Source code for ymp.exceptions

"""Exceptions raised by YMP"""

import textwrap
from inspect import stack
from typing import Optional

from click import ClickException, echo


class YmpException(Exception):
    """Base class of all YMP Exceptions"""


class YmpNoStackException(YmpException, ClickException):
    """Exception that does not lead to stack trace on CLI

    Inheriting from ClickException makes ``click`` print only the
    ``self.msg`` value of the exception, rather than allowing Python
    to print a full stack trace.

    This is useful for exceptions indicating usage or configuration
    errors. We use this, instead of `click.UsageError` and friends so
    that the exceptions can be caught and handled explicitly where
    needed.

    Note that click will call the ``show`` method on this object to
    print the exception. The default implementation from click will
    just prefix the ``msg`` with ``Error:``.

    FIXME: This does not work if the exception is raised from within
        the snakemake workflow as snakemake.snakemake catches and
        reformats exceptions.
    """


class YmpUsageError(YmpNoStackException):
    pass


class YmpSystemError(YmpNoStackException):
    """Indicates problem running YMP with available system software"""


class YmpRuleError(YmpNoStackException):
    """Indicates an error in the rules files

    This could e.g. be a Stage or Environment defined twice.

    Args:
      obj: The object causing the exception. Must have ``lineno``
        and ``filename`` as these will be shown as part of the error
        message on the command line.
      msg: The message to display
    """
    def __init__(self, obj: object, msg: str) -> None:
        self.obj = obj
        self.stack = stack()
        super().__init__(msg)

    def show(self) -> None:
        echo('Error in line %i of %s:\n%s' % (
            getattr(self.obj, "lineno", -1),
            getattr(self.obj, "filename", "<NOT FOUND>"),
            self.format_message()
        ), err=True)
        for fi in self.stack:
            if not fi.filename.endswith(".py"):
                echo(f"  included from {fi.filename}:{fi.lineno}")


class YmpConfigError(YmpNoStackException):
    """Indicates an error in the ymp.yml config files

    Args:
      obj: Subtree of config causing error
      msg: The message to display
      key: Key indicating part of ``obj`` causing error
      exc: Upstream exception causing error
    """
    def __init__(self, obj: object, msg: str, key: Optional[object]=None,
                 exc: Optional[Exception]=None) -> None:
        self.obj = obj
        self.stack = stack()
        self.exc = exc
        super().__init__(msg)


class YmpStageError(YmpNoStackException):
    """Indicates an error in the requested stage stack
    """
    def __init__(self, msg: str) -> None:
        super().__init__(textwrap.dedent(msg))

    def show(self) -> None:
        echo(self.format_message(), err=True)


class YmpWorkflowError(YmpNoStackException):
    """Indicates an error during workflow execution

    E.g. failures to expand dynamic variables
    """