File: parameter_validators.py

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from typing import (
    Any,
    List,
    Optional,
    Union,
)

from pydantic import (
    BaseModel,
    ConfigDict,
    Field,
    model_validator,
    PrivateAttr,
    TypeAdapter,
)
from typing_extensions import (
    Annotated,
    Literal,
    Protocol,
    Self,
)

try:
    import regex
except ImportError:
    import re as regex


class ValidationArgument:
    doc: Optional[str]
    xml_body: bool
    xml_allow_json_load: bool

    def __init__(
        self,
        doc: Optional[str],
        xml_body: bool = False,
        xml_allow_json_load: bool = False,
    ):
        self.doc = doc
        self.xml_body = xml_body
        self.xml_allow_json_load = xml_allow_json_load


Negate = Annotated[
    bool,
    ValidationArgument("Negates the result of the validator."),
]
NEGATE_DEFAULT = False
SPLIT_DEFAULT = "\t"
DEFAULT_VALIDATOR_MESSAGE = "Parameter validation error."

ValidatorType = Literal[
    "expression",
    "regex",
    "in_range",
    "length",
    "metadata",
    "dataset_metadata_equal",
    "unspecified_build",
    "no_options",
    "empty_field",
    "empty_dataset",
    "empty_extra_files_path",
    "dataset_metadata_in_data_table",
    "dataset_metadata_not_in_data_table",
    "dataset_metadata_in_range",
    "value_in_data_table",
    "value_not_in_data_table",
    "dataset_ok_validator",
    "dataset_metadata_in_file",
]


class ValidatorDescription(Protocol):

    @property
    def negate(self) -> bool: ...

    @property
    def message(self) -> Optional[str]: ...


class StrictModel(BaseModel):
    model_config = ConfigDict(extra="forbid")


class ParameterValidatorModel(StrictModel):
    type: ValidatorType
    message: Annotated[
        Optional[str],
        ValidationArgument(
            """The error message displayed on the tool form if validation fails. A placeholder string ``%s`` will be repaced by the ``value``"""
        ),
    ] = None
    # track validators setup by other input parameters and not validation explicitly
    implicit: bool = False
    _static: bool = PrivateAttr(False)
    _deprecated: bool = PrivateAttr(False)
    # validators must be explicitly set as 'safe' to operate as user-defined workflow parameters or to be used
    # within future user-defined tool parameters
    _safe: bool = PrivateAttr(False)

    @model_validator(mode="after")
    def set_default_message(self) -> Self:
        if self.message is None:
            self.message = self.default_message
        return self

    @property
    def default_message(self) -> str:
        return DEFAULT_VALIDATOR_MESSAGE


class StaticValidatorModel(ParameterValidatorModel):
    _static: bool = PrivateAttr(True)

    def statically_validate(self, v: Any) -> None: ...


class ExpressionParameterValidatorModel(StaticValidatorModel):
    """Check if a one line python expression given expression evaluates to True.

    The expression is given is the content of the validator tag."""

    type: Literal["expression"] = "expression"
    negate: Negate = NEGATE_DEFAULT
    expression: Annotated[str, ValidationArgument("Python expression to validate.", xml_body=True)]

    def statically_validate(self, value: Any) -> None:
        ExpressionParameterValidatorModel.expression_validation(self.expression, value, self)

    @staticmethod
    def ensure_compiled(expression: Union[str, Any]) -> Any:
        if isinstance(expression, str):
            return compile(expression, "<string>", "eval")
        else:
            return expression

    @staticmethod
    def expression_validation(
        expression: str, value: Any, validator: "ValidatorDescription", compiled_expression: Optional[Any] = None
    ):
        if compiled_expression is None:
            compiled_expression = ExpressionParameterValidatorModel.ensure_compiled(expression)
        message = None
        try:
            evalresult = eval(compiled_expression, dict(value=value))
        except Exception:
            message = f"Validator '{expression}' could not be evaluated on '{value}'"
            evalresult = False

        raise_error_if_validation_fails(bool(evalresult), validator, message=message, value_to_show=value)

    @property
    def default_message(self) -> str:
        return f"Value '%s' does not evaluate to {'True' if not self.negate else 'False'} for '{self.expression}'"


class RegexParameterValidatorModel(StaticValidatorModel):
    """Check if a regular expression **matches** the value, i.e. appears
    at the beginning of the value. To enforce a match of the complete value use
    ``$`` at the end of the expression. The expression is given is the content
    of the validator tag. Note that for ``selects`` each option is checked
    separately."""

    type: Literal["regex"] = "regex"
    negate: Negate = NEGATE_DEFAULT
    expression: Annotated[str, ValidationArgument("Regular expression to validate against.", xml_body=True)]
    _safe: bool = PrivateAttr(True)

    @property
    def default_message(self) -> str:
        return f"Value '%s' does {'not ' if not self.negate else ''}match regular expression '{self.expression.replace('%', '%%')}'"

    def statically_validate(self, value: Any) -> None:
        if value and not isinstance(value, str):
            raise ValueError(f"Wrong type found value {value}")
        RegexParameterValidatorModel.regex_validation(self.expression, value, self)

    @staticmethod
    def regex_validation(expression: str, value: Any, validator: "ValidatorDescription"):
        if not isinstance(value, list):
            value = [value]
        for val in value:
            match = regex.match(expression, val or "")
            raise_error_if_validation_fails(match is not None, validator, value_to_show=val)


class InRangeParameterValidatorModel(StaticValidatorModel):
    type: Literal["in_range"] = "in_range"
    min: Optional[Union[float, int]] = None
    max: Optional[Union[float, int]] = None
    exclude_min: bool = False
    exclude_max: bool = False
    negate: Negate = NEGATE_DEFAULT
    _safe: bool = PrivateAttr(True)

    def statically_validate(self, value: Any):
        if isinstance(value, (int, float)):
            validates = True
            if self.min is not None and value == self.min and self.exclude_min:
                validates = False
            elif self.min is not None and value < self.min:
                validates = False
            elif self.max is not None and value == self.max and self.exclude_max:
                validates = False
            if self.max is not None and value > self.max:
                validates = False
            raise_error_if_validation_fails(validates, self)

    @property
    def default_message(self) -> str:
        op1 = "<="
        op2 = "<="
        if self.exclude_min:
            op1 = "<"
        if self.exclude_max:
            op2 = "<"
        min_str = str(self.min) if self.min is not None else "-infinity"
        max_str = str(self.max) if self.max is not None else "+infinity"
        range_description_str = f"({min_str} {op1} value {op2} {max_str})"
        return f"Value ('%s') must {'not ' if self.negate else ''}fulfill {range_description_str}"


class LengthParameterValidatorModel(StaticValidatorModel):
    type: Literal["length"] = "length"
    min: Optional[int] = None
    max: Optional[int] = None
    negate: Negate = NEGATE_DEFAULT
    _safe: bool = PrivateAttr(True)

    def statically_validate(self, value: Any):
        if isinstance(value, str):
            length = len(value)
            validates = True
            if self.min is not None and length < self.min:
                validates = False
            if self.max is not None and length > self.max:
                validates = False
            raise_error_if_validation_fails(validates, self)

    @property
    def default_message(self) -> str:
        return f"Must {'not ' if self.negate else ''}have length of at least {self.min} and at most {self.max}"


class MetadataParameterValidatorModel(ParameterValidatorModel):
    type: Literal["metadata"] = "metadata"
    check: Optional[List[str]] = None
    skip: Optional[List[str]] = None
    negate: Negate = NEGATE_DEFAULT

    @property
    def default_message(self) -> str:
        check = self.check
        skip = self.skip
        message = DEFAULT_VALIDATOR_MESSAGE
        if not self.negate:
            message = "Metadata '%s' missing, click the pencil icon in the history item to edit / save the metadata attributes"
        else:
            if check:
                message = f"""At least one of the checked metadata '{",".join(check)}' is set, click the pencil icon in the history item to edit / save the metadata attributes"""
            elif skip:
                message = f"""At least one of the non skipped metadata '{",".join(skip)}' is set, click the pencil icon in the history item to edit / save the metadata attributes"""
        return message


class DatasetMetadataEqualParameterValidatorModel(ParameterValidatorModel):
    type: Literal["dataset_metadata_equal"] = "dataset_metadata_equal"
    metadata_name: str
    value: Annotated[Any, ValidationArgument("Value to test against", xml_allow_json_load=True)]
    negate: Negate = NEGATE_DEFAULT

    @property
    def default_message(self) -> str:
        if not self.negate:
            message = f"Metadata value for '{self.metadata_name}' must be '{self.value}', but it is '%s'."
        else:
            message = f"Metadata value for '{self.metadata_name}' must not be '{self.value}' but it is."
        return message


class UnspecifiedBuildParameterValidatorModel(ParameterValidatorModel):
    type: Literal["unspecified_build"] = "unspecified_build"
    negate: Negate = NEGATE_DEFAULT

    @property
    def default_message(self) -> str:
        return f"{'Unspecified' if not self.negate else 'Specified'} genome build, click the pencil icon in the history item to {'set' if not self.negate else 'remove'} the genome build"


class NoOptionsParameterValidatorModel(StaticValidatorModel):
    type: Literal["no_options"] = "no_options"
    negate: Negate = NEGATE_DEFAULT

    @staticmethod
    def no_options_validate(value: Any, validator: "ValidatorDescription"):
        raise_error_if_validation_fails(value is not None, validator)

    def statically_validate(self, value: Any) -> None:
        NoOptionsParameterValidatorModel.no_options_validate(value, self)

    @property
    def default_message(self) -> str:
        return f"{'No options' if not self.negate else 'Options'} available for selection"


class EmptyFieldParameterValidatorModel(StaticValidatorModel):
    type: Literal["empty_field"] = "empty_field"
    negate: Negate = NEGATE_DEFAULT

    @staticmethod
    def empty_validate(value: Any, validator: "ValidatorDescription"):
        raise_error_if_validation_fails((value not in ("", None)), validator)

    def statically_validate(self, value: Any) -> None:
        EmptyFieldParameterValidatorModel.empty_validate(value, self)

    @property
    def default_message(self) -> str:
        if not self.negate:
            message = "Field requires a value"
        else:
            message = "Field must not set a value"
        return message


class EmptyDatasetParameterValidatorModel(ParameterValidatorModel):
    type: Literal["empty_dataset"] = "empty_dataset"
    negate: Negate = NEGATE_DEFAULT

    @property
    def default_message(self) -> str:
        return f"The selected dataset is {'non-' if self.negate else ''}empty, this tool expects {'non-' if not self.negate else ''}empty files."


class EmptyExtraFilesPathParameterValidatorModel(ParameterValidatorModel):
    type: Literal["empty_extra_files_path"] = "empty_extra_files_path"
    negate: Negate = NEGATE_DEFAULT

    @property
    def default_message(self) -> str:
        negate = self.negate
        return f"The selected dataset's extra_files_path directory is {'non-' if negate else ''}empty or does {'not ' if not negate else ''}exist, this tool expects {'non-' if not negate else ''}empty extra_files_path directories associated with the selected input."


class DatasetMetadataInDataTableParameterValidatorModel(ParameterValidatorModel):
    type: Literal["dataset_metadata_in_data_table"] = "dataset_metadata_in_data_table"
    table_name: str
    metadata_name: str
    metadata_column: Union[int, str]
    negate: Negate = NEGATE_DEFAULT

    @property
    def default_message(self) -> str:
        return f"Value for metadata {self.metadata_name} was not found in {self.table_name}."


class DatasetMetadataNotInDataTableParameterValidatorModel(ParameterValidatorModel):
    type: Literal["dataset_metadata_not_in_data_table"] = "dataset_metadata_not_in_data_table"
    table_name: str
    metadata_name: str
    metadata_column: Union[int, str]
    negate: Negate = NEGATE_DEFAULT

    @property
    def default_message(self) -> str:
        return f"Value for metadata {self.metadata_name} was not found in {self.table_name}."


class DatasetMetadataInRangeParameterValidatorModel(ParameterValidatorModel):
    type: Literal["dataset_metadata_in_range"] = "dataset_metadata_in_range"
    metadata_name: str
    min: Optional[Union[float, int]] = None
    max: Optional[Union[float, int]] = None
    exclude_min: bool = False
    exclude_max: bool = False
    negate: Negate = NEGATE_DEFAULT

    @property
    def default_message(self) -> str:
        op1 = "<="
        op2 = "<="
        if self.exclude_min:
            op1 = "<"
        if self.exclude_max:
            op2 = "<"
        range_description_str = f"({self.min} {op1} value {op2} {self.max})"
        return f"Value ('%s') must {'not ' if self.negate else ''}fulfill {range_description_str}"


class ValueInDataTableParameterValidatorModel(ParameterValidatorModel):
    type: Literal["value_in_data_table"] = "value_in_data_table"
    table_name: str
    metadata_column: Union[int, str]
    negate: Negate = NEGATE_DEFAULT

    @property
    def default_message(self) -> str:
        return "Value for metadata not found."


class ValueNotInDataTableParameterValidatorModel(ParameterValidatorModel):
    type: Literal["value_not_in_data_table"] = "value_not_in_data_table"
    table_name: str
    metadata_column: Union[int, str]
    negate: Negate = NEGATE_DEFAULT

    @property
    def default_message(self) -> str:
        return f"Value was not found in {self.table_name}."


class DatasetOkValidatorParameterValidatorModel(ParameterValidatorModel):
    type: Literal["dataset_ok_validator"] = "dataset_ok_validator"
    negate: Negate = NEGATE_DEFAULT

    @property
    def default_message(self) -> str:
        if not self.negate:
            message = (
                "The selected dataset is still being generated, select another dataset or wait until it is completed"
            )
        else:
            message = "The selected dataset must not be in state OK"
        return message


class DatasetMetadataInFileParameterValidatorModel(ParameterValidatorModel):
    type: Literal["dataset_metadata_in_file"] = "dataset_metadata_in_file"
    filename: str
    metadata_name: str
    metadata_column: Union[int, str]
    line_startswith: Optional[str] = None
    split: str = SPLIT_DEFAULT
    negate: Negate = NEGATE_DEFAULT
    _deprecated: bool = PrivateAttr(True)

    @property
    def default_message(self) -> str:
        return f"Value for metadata {self.metadata_name} was not found in {self.filename}."


AnyValidatorModel = Annotated[
    Union[
        ExpressionParameterValidatorModel,
        RegexParameterValidatorModel,
        InRangeParameterValidatorModel,
        LengthParameterValidatorModel,
        MetadataParameterValidatorModel,
        DatasetMetadataEqualParameterValidatorModel,
        UnspecifiedBuildParameterValidatorModel,
        NoOptionsParameterValidatorModel,
        EmptyFieldParameterValidatorModel,
        EmptyDatasetParameterValidatorModel,
        EmptyExtraFilesPathParameterValidatorModel,
        DatasetMetadataInDataTableParameterValidatorModel,
        DatasetMetadataNotInDataTableParameterValidatorModel,
        DatasetMetadataInRangeParameterValidatorModel,
        ValueInDataTableParameterValidatorModel,
        ValueNotInDataTableParameterValidatorModel,
        DatasetOkValidatorParameterValidatorModel,
        DatasetMetadataInFileParameterValidatorModel,
    ],
    Field(discriminator="type"),
]

AnySafeValidatorModel = Annotated[
    Union[
        RegexParameterValidatorModel,
        InRangeParameterValidatorModel,
        LengthParameterValidatorModel,
    ],
    Field(discriminator="type"),
]

DiscriminatedAnyValidatorModel = TypeAdapter(AnyValidatorModel)  # type:ignore[var-annotated]
DiscriminatedAnySafeValidatorModel = TypeAdapter(AnySafeValidatorModel)  # type:ignore[var-annotated]


def raise_error_if_validation_fails(
    value: bool, validator: ValidatorDescription, message: Optional[str] = None, value_to_show: Optional[str] = None
):
    if not isinstance(value, bool):
        raise AssertionError("Validator logic problem - computed validation value must be boolean")
    if message is None:
        message = validator.message
    if not message:
        message = DEFAULT_VALIDATOR_MESSAGE
    assert message is not None
    if value_to_show and "%s" in message:
        message = message % value_to_show
    negate = validator.negate
    if (not negate and value) or (negate and not value):
        return
    else:
        raise ValueError(message)


__all__ = (
    "AnyValidatorModel",
    "DiscriminatedAnyValidatorModel",
    "ValidatorType",
    "ParameterValidatorModel",
    "SPLIT_DEFAULT",
    "StaticValidatorModel",
    "ExpressionParameterValidatorModel",
    "RegexParameterValidatorModel",
    "InRangeParameterValidatorModel",
    "LengthParameterValidatorModel",
    "MetadataParameterValidatorModel",
    "DatasetMetadataEqualParameterValidatorModel",
    "UnspecifiedBuildParameterValidatorModel",
    "NoOptionsParameterValidatorModel",
    "EmptyFieldParameterValidatorModel",
    "EmptyDatasetParameterValidatorModel",
    "EmptyExtraFilesPathParameterValidatorModel",
    "DatasetMetadataInDataTableParameterValidatorModel",
    "DatasetMetadataNotInDataTableParameterValidatorModel",
    "DatasetMetadataInRangeParameterValidatorModel",
    "ValueInDataTableParameterValidatorModel",
    "ValueNotInDataTableParameterValidatorModel",
    "DatasetOkValidatorParameterValidatorModel",
    "DatasetMetadataInFileParameterValidatorModel",
)