr"]
            if stderr is not None:
                try:
                    statinfo = os.stat(stderr, follow_symlinks=False)
                except Exception:
                    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)

        elif p.returncode == 1:
            traceback_warning = True

            stderr_file = command_dict["stderr"]
            if stderr_file is None:
                traceback_warning = False
            else:
                with open(stderr_file) as f:
                    for stderr_line in f:
                        stderr_line = stderr_line.strip()
                        if (
                            not truncation_regex.match(stderr_line)
                            and stderr_line != truncation_msg
                        ):
                            traceback_warning = False

            if traceback_warning:
                elapsed = time.perf_counter() - begin
                output_queue.put(elapsed)
            else:
                sys.exit(f"command failed: {' '.join(args)}")

        else:
            sys.exit(f"command failed: {' '.join(args)}")

        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

                        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)

        for file_type, file_list in self.output_files.items():
            with open(f"output.{final_output_format}", "w") as ofh:
                if final_output_format == "maf":
                    print("##maf version=1", file=ofh)
                for filename in file_list:
                    with open(f"galaxy/files/{filename}") as ifh:
                        for line in ifh:
                            ofh.write(line)

11:aa5586d83ae3

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

    # These are not considered errors even though
    # we will end up with a segmented alignment
    truncation_regex = re.compile(

    while True:
        command_dict = input_queue.get()

        if not command_dict:
            return None

        args = ["lastz", "--allocate:traceback=1.99G"]
        args.extend(command_dict["args"])

        stdin = command_dict["stdin"]

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

        # if there is a stderr_file, make sure it is
        # empty or only contains truncation messages
        stderr_ok = True
        stderr_file = command_dict["stderr"]

        if stderr_file is not None:
            try:
                statinfo = os.stat(stderr_file, follow_symlinks=False)
                if statinfo.st_size != 0:
                    with open(stderr_file) as f:
                        for stderr_line in f:
                            stderr_line = stderr_line.strip()
                            if (not truncation_regex.match(stderr_line) and stderr_line != truncation_msg):
                                stderr_ok = False
            except Exception:
                stderr_ok = False

        if p.returncode in [0, 1] and stderr_ok:
            elapsed = time.perf_counter() - begin
            output_queue.put(elapsed)
        else:
            return f"command failed (rc={p.returncode}): {' '.join(args)}"


class BatchTar:
    def __init__(self, pathname: str, debug: bool = False) -> None:
        self.pathname = pathname

                        debug=self.debug,
                    )
                    for instance in range(self.parallel)
                ]

            found_falures = False

            for f in concurrent.futures.as_completed(futures):
                result = f.result()
                if result is not None:
                    print(f"lastz: {result}", file=sys.stderr, flush=True)

                if not f.done() or f.cancelled() or f.exception() is not None:
                    found_falures = True

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

            if found_falures:
                sys.exit("lastz command failed")

        elapsed = time.perf_counter() - begin

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

        for file_type, file_list in self.output_files.items():
            with open(f"output.{final_output_format}", "w") as ofh:
                if final_output_format == "maf":
                    print("##maf version=1", file=ofh)

                for filename in file_list:
                    with open(f"galaxy/files/{filename}") as ifh:
                        for line in ifh:
                            ofh.write(line)