input4mips_validation.validation.cf_checker

input4mips_validation.validation.cf_checker

Validation with the cf-checker

check_with_cf_checker(filepath, ds, no_raise_if_only_warnings=False, conventions_attribute='Conventions')

Check a file with the cf-checker

Parameters:

Name	Type	Description	Default
filepath	Path | str	Filepath to check	required
ds	Dataset	Dataset that corresponds to filepath. This is required to we can tell cf-checker which CF conventions to use while checking the file.	required
no_raise_if_only_warnings	bool	If True, no error is raised if the CF-checker only raises warnings.	False
conventions_attribute	str	The attribute which contains the conventions information used by cf-checker. We provide this as an argument just in case, it is very unlikely that you will want to change this.	'Conventions'

Raises:

Type	Description
ValueError	If no_raise_if_only_warnings is False, an error is raised if the CF-checker found any issues, including warnings. If no_raise_if_only_warnings is True, an error is raised if the CF-checker found any errors, excluding warnings.

Source code in src/input4mips_validation/validation/cf_checker.py

def check_with_cf_checker(
    filepath: Path | str,
    ds: xr.Dataset,
    no_raise_if_only_warnings: bool = False,
    conventions_attribute: str = "Conventions",
) -> None:
    """
    Check a file with the cf-checker

    Parameters
    ----------
    filepath
        Filepath to check

    ds
        Dataset that corresponds to `filepath`.

        This is required to we can tell cf-checker
        which CF conventions to use while checking the file.

    no_raise_if_only_warnings
        If `True`, no error is raised if the CF-checker only raises warnings.

    conventions_attribute
        The attribute which contains the conventions information used by cf-checker.

        We provide this as an argument just in case,
        it is very unlikely that you will want to change this.

    Raises
    ------
    ValueError
        If `no_raise_if_only_warnings` is `False`, an error is raised
        if the CF-checker found any issues, including warnings.

        If `no_raise_if_only_warnings` is `True`, an error is raised
        if the CF-checker found any errors, excluding warnings.
    """
    if conventions_attribute not in ds.attrs:
        raise MissingAttributeError(conventions_attribute)

    Conventions = ds.attrs[conventions_attribute]
    validate_Conventions(Conventions)

    conventions_match = re.match(r"CF-(?P<conventions_id>[0-9]+\.[0-9]+)", Conventions)
    if conventions_match is not None:
        cf_conventions = conventions_match.group("conventions_id").strip()
    else:
        cf_conventions = None

    if cf_conventions is None:  # pragma: no cover
        msg = (
            "Somehow failed to get the conventions from "
            f"{ds.attrs[conventions_attribute]=}"
        )
        raise AssertionError(msg)

    cf_checks_loc = shutil.which("cfchecks")
    if cf_checks_loc is None:
        msg = "Could not find cfchecks executable"
        raise AssertionError(msg)

    try:
        subprocess.check_output(
            [cf_checks_loc, "-v", cf_conventions, str(filepath)],  # noqa: S603
        )
    except subprocess.CalledProcessError as exc:
        output = exc.output.decode()

        # If only warnings should not raise an error,
        # parse the output to work out what happened.
        # This is a terrible way to do this, but the cf-checker's
        # return codes don't play nice with subprocess so here we are
        if no_raise_if_only_warnings and only_cf_checker_warnings_raised(output):
            logger.debug(f"Ignoring cf-checker warnings:\n\n{output}")

            return

        error_msg = f"cf-checker validation failed. cfchecks output:\n\n{output}"
        raise ValueError(error_msg) from exc

only_cf_checker_warnings_raised(cf_checker_output)

Determine if the CF-checker only raised warnings

This is extremely sensitive to the implementation of the cf-checker, particularly its error reporting (status of error reporting at last check).

Parameters:

Name	Type	Description	Default
cf_checker_output	str	CF-checker output to parse	required

Returns:

Type	Description
bool	True if only warnings and below were raised by the CF-checker, False otherwise.

Source code in src/input4mips_validation/validation/cf_checker.py

def only_cf_checker_warnings_raised(cf_checker_output: str) -> bool:
    """
    Determine if the CF-checker only raised warnings

    This is extremely sensitive to the implementation of the
    [cf-checker](https://github.com/cedadev/cf-checker),
    particularly its error reporting
    ([status of error reporting at last check](https://github.com/cedadev/cf-checker/blob/c0486c606f7cf4d38d3b484b427726ce1bde73ee/src/cfchecker/cfchecks.py#L675)).

    Parameters
    ----------
    cf_checker_output
        CF-checker output to parse

    Returns
    -------
    :
        `True` if only warnings and below were raised by the CF-checker,
        `False` otherwise.
    """
    cf_checker_output_no_new_lines = " ".join(cf_checker_output.splitlines())

    counts: dict[str, Union[int, None]] = {}
    for key, id_string in {
        "fatal": "FATAL ERRORS",
        "errors": "ERRORS detected",
        "warnings": "WARNINGS given",
    }.items():
        check_regexp = rf".*(?P<checker_output_string>{id_string}:\s\d+).*"
        match = re.match(check_regexp, cf_checker_output_no_new_lines)
        if match:
            matching_text = match.group("checker_output_string")
            count = int(matching_text.split(":")[-1].strip())

            counts[key] = count

        else:
            counts[key] = None

    return all(counts[k] is None or counts[k] == 0 for k in ("fatal", "errors"))