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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",
)
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