comparison package_output.py @ 4:36cafb694dd2 draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit b8aa943b38b865defab8a27e4404bb8a2131f919

3:6f46cebc9ed8

        if self.tarfile is None:
            self.tarfile = tarfile.open(
                name=self.pathname,
                mode="w:gz",
                format=tarfile.GNU_FORMAT,
                compresslevel=1,
            )

    def add_config(self, pathname: str) -> None:
        if self.tarfile is None:
            self._initialize()

        self.package_file.add_config("commands.json")

    def _parse_line(self, line: str) -> typing.Dict[str, typing.Any]:
        # resolve shell redirects
        trees: typing.List[typing.Any] = bashlex.parse(line, strictmode=False)  # type: ignore[attr-defined]
        positions: typing.List[typing.Tuple[int, int]] = []

        for tree in trees:
            visitor = nodevisitor(positions)
            visitor.visit(tree)

        command_dict["stderr"] = visitor.stderr

        return command_dict

    def _parse_processed_line(self, line: str) -> typing.Dict[str, typing.Any]:
        argv: typing.List[str] = list(bashlex.split(line))  # type: ignore[attr-defined]
        self.executable = argv.pop(0)

        parser: argparse.ArgumentParser = argparse.ArgumentParser(add_help=False)
        if "arguments" in self.config:
            arguments_section = self.config["arguments"]

            command_dict["args"].append(f"--query={value}")

        return command_dict


class nodevisitor(bashlex.ast.nodevisitor):  # type: ignore[name-defined,misc]
    def __init__(self, positions: typing.List[typing.Tuple[int, int]]) -> None:
        self.positions = positions
        self.stdin = None
        self.stdout = None
        self.stderr = None

    def visitredirect(
        self,
        n: bashlex.ast.node,  # type: ignore[name-defined]
        n_input: int,
        n_type: str,
        output: typing.Any,
        heredoc: typing.Any,
    ) -> None:
        if isinstance(n_input, int) and 0 <= n_input <= 2:
            if isinstance(output, bashlex.ast.node) and output.kind == "word":  # type: ignore[attr-defined]
                self.positions.append(n.pos)
                if n_input == 0:
                    self.stdin = output.word
                elif n_input == 1:
                    self.stdout = output.word

            else:
                sys.exit(f"oops 1: {type(n_input)}")
        else:
            sys.exit(f"oops 2: {type(n_input)}")

    def visitheredoc(self, n: bashlex.ast.node, value: typing.Any) -> None:  # type: ignore[name-defined]
        pass


def main() -> None:
    our_dirname: str = os.path.dirname(os.path.realpath(__file__))

4:36cafb694dd2

        if self.tarfile is None:
            self.tarfile = tarfile.open(
                name=self.pathname,
                mode="w:gz",
                format=tarfile.GNU_FORMAT,
                compresslevel=6,
            )

    def add_config(self, pathname: str) -> None:
        if self.tarfile is None:
            self._initialize()

        self.package_file.add_config("commands.json")

    def _parse_line(self, line: str) -> typing.Dict[str, typing.Any]:
        # resolve shell redirects
        trees: typing.List[typing.Any] = bashlex.parse(line, strictmode=False)
        positions: typing.List[typing.Tuple[int, int]] = []

        for tree in trees:
            visitor = nodevisitor(positions)
            visitor.visit(tree)

        command_dict["stderr"] = visitor.stderr

        return command_dict

    def _parse_processed_line(self, line: str) -> typing.Dict[str, typing.Any]:
        argv: typing.List[str] = list(bashlex.split(line))
        self.executable = argv.pop(0)

        parser: argparse.ArgumentParser = argparse.ArgumentParser(add_help=False)
        if "arguments" in self.config:
            arguments_section = self.config["arguments"]

            command_dict["args"].append(f"--query={value}")

        return command_dict


class nodevisitor(bashlex.ast.nodevisitor):  # type: ignore[misc]
    def __init__(self, positions: typing.List[typing.Tuple[int, int]]) -> None:
        self.positions = positions
        self.stdin = None
        self.stdout = None
        self.stderr = None

    def visitredirect(
        self,
        n: bashlex.ast.node,
        n_input: int,
        n_type: str,
        output: typing.Any,
        heredoc: typing.Any,
    ) -> None:
        if isinstance(n_input, int) and 0 <= n_input <= 2:
            if isinstance(output, bashlex.ast.node) and output.kind == "word":
                self.positions.append(n.pos)
                if n_input == 0:
                    self.stdin = output.word
                elif n_input == 1:
                    self.stdout = output.word

            else:
                sys.exit(f"oops 1: {type(n_input)}")
        else:
            sys.exit(f"oops 2: {type(n_input)}")

    def visitheredoc(self, n: bashlex.ast.node, value: typing.Any) -> None:
        pass


def main() -> None:
    our_dirname: str = os.path.dirname(os.path.realpath(__file__))