medcat.utils.regression.results

Attributes

STRICTNESS_MATRIX

Exceptions

MalformedFinding

Inappropriate argument value (of correct type).

Classes

TranslationLayer	The translation layer for translating:
FinalTarget	The final target.
Entity	dict() -> new empty dictionary
Finding	Describes whether or how the finding verified.
FindingDeterminer	A helper class to determine the type of finding.
Strictness	The total strictness on which to judge the results.
SingleResultDescriptor	The result descriptor.
ResultDescriptor	The overarching result descriptor that handles multiple phrases.
MultiDescriptor	The descriptor of results over multiple different results (parts).

Functions

limit_str_len(input_str[, max_length, keep_front, ...])	Limits the length of a string.
add_doc_strings_to_enum(cls)	Add doc strings to Enum as they are described in code right below

Module Contents

class medcat.utils.regression.results.TranslationLayer(cui2info, name2info, cui2children, separator, whitespace=' ')

The translation layer for translating: - CUIs to names - names to CUIs - type_ids to CUIs - CUIs to chil CUIs

The idea is to decouple these translations from the CDB instance in case something changes there.

Parameters:

• cui2info (dict[str, CUIInfo]) – The map from CUI to names

• name2info (dict[str, NameInfo]) – The map from name to CUIs

• cui2type_ids (dict[str, set[str]]) – The map from CUI to type_ids

• cui2children (dict[str, set[str]]) – The map from CUI to child CUIs

• separator (str)

• whitespace (str)

__init__(cui2info, name2info, cui2children, separator, whitespace=' ')

Parameters:

• cui2info (dict[str, medcat.cdb.concepts.CUIInfo])

• name2info (dict[str, medcat.cdb.concepts.NameInfo])

• cui2children (dict[str, set[str]])

• separator (str)

• whitespace (str)

Return type:

None

cui2info

name2info

separator

whitespace = ' '

type_id2cuis: dict[str, set[str]]

cui2children

get_names_of(cui, only_prefnames)

Get the preprocessed names of a CUI.

This method preporcesses the names by replacing the separator (generally ~) with the appropriate whitespace (` `).

If the concept is not in the underlying CDB, an empty list is returned.

Parameters:

• cui (str) – The concept in question.

• only_prefnames (bool) – Whether to only return a preferred name.

Returns:

list[str] – The list of names.

Return type:

list[str]

get_preferred_name(cui)

Get the preferred name of a concept.

If no preferred name is found, the random ‘first’ name is selected.

Parameters:

cui (str) – The concept ID.

Returns:

str – The preferred name.

Return type:

str

get_first_name(cui)

Get the preprocessed (potentially) arbitrarily first name of the given concept.

If the concept does not exist, the CUI itself is returned.

PS: The “first” name may not be consistent across runs since it relies on set order.

Parameters:

cui (str) – The concept ID.

Returns:

str – The first name.

Return type:

str

get_direct_children(cui)

Get the direct children of a concept.

This means only the children, but not grandchildren.

If the underlying CDB doesn’t list children for this CUI, an empty list is returned.

Parameters:

cui (str) – The concept in question.

Returns:

list[str] – The (potentially empty) list of direct children.

Return type:

list[str]

get_direct_parents(cui)

Get the direct parent(s) of a concept.

PS: This method can be quite a CPU heavy one since it relies

on running through all the parent-children relationships since the child->parent(s) relationship isn’t normally kept track of.

Parameters:

cui (str) – _description_

Returns:

list[str] – _description_

Return type:

list[str]

get_children_of(found_cuis, cui, depth=1)

Get the children of the specifeid CUI in the listed CUIs (if they exist).

Parameters:

• found_cuis (Iterable[str]) – The list of CUIs to look in

• cui (str) – The target parent CUI

• depth (int) – The depth to carry out the search for

Returns:

list[str] – The list of children found

Return type:

list[str]

classmethod from_CDB(cdb)

Construct a TranslationLayer object from a context database (CDB).

This translation layer will refer to the same dicts that the CDB refers to. While there is no obvious reason these should be modified, it’s something to keep in mind.

Parameters:

cdb (CDB) – The CDB

Returns:

TranslationLayer – The subsequent TranslationLayer

Return type:

TranslationLayer

class medcat.utils.regression.results.FinalTarget(/, **data)

Bases: pydantic.BaseModel

The final target.

This involves the final phrase (which (potentially) has other placeholder replaced in it), the placeholder to be replaced, and the CUI and specific name being used.

Parameters:

data (Any)

placeholder: str

cui: str

name: str

final_phrase: str

model_config: ClassVar[pydantic.config.ConfigDict]

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[Dict[str, pydantic.fields.FieldInfo]]

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

model_computed_fields: ClassVar[Dict[str, pydantic.fields.ComputedFieldInfo]]

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

__class_vars__: ClassVar[set[str]]

The names of the class variables defined on the model.

__private_attributes__: ClassVar[Dict[str, pydantic.fields.ModelPrivateAttr]]

Metadata about the private attributes of the model.

__signature__: ClassVar[inspect.Signature]

The synthesized __init__ [Signature][inspect.Signature] of the model.

__pydantic_complete__: ClassVar[bool] = False

Whether model building is completed, or if there are still undefined fields.

__pydantic_core_schema__: ClassVar[pydantic_core.CoreSchema]

The core schema of the model.

__pydantic_custom_init__: ClassVar[bool]

Whether the model has a custom __init__ method.

__pydantic_decorators__: ClassVar[pydantic._internal._decorators.DecoratorInfos]

Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.

__pydantic_generic_metadata__: ClassVar[pydantic._internal._generics.PydanticGenericMetadata]

Metadata for generic models; contains data used for a similar purpose to __args__, __origin__, __parameters__ in typing-module generics. May eventually be replaced by these.

__pydantic_parent_namespace__: ClassVar[Dict[str, Any] | None] = None

Parent namespace of the model, used for automatic rebuilding of models.

__pydantic_post_init__: ClassVar[None | Literal['model_post_init']]

The name of the post-init method for the model, if defined.

__pydantic_root_model__: ClassVar[bool] = False

Whether the model is a [RootModel][pydantic.root_model.RootModel].

__pydantic_serializer__: ClassVar[pydantic_core.SchemaSerializer]

The pydantic-core SchemaSerializer used to dump instances of the model.

__pydantic_validator__: ClassVar[pydantic_core.SchemaValidator | pydantic.plugin._schema_validator.PluggableSchemaValidator]

The pydantic-core SchemaValidator used to validate instances of the model.

__pydantic_extra__: dict[str, Any] | None

A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.

__pydantic_fields_set__: set[str]

The names of fields explicitly set during instantiation.

__pydantic_private__: dict[str, Any] | None

Values of private attributes set on the model instance.

__slots__ = ('__dict__', '__pydantic_fields_set__', '__pydantic_extra__', '__pydantic_private__')

__init__(/, **data)

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Parameters:

data (Any)

Return type:

None

property model_extra: dict[str, Any] | None

Get extra fields set during validation.

Returns:

A dictionary of extra fields, or `None` if `config.extra` is not set to `”allow”`.

Return type:

dict[str, Any] | None

property model_fields_set: set[str]

Returns the set of fields that have been explicitly set on this model instance.

Returns:

A set of strings representing the fields that have been set, – i.e. that were not filled from defaults.

Return type:

set[str]

classmethod model_construct(_fields_set=None, **values)

Creates a new instance of the Model class with validated data.

Creates a new model setting __dict__ and __pydantic_fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed.

!!! note

model_construct() generally respects the model_config.extra setting on the provided model. That is, if model_config.extra == ‘allow’, then all extra passed values are added to the model instance’s __dict__ and __pydantic_extra__ fields. If model_config.extra == ‘ignore’ (the default), then all extra passed values are ignored. Because no validation is performed with a call to model_construct(), having model_config.extra == ‘forbid’ does not result in an error if extra values are passed, but they will be ignored.

Parameters:

• _fields_set (set[str] | None) – A set of field names that were originally explicitly set during instantiation. If provided, this is directly used for the [model_fields_set][pydantic.BaseModel.model_fields_set] attribute. Otherwise, the field names from the values argument will be used.

• values (Any) – Trusted or pre-validated data dictionary.

Returns:

A new instance of the `Model` class with validated data.

Return type:

typing_extensions.Self

model_copy(*, update=None, deep=False)

Usage docs: https://docs.pydantic.dev/2.9/concepts/serialization/#model_copy

Returns a copy of the model.

Parameters:

• update (dict[str, Any] | None) – Values to change/add in the new model. Note: the data is not validated before creating the new model. You should trust this data.

• deep (bool) – Set to True to make a deep copy of the model.

Returns:

New model instance.

Return type:

typing_extensions.Self

model_dump(*, mode='python', include=None, exclude=None, context=None, by_alias=False, exclude_unset=False, exclude_defaults=False, exclude_none=False, round_trip=False, warnings=True, serialize_as_any=False)

Usage docs: https://docs.pydantic.dev/2.9/concepts/serialization/#modelmodel_dump

Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

Parameters:

• mode (Literal['json', 'python'] | str) – The mode in which to_python should run. If mode is ‘json’, the output will only contain JSON serializable types. If mode is ‘python’, the output may contain non-JSON-serializable Python objects.

• include (IncEx | None) – A set of fields to include in the output.

• exclude (IncEx | None) – A set of fields to exclude from the output.

• context (Any | None) – Additional context to pass to the serializer.

• by_alias (bool) – Whether to use the field’s alias in the dictionary key if defined.

• exclude_unset (bool) – Whether to exclude fields that have not been explicitly set.

• exclude_defaults (bool) – Whether to exclude fields that are set to their default value.

• exclude_none (bool) – Whether to exclude fields that have a value of None.

• round_trip (bool) – If True, dumped values should be valid as input for non-idempotent types such as Json[T].

• warnings (bool | Literal['none', 'warn', 'error']) – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].

• serialize_as_any (bool) – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A dictionary representation of the model.

Return type:

dict[str, Any]

model_dump_json(*, indent=None, include=None, exclude=None, context=None, by_alias=False, exclude_unset=False, exclude_defaults=False, exclude_none=False, round_trip=False, warnings=True, serialize_as_any=False)

Usage docs: https://docs.pydantic.dev/2.9/concepts/serialization/#modelmodel_dump_json

Generates a JSON representation of the model using Pydantic’s to_json method.

Parameters:

• indent (int | None) – Indentation to use in the JSON output. If None is passed, the output will be compact.

• include (IncEx | None) – Field(s) to include in the JSON output.

• exclude (IncEx | None) – Field(s) to exclude from the JSON output.

• context (Any | None) – Additional context to pass to the serializer.

• by_alias (bool) – Whether to serialize using field aliases.

• exclude_unset (bool) – Whether to exclude fields that have not been explicitly set.

• exclude_defaults (bool) – Whether to exclude fields that are set to their default value.

• exclude_none (bool) – Whether to exclude fields that have a value of None.

• round_trip (bool) – If True, dumped values should be valid as input for non-idempotent types such as Json[T].

• warnings (bool | Literal['none', 'warn', 'error']) – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].

• serialize_as_any (bool) – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A JSON string representation of the model.

Return type:

str

classmethod model_json_schema(by_alias=True, ref_template=DEFAULT_REF_TEMPLATE, schema_generator=GenerateJsonSchema, mode='validation')

Generates a JSON schema for a model class.

Parameters:

• by_alias (bool) – Whether to use attribute aliases or not.

• ref_template (str) – The reference template.

• schema_generator (type[pydantic.json_schema.GenerateJsonSchema]) – To override the logic used to generate the JSON schema, as a subclass of GenerateJsonSchema with your desired modifications

• mode (pydantic.json_schema.JsonSchemaMode) – The mode in which to generate the schema.

Returns:

The JSON schema for the given model class.

Return type:

dict[str, Any]

classmethod model_parametrized_name(params)

Compute the class name for parametrizations of generic classes.

This method can be overridden to achieve a custom naming scheme for generic BaseModels.

Parameters:

params (tuple[type[Any], Ellipsis]) – Tuple of types of the class. Given a generic class Model with 2 type variables and a concrete model Model[str, int], the value (str, int) would be passed to params.

Returns:

String representing the new class where `params` are passed to `cls` as type variables.

Raises:

TypeError – Raised when trying to generate concrete names for non-generic models.

Return type:

str

model_post_init(__context)

Override this method to perform additional initialization after __init__ and model_construct. This is useful if you want to do some validation that requires the entire model to be initialized.

Parameters:

__context (Any)

Return type:

None

classmethod model_rebuild(*, force=False, raise_errors=True, _parent_namespace_depth=2, _types_namespace=None)

Try to rebuild the pydantic-core schema for the model.

This may be necessary when one of the annotations is a ForwardRef which could not be resolved during the initial attempt to build the schema, and automatic rebuilding fails.

Parameters:

• force (bool) – Whether to force the rebuilding of the model schema, defaults to False.

• raise_errors (bool) – Whether to raise errors, defaults to True.

• _parent_namespace_depth (int) – The depth level of the parent namespace, defaults to 2.

• _types_namespace (dict[str, Any] | None) – The types namespace, defaults to None.

Returns:

• Returns `None` if the schema is already “complete” and rebuilding was not required.

• If rebuilding _was_ required, returns `True` if rebuilding was successful, otherwise `False`.

Return type:

bool | None

classmethod model_validate(obj, *, strict=None, from_attributes=None, context=None)

Validate a pydantic model instance.

Parameters:

• obj (Any) – The object to validate.

• strict (bool | None) – Whether to enforce types strictly.

• from_attributes (bool | None) – Whether to extract data from object attributes.

• context (Any | None) – Additional context to pass to the validator.

Raises:

ValidationError – If the object could not be validated.

Returns:

The validated model instance.

Return type:

typing_extensions.Self

classmethod model_validate_json(json_data, *, strict=None, context=None)

Usage docs: https://docs.pydantic.dev/2.9/concepts/json/#json-parsing

Validate the given JSON data against the Pydantic model.

Parameters:

• json_data (str | bytes | bytearray) – The JSON data to validate.

• strict (bool | None) – Whether to enforce types strictly.

• context (Any | None) – Extra variables to pass to the validator.

Returns:

The validated Pydantic model.

Raises:

ValidationError – If json_data is not a JSON string or the object could not be validated.

Return type:

typing_extensions.Self

classmethod model_validate_strings(obj, *, strict=None, context=None)

Validate the given object with string data against the Pydantic model.

Parameters:

• obj (Any) – The object containing string data to validate.

• strict (bool | None) – Whether to enforce types strictly.

• context (Any | None) – Extra variables to pass to the validator.

Returns:

The validated Pydantic model.

Return type:

typing_extensions.Self

classmethod __get_pydantic_core_schema__(source, handler, /)

Hook into generating the model’s CoreSchema.

Parameters:

• source (type[BaseModel]) – The class we are generating a schema for. This will generally be the same as the cls argument if this is a classmethod.

• handler (pydantic.annotated_handlers.GetCoreSchemaHandler) – A callable that calls into Pydantic’s internal CoreSchema generation logic.

Returns:

A `pydantic-core` `CoreSchema`.

Return type:

pydantic_core.CoreSchema

classmethod __get_pydantic_json_schema__(core_schema, handler, /)

Hook into generating the model’s JSON schema.

Parameters:

• core_schema (pydantic_core.CoreSchema) – A pydantic-core CoreSchema. You can ignore this argument and call the handler with a new CoreSchema, wrap this CoreSchema ({‘type’: ‘nullable’, ‘schema’: current_schema}), or just call the handler with the original schema.

• handler (pydantic.annotated_handlers.GetJsonSchemaHandler) – Call into Pydantic’s internal JSON schema generation. This will raise a pydantic.errors.PydanticInvalidForJsonSchema if JSON schema generation fails. Since this gets called by BaseModel.model_json_schema you can override the schema_generator argument to that function to change JSON schema generation globally for a type.

Returns:

A JSON schema, as a Python object.

Return type:

pydantic.json_schema.JsonSchemaValue

classmethod __pydantic_init_subclass__(**kwargs)

This is intended to behave just like __init_subclass__, but is called by ModelMetaclass only after the class is actually fully initialized. In particular, attributes like model_fields will be present when this is called.

This is necessary because __init_subclass__ will always be called by type.__new__, and it would require a prohibitively large refactor to the ModelMetaclass to ensure that type.__new__ was called in such a manner that the class would already be sufficiently initialized.

This will receive the same kwargs that would be passed to the standard __init_subclass__, namely, any kwargs passed to the class definition that aren’t used internally by pydantic.

Parameters:

**kwargs (Any) – Any keyword arguments passed to the class definition that aren’t used internally by pydantic.

Return type:

None

classmethod __class_getitem__(typevar_values)

Parameters:

typevar_values (type[Any] | tuple[type[Any], Ellipsis])

Return type:

type[BaseModel] | pydantic._internal._forward_ref.PydanticRecursiveRef

__copy__()

Returns a shallow copy of the model.

Return type:

typing_extensions.Self

__deepcopy__(memo=None)

Returns a deep copy of the model.

Parameters:

memo (dict[int, Any] | None)

Return type:

typing_extensions.Self

__getattr__(item)

Parameters:

item (str)

Return type:

Any

_check_frozen(name, value)

Parameters:

• name (str)

• value (Any)

Return type:

None

__getstate__()

Return type:

dict[Any, Any]

__setstate__(state)

Parameters:

state (dict[Any, Any])

Return type:

None

__eq__(other)

Parameters:

other (Any)

Return type:

bool

classmethod __init_subclass__(**kwargs)

This signature is included purely to help type-checkers check arguments to class declaration, which provides a way to conveniently set model_config key/value pairs.

```py from pydantic import BaseModel

class MyModel(BaseModel, extra=’allow’): … ```

However, this may be deceiving, since the _actual_ calls to __init_subclass__ will not receive any of the config arguments, and will only receive any keyword arguments passed during class initialization that are _not_ expected keys in ConfigDict. (This is due to the way ModelMetaclass.__new__ works.)

Parameters:

**kwargs (typing_extensions.Unpack[pydantic.config.ConfigDict]) – Keyword arguments passed to the class definition, which set model_config

Note

You may want to override __pydantic_init_subclass__ instead, which behaves similarly but is called after the class is fully initialized.

__iter__()

So dict(model) works.

Return type:

TupleGenerator

__repr__()

Return type:

str

__repr_args__()

Return type:

pydantic._internal._repr.ReprArgs

__repr_name__

__repr_str__

__pretty__

__rich_repr__

__str__()

Return type:

str

property __fields__: dict[str, pydantic.fields.FieldInfo]

Return type:

dict[str, pydantic.fields.FieldInfo]

property __fields_set__: set[str]

Return type:

set[str]

dict(*, include=None, exclude=None, by_alias=False, exclude_unset=False, exclude_defaults=False, exclude_none=False)

Parameters:

• include (IncEx | None)

• exclude (IncEx | None)

• by_alias (bool)

• exclude_unset (bool)

• exclude_defaults (bool)

• exclude_none (bool)

Return type:

Dict[str, Any]

json(*, include=None, exclude=None, by_alias=False, exclude_unset=False, exclude_defaults=False, exclude_none=False, encoder=PydanticUndefined, models_as_dict=PydanticUndefined, **dumps_kwargs)

Parameters:

• include (IncEx | None)

• exclude (IncEx | None)

• by_alias (bool)

• exclude_unset (bool)

• exclude_defaults (bool)

• exclude_none (bool)

• encoder (Callable[[Any], Any] | None)

• models_as_dict (bool)

• dumps_kwargs (Any)

Return type:

str

classmethod parse_obj(obj)

Parameters:

obj (Any)

Return type:

typing_extensions.Self

classmethod parse_raw(b, *, content_type=None, encoding='utf8', proto=None, allow_pickle=False)

Parameters:

• b (str | bytes)

• content_type (str | None)

• encoding (str)

• proto (pydantic.deprecated.parse.Protocol | None)

• allow_pickle (bool)

Return type:

typing_extensions.Self

classmethod parse_file(path, *, content_type=None, encoding='utf8', proto=None, allow_pickle=False)

Parameters:

• path (str | pathlib.Path)

• content_type (str | None)

• encoding (str)

• proto (pydantic.deprecated.parse.Protocol | None)

• allow_pickle (bool)

Return type:

typing_extensions.Self

classmethod from_orm(obj)

Parameters:

obj (Any)

Return type:

typing_extensions.Self

classmethod construct(_fields_set=None, **values)

Parameters:

• _fields_set (set[str] | None)

• values (Any)

Return type:

typing_extensions.Self

copy(*, include=None, exclude=None, update=None, deep=False)

Returns a copy of the model.

!!! warning “Deprecated”

This method is now deprecated; use model_copy instead.

If you need include or exclude, use:

`py data = self.model_dump(include=include, exclude=exclude, round_trip=True) data = {**data, **(update or {})} copied = self.model_validate(data) `

Parameters:

• include (pydantic._internal._utils.AbstractSetIntStr | pydantic._internal._utils.MappingIntStrAny | None) – Optional set or mapping specifying which fields to include in the copied model.

• exclude (pydantic._internal._utils.AbstractSetIntStr | pydantic._internal._utils.MappingIntStrAny | None) – Optional set or mapping specifying which fields to exclude in the copied model.

• update (Dict[str, Any] | None) – Optional dictionary of field-value pairs to override field values in the copied model.

• deep (bool) – If True, the values of fields that are Pydantic models will be deep-copied.

Returns:

A copy of the model with included, excluded and updated fields as specified.

Return type:

typing_extensions.Self

classmethod schema(by_alias=True, ref_template=DEFAULT_REF_TEMPLATE)

Parameters:

• by_alias (bool)

• ref_template (str)

Return type:

Dict[str, Any]

classmethod schema_json(*, by_alias=True, ref_template=DEFAULT_REF_TEMPLATE, **dumps_kwargs)

Parameters:

• by_alias (bool)

• ref_template (str)

• dumps_kwargs (Any)

Return type:

str

classmethod validate(value)

Parameters:

value (Any)

Return type:

typing_extensions.Self

classmethod update_forward_refs(**localns)

Parameters:

localns (Any)

Return type:

None

_iter(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

_copy_and_set_values(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

classmethod _get_value(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

_calculate_keys(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

medcat.utils.regression.results.limit_str_len(input_str, max_length=40, keep_front=20, keep_rear=10)

Limits the length of a string.

If the length of the string is less than or equal to max_length, the same string is returned. If it’s longer, the first keep_front are kept, then the number of chars is included in brackets (e.g “ [123 chars] “), and finally the last keep_rear characters are included.

Parameters:

• input_str (str) – The input (potentially) long string.

• max_length (int) – The maximum number of characters at which the string will remain unchanged. Defaults to 40.

• keep_front (int) – How many starting characters to keep. Defaults to 20.

• keep_rear (int) – How many ending characters to keep. Defaults to 10.

Returns:

str – _description_

Return type:

str

medcat.utils.regression.results.add_doc_strings_to_enum(cls)

Add doc strings to Enum as they are described in code right below each constant.

The way python works means that the doc strings defined after an Enum constant do not get stored with the constant. When accessing the doc string of an Enum constant, the doc string of the class is returned instead.

So what this method does is gets the doc strings by traversing the abstract syntax tree.

While there would be easier ways to accomplish this, they would require the doc strings for the Enum constant to be further from the constants themselves.

If the class itself has a doc string, it is omitted. Otherwise the Enum constants are given the doc strings in the order in which they appear.

Parameters:

cls (Type[Enum]) – The Enum class to do this for.

Return type:

None

class medcat.utils.regression.results.Entity

Bases: TypedDict

dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object’s

(key, value) pairs

dict(iterable) -> new dictionary initialized as if via:

d = {} for k, v in iterable:

d[k] = v

dict(**kwargs) -> new dictionary initialized with the name=value pairs

in the keyword argument list. For example: dict(one=1, two=2)

pretty_name: str

cui: str

type_ids: list[str]

source_value: str

detected_name: str

acc: float

context_similarity: float

start: int

end: int

id: int

meta_anns: dict[str, MetaAnnotation]

context_left: list[str]

context_center: list[str]

context_right: list[str]

__contains__()

True if the dictionary has the specified key, else False.

__delattr__()

Implement delattr(self, name).

__delitem__()

Delete self[key].

__dir__()

Default dir() implementation.

__eq__()

Return self==value.

__format__()

Default object formatter.

__ge__()

Return self>=value.

__getattribute__()

Return getattr(self, name).

__getitem__()

x.__getitem__(y) <==> x[y]

__gt__()

Return self>value.

__init__()

Initialize self. See help(type(self)) for accurate signature.

__ior__()

Return self|=value.

__iter__()

Implement iter(self).

__le__()

Return self<=value.

__len__()

Return len(self).

__lt__()

Return self<value.

__ne__()

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__or__()

Return self|value.

__reduce__()

Helper for pickle.

__reduce_ex__()

Helper for pickle.

__repr__()

Return repr(self).

__reversed__()

Return a reverse iterator over the dict keys.

__ror__()

Return value|self.

__setattr__()

Implement setattr(self, name, value).

__setitem__()

Set self[key] to value.

__sizeof__()

D.__sizeof__() -> size of D in memory, in bytes

__str__()

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

clear()

D.clear() -> None. Remove all items from D.

copy()

D.copy() -> a shallow copy of D

get()

Return the value for key if key is in the dictionary, else default.

items()

D.items() -> a set-like object providing a view on D’s items

keys()

D.keys() -> a set-like object providing a view on D’s keys

pop()

D.pop(k[,d]) -> v, remove specified key and return the corresponding value.

If the key is not found, return the default if given; otherwise, raise a KeyError.

popitem()

Remove and return a (key, value) pair as a 2-tuple.

Pairs are returned in LIFO (last-in, first-out) order. Raises KeyError if the dict is empty.

setdefault()

Insert key with a value of default if key is not in the dictionary.

Return the value for key if key is in the dictionary, else default.

update()

D.update([E, ]**F) -> None. Update D from dict/iterable E and F. If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]

values()

D.values() -> an object providing a view on D’s values

class medcat.utils.regression.results.Finding

Bases: enum.Enum

Describes whether or how the finding verified.

The idea is that we know where we expect the entity to be recognised and the enum constants describe how the recognition compared to the expectation.

In essence, we want to know the relative positions of the two pairs of numbers (character numbers): - Expected Start, Expected End - Recognised Start, Recognised End

We can model this as 4 numbers on the number line. And we want to know their position relative to each other. For example, if the expected positions are marked with * and recognised positions with #, we may have something like: ___*__#_______#*______________ Which would indicate that there is a partial, but smaller span recognised.

IDENTICAL

The CUI and the span recognised are identical to what was expected.

BIGGER_SPAN_RIGHT

The CUI is the same, but the recognised span is longer on the right.

If we use the notation from the class doc string, e.g: _*#__*__#

BIGGER_SPAN_LEFT

The CUI is the same, but the recognised span is longer on the left.

If we use the notation from the class doc string, e.g: _#_*__*#_

BIGGER_SPAN_BOTH

The CUI is the same, but the recognised span is longer on both sides.

If we use the notation from the class doc string, e.g: _#__*__*__#_

SMALLER_SPAN

The CUI is the same, but the recognised span is smaller.

If we use the notation from the class doc string, e.g: _*_#_#_*_ (neither start nor end match) _*#_#_*__ (start matches, but end is before expected) _*__#_#*_ (end matches, but start is after expected)

PARTIAL_OVERLAP

The CUI is the same, but the span overlaps partially.

If we use the notation from the class doc string, e.g: _*_#__*_#_ (starts between expected start and end, but ends beyond) _#_*_#_*__ (start before expected start, but ends between expected start and end)

FOUND_DIR_PARENT

The recognised CUI is a parent of the expected CUI but the span is an exact match.

FOUND_DIR_GRANDPARENT

The recognised CUI is a grandparent of the expected CUI but the span is an exact match.

FOUND_ANY_CHILD

The recognised CUI is a child of the expected CUI but the span is an exact match.

FOUND_CHILD_PARTIAL

The recognised CUI is a child yet the match is only partial (smaller/bigger/partial).

FOUND_OTHER

Found another CUI in the same span.

FAIL

The concept was not recognised in any meaningful way.

has_correct_cui()

Whether the finding found the correct concept.

Returns:

bool – Whether the correct concept was found.

Return type:

bool

classmethod determine(exp_cui, exp_start, exp_end, tl, found_entities, strict_only=False, check_children=True, check_parent=True, check_grandparent=True)

Determine the finding type based on the input

Parameters:

• exp_cui (str) – Expected CUI.

• exp_start (int) – Expected span start.

• exp_end (int) – Expected span end.

• tl (TranslationLayer) – The translation layer.

• found_entities (dict[int, Entity]) – The entities found by the model.

• strict_only (bool) – Whether to use a strict-only mode (either identical or fail). Defaults to False.

• check_children (bool) – Whether to check the children. Defaults to True.

• check_parent (bool) – Whether to check for parent(s). Defaults to True.

• check_grandparent (bool) – Whether to check for grandparent(s). Defaults to True.

Returns:

tuple[‘Finding’, Optional[str]] – The type of finding determined, and the alternative.

Return type:

tuple[Finding, Optional[str]]

__new__(value)

_generate_next_value_(start, count, last_values)

Generate the next value when not given.

name: the name of the member start: the initial start value or None count: the number of existing members last_value: the last value assigned or None

classmethod _missing_(value)

__repr__()

__str__()

__dir__()

Returns all members and all public methods

__format__(format_spec)

Returns format using actual value type unless __str__ has been overridden.

__hash__()

__reduce_ex__(proto)

name()

The name of the Enum member.

value()

The value of the Enum member.

class medcat.utils.regression.results.FindingDeterminer(exp_cui, exp_start, exp_end, tl, found_entities, strict_only=False, check_children=True, check_parent=True, check_grandparent=True)

A helper class to determine the type of finding.

This is mostly useful to split the responsibilities of looking at children/parents as well as to keep track of the already-checked children to avoid infinite recursion (which could happen in - e.g - a SNOMED model).

Parameters:

• exp_cui (str) – The expected CUI.

• exp_start (int) – The expected span start.

• exp_end (int) – The expected span end.

• tl (TranslationLayer) – The translation layer.

• found_entities (dict[str, Entity]) – The entities found by the model.

• strict_only (bool) – Whether to use strict-only mode (either identical or fail). Defaults to False.

• check_children (bool) – Whether or not to check the children. Defaults to True.

• check_parent (bool) – Whether to check for parent(s). Defaults to True.

• check_grandparent (bool) – Whether to check for granparent(s). Defaults to True.

__init__(exp_cui, exp_start, exp_end, tl, found_entities, strict_only=False, check_children=True, check_parent=True, check_grandparent=True)

Parameters:

• exp_cui (str)

• exp_start (int)

• exp_end (int)

• tl (medcat.utils.regression.targeting.TranslationLayer)

• found_entities (dict[int, medcat.data.entities.Entity])

• strict_only (bool)

• check_children (bool)

• check_parent (bool)

• check_grandparent (bool)

Return type:

None

exp_cui

exp_start

exp_end

tl

found_entities

strict_only = False

check_children = True

check_parent = True

check_grandparent = True

_checked_children: set[str]

_determine_raw(start, end)

Determines the raw SPAN-ONLY finding.

I.e this assumes the concept is appropriate. It will return None if there is no overlapping span.

Parameters:

• start (int) – The start of the span.

• end (int) – The end of the span.

Raises:

• MalformedFinding – If the start is greater than the end.

• MalformedFinding – If the expected start is greater than the expected end.

Returns:

Optional[Finding] – The finding, if a match is found.

Return type:

Optional[Finding]

_get_strict()

Return type:

Optional[Finding]

_check_parents()

Return type:

Optional[tuple[Finding, Optional[str]]]

_check_children()

Return type:

Optional[tuple[Finding, Optional[str]]]

_descr_cui(cui)

Parameters:

cui (Optional[str])

Return type:

Optional[str]

_find_diff_cui()

Return type:

Optional[tuple[Finding, str]]

determine()

Determine the finding based on the given information.

First, the strict check is done (either identical or not). Then, parents are checked (if required). After that, children are checked (if required).

Returns:

tuple[Finding, Optional[str]] – The appropriate finding, and the alternative (if applicable).

Return type:

tuple[Finding, Optional[str]]

_determine()

Return type:

tuple[Finding, Optional[str]]

class medcat.utils.regression.results.Strictness

Bases: enum.Enum

The total strictness on which to judge the results.

STRICTEST

The strictest option which only allows identical findings.

STRICT

A strict option which allows identical or children.

NORMAL

Normal strictness also allows partial overlaps on target concept and children.

LENIENT

Lenient stictness also allows parents and grandparents.

ANYTHING

Anything stricness allows ANY finding.

This would generally only be relevant when disabling examples for results descriptors.

__new__(value)

_generate_next_value_(start, count, last_values)

Generate the next value when not given.

name: the name of the member start: the initial start value or None count: the number of existing members last_value: the last value assigned or None

classmethod _missing_(value)

__repr__()

__str__()

__dir__()

Returns all members and all public methods

__format__(format_spec)

Returns format using actual value type unless __str__ has been overridden.

__hash__()

__reduce_ex__(proto)

name()

The name of the Enum member.

value()

The value of the Enum member.

medcat.utils.regression.results.STRICTNESS_MATRIX: dict[Strictness, set[Finding]]

class medcat.utils.regression.results.SingleResultDescriptor(/, **data)

Bases: pydantic.BaseModel

The result descriptor.

This class is responsible for keeping track of all the findings (i.e how many were found to be identical) as well as the examples of the finding on a per-target basis for further analysis.

Parameters:

data (Any)

name: str

The name of the part that was checked

findings: dict[Finding, int]

The description of failures

examples: list[tuple[medcat.utils.regression.targeting.FinalTarget, tuple[Finding, str | None]]] = []

The examples of non-perfect alignment.

report_success(target, found)

Report a test case and its successfulness.

Parameters:

• target (FinalTarget) – The target configuration

• found (tuple[Finding, Optional[str]]) – Whether or not the check was successful

Return type:

None

get_report()

Get the report associated with this descriptor

Returns:

str – The report string

Return type:

str

model_dump(**kwargs)

Usage docs: https://docs.pydantic.dev/2.9/concepts/serialization/#modelmodel_dump

Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

Parameters:

• mode – The mode in which to_python should run. If mode is ‘json’, the output will only contain JSON serializable types. If mode is ‘python’, the output may contain non-JSON-serializable Python objects.

• include – A set of fields to include in the output.

• exclude – A set of fields to exclude from the output.

• context – Additional context to pass to the serializer.

• by_alias – Whether to use the field’s alias in the dictionary key if defined.

• exclude_unset – Whether to exclude fields that have not been explicitly set.

• exclude_defaults – Whether to exclude fields that are set to their default value.

• exclude_none – Whether to exclude fields that have a value of None.

• round_trip – If True, dumped values should be valid as input for non-idempotent types such as Json[T].

• warnings – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].

• serialize_as_any – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A dictionary representation of the model.

Return type:

dict

json(**kwargs)

Return type:

str

model_config: ClassVar[pydantic.config.ConfigDict]

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[Dict[str, pydantic.fields.FieldInfo]]

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

model_computed_fields: ClassVar[Dict[str, pydantic.fields.ComputedFieldInfo]]

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

__class_vars__: ClassVar[set[str]]

The names of the class variables defined on the model.

__private_attributes__: ClassVar[Dict[str, pydantic.fields.ModelPrivateAttr]]

Metadata about the private attributes of the model.

__signature__: ClassVar[inspect.Signature]

The synthesized __init__ [Signature][inspect.Signature] of the model.

__pydantic_complete__: ClassVar[bool] = False

Whether model building is completed, or if there are still undefined fields.

__pydantic_core_schema__: ClassVar[pydantic_core.CoreSchema]

The core schema of the model.

__pydantic_custom_init__: ClassVar[bool]

Whether the model has a custom __init__ method.

__pydantic_decorators__: ClassVar[pydantic._internal._decorators.DecoratorInfos]

Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.

__pydantic_generic_metadata__: ClassVar[pydantic._internal._generics.PydanticGenericMetadata]

Metadata for generic models; contains data used for a similar purpose to __args__, __origin__, __parameters__ in typing-module generics. May eventually be replaced by these.

__pydantic_parent_namespace__: ClassVar[Dict[str, Any] | None] = None

Parent namespace of the model, used for automatic rebuilding of models.

__pydantic_post_init__: ClassVar[None | Literal['model_post_init']]

The name of the post-init method for the model, if defined.

__pydantic_root_model__: ClassVar[bool] = False

Whether the model is a [RootModel][pydantic.root_model.RootModel].

__pydantic_serializer__: ClassVar[pydantic_core.SchemaSerializer]

The pydantic-core SchemaSerializer used to dump instances of the model.

__pydantic_validator__: ClassVar[pydantic_core.SchemaValidator | pydantic.plugin._schema_validator.PluggableSchemaValidator]

The pydantic-core SchemaValidator used to validate instances of the model.

__pydantic_extra__: dict[str, Any] | None

A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.

__pydantic_fields_set__: set[str]

The names of fields explicitly set during instantiation.

__pydantic_private__: dict[str, Any] | None

Values of private attributes set on the model instance.

__slots__ = ('__dict__', '__pydantic_fields_set__', '__pydantic_extra__', '__pydantic_private__')

__init__(/, **data)

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Parameters:

data (Any)

Return type:

None

property model_extra: dict[str, Any] | None

Get extra fields set during validation.

Returns:

A dictionary of extra fields, or `None` if `config.extra` is not set to `”allow”`.

Return type:

dict[str, Any] | None

property model_fields_set: set[str]

Returns the set of fields that have been explicitly set on this model instance.

Returns:

A set of strings representing the fields that have been set, – i.e. that were not filled from defaults.

Return type:

set[str]

classmethod model_construct(_fields_set=None, **values)

Creates a new instance of the Model class with validated data.

Creates a new model setting __dict__ and __pydantic_fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed.

!!! note

model_construct() generally respects the model_config.extra setting on the provided model. That is, if model_config.extra == ‘allow’, then all extra passed values are added to the model instance’s __dict__ and __pydantic_extra__ fields. If model_config.extra == ‘ignore’ (the default), then all extra passed values are ignored. Because no validation is performed with a call to model_construct(), having model_config.extra == ‘forbid’ does not result in an error if extra values are passed, but they will be ignored.

Parameters:

• _fields_set (set[str] | None) – A set of field names that were originally explicitly set during instantiation. If provided, this is directly used for the [model_fields_set][pydantic.BaseModel.model_fields_set] attribute. Otherwise, the field names from the values argument will be used.

• values (Any) – Trusted or pre-validated data dictionary.

Returns:

A new instance of the `Model` class with validated data.

Return type:

typing_extensions.Self

model_copy(*, update=None, deep=False)

Usage docs: https://docs.pydantic.dev/2.9/concepts/serialization/#model_copy

Returns a copy of the model.

Parameters:

• update (dict[str, Any] | None) – Values to change/add in the new model. Note: the data is not validated before creating the new model. You should trust this data.

• deep (bool) – Set to True to make a deep copy of the model.

Returns:

New model instance.

Return type:

typing_extensions.Self

model_dump_json(*, indent=None, include=None, exclude=None, context=None, by_alias=False, exclude_unset=False, exclude_defaults=False, exclude_none=False, round_trip=False, warnings=True, serialize_as_any=False)

Usage docs: https://docs.pydantic.dev/2.9/concepts/serialization/#modelmodel_dump_json

Generates a JSON representation of the model using Pydantic’s to_json method.

Parameters:

• indent (int | None) – Indentation to use in the JSON output. If None is passed, the output will be compact.

• include (IncEx | None) – Field(s) to include in the JSON output.

• exclude (IncEx | None) – Field(s) to exclude from the JSON output.

• context (Any | None) – Additional context to pass to the serializer.

• by_alias (bool) – Whether to serialize using field aliases.

• exclude_unset (bool) – Whether to exclude fields that have not been explicitly set.

• exclude_defaults (bool) – Whether to exclude fields that are set to their default value.

• exclude_none (bool) – Whether to exclude fields that have a value of None.

• round_trip (bool) – If True, dumped values should be valid as input for non-idempotent types such as Json[T].

• warnings (bool | Literal['none', 'warn', 'error']) – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].

• serialize_as_any (bool) – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A JSON string representation of the model.

Return type:

str

classmethod model_json_schema(by_alias=True, ref_template=DEFAULT_REF_TEMPLATE, schema_generator=GenerateJsonSchema, mode='validation')

Generates a JSON schema for a model class.

Parameters:

• by_alias (bool) – Whether to use attribute aliases or not.

• ref_template (str) – The reference template.

• schema_generator (type[pydantic.json_schema.GenerateJsonSchema]) – To override the logic used to generate the JSON schema, as a subclass of GenerateJsonSchema with your desired modifications

• mode (pydantic.json_schema.JsonSchemaMode) – The mode in which to generate the schema.

Returns:

The JSON schema for the given model class.

Return type:

dict[str, Any]

classmethod model_parametrized_name(params)

Compute the class name for parametrizations of generic classes.

This method can be overridden to achieve a custom naming scheme for generic BaseModels.

Parameters:

params (tuple[type[Any], Ellipsis]) – Tuple of types of the class. Given a generic class Model with 2 type variables and a concrete model Model[str, int], the value (str, int) would be passed to params.

Returns:

String representing the new class where `params` are passed to `cls` as type variables.

Raises:

TypeError – Raised when trying to generate concrete names for non-generic models.

Return type:

str

model_post_init(__context)

Override this method to perform additional initialization after __init__ and model_construct. This is useful if you want to do some validation that requires the entire model to be initialized.

Parameters:

__context (Any)

Return type:

None

classmethod model_rebuild(*, force=False, raise_errors=True, _parent_namespace_depth=2, _types_namespace=None)

Try to rebuild the pydantic-core schema for the model.

This may be necessary when one of the annotations is a ForwardRef which could not be resolved during the initial attempt to build the schema, and automatic rebuilding fails.

Parameters:

• force (bool) – Whether to force the rebuilding of the model schema, defaults to False.

• raise_errors (bool) – Whether to raise errors, defaults to True.

• _parent_namespace_depth (int) – The depth level of the parent namespace, defaults to 2.

• _types_namespace (dict[str, Any] | None) – The types namespace, defaults to None.

Returns:

• Returns `None` if the schema is already “complete” and rebuilding was not required.

• If rebuilding _was_ required, returns `True` if rebuilding was successful, otherwise `False`.

Return type:

bool | None

classmethod model_validate(obj, *, strict=None, from_attributes=None, context=None)

Validate a pydantic model instance.

Parameters:

• obj (Any) – The object to validate.

• strict (bool | None) – Whether to enforce types strictly.

• from_attributes (bool | None) – Whether to extract data from object attributes.

• context (Any | None) – Additional context to pass to the validator.

Raises:

ValidationError – If the object could not be validated.

Returns:

The validated model instance.

Return type:

typing_extensions.Self

classmethod model_validate_json(json_data, *, strict=None, context=None)

Usage docs: https://docs.pydantic.dev/2.9/concepts/json/#json-parsing

Validate the given JSON data against the Pydantic model.

Parameters:

• json_data (str | bytes | bytearray) – The JSON data to validate.

• strict (bool | None) – Whether to enforce types strictly.

• context (Any | None) – Extra variables to pass to the validator.

Returns:

The validated Pydantic model.

Raises:

ValidationError – If json_data is not a JSON string or the object could not be validated.

Return type:

typing_extensions.Self

classmethod model_validate_strings(obj, *, strict=None, context=None)

Validate the given object with string data against the Pydantic model.

Parameters:

• obj (Any) – The object containing string data to validate.

• strict (bool | None) – Whether to enforce types strictly.

• context (Any | None) – Extra variables to pass to the validator.

Returns:

The validated Pydantic model.

Return type:

typing_extensions.Self

classmethod __get_pydantic_core_schema__(source, handler, /)

Hook into generating the model’s CoreSchema.

Parameters:

• source (type[BaseModel]) – The class we are generating a schema for. This will generally be the same as the cls argument if this is a classmethod.

• handler (pydantic.annotated_handlers.GetCoreSchemaHandler) – A callable that calls into Pydantic’s internal CoreSchema generation logic.

Returns:

A `pydantic-core` `CoreSchema`.

Return type:

pydantic_core.CoreSchema

classmethod __get_pydantic_json_schema__(core_schema, handler, /)

Hook into generating the model’s JSON schema.

Parameters:

• core_schema (pydantic_core.CoreSchema) – A pydantic-core CoreSchema. You can ignore this argument and call the handler with a new CoreSchema, wrap this CoreSchema ({‘type’: ‘nullable’, ‘schema’: current_schema}), or just call the handler with the original schema.

• handler (pydantic.annotated_handlers.GetJsonSchemaHandler) – Call into Pydantic’s internal JSON schema generation. This will raise a pydantic.errors.PydanticInvalidForJsonSchema if JSON schema generation fails. Since this gets called by BaseModel.model_json_schema you can override the schema_generator argument to that function to change JSON schema generation globally for a type.

Returns:

A JSON schema, as a Python object.

Return type:

pydantic.json_schema.JsonSchemaValue

classmethod __pydantic_init_subclass__(**kwargs)

This is intended to behave just like __init_subclass__, but is called by ModelMetaclass only after the class is actually fully initialized. In particular, attributes like model_fields will be present when this is called.

This is necessary because __init_subclass__ will always be called by type.__new__, and it would require a prohibitively large refactor to the ModelMetaclass to ensure that type.__new__ was called in such a manner that the class would already be sufficiently initialized.

This will receive the same kwargs that would be passed to the standard __init_subclass__, namely, any kwargs passed to the class definition that aren’t used internally by pydantic.

Parameters:

**kwargs (Any) – Any keyword arguments passed to the class definition that aren’t used internally by pydantic.

Return type:

None

classmethod __class_getitem__(typevar_values)

Parameters:

typevar_values (type[Any] | tuple[type[Any], Ellipsis])

Return type:

type[BaseModel] | pydantic._internal._forward_ref.PydanticRecursiveRef

__copy__()

Returns a shallow copy of the model.

Return type:

typing_extensions.Self

__deepcopy__(memo=None)

Returns a deep copy of the model.

Parameters:

memo (dict[int, Any] | None)

Return type:

typing_extensions.Self

__getattr__(item)

Parameters:

item (str)

Return type:

Any

_check_frozen(name, value)

Parameters:

• name (str)

• value (Any)

Return type:

None

__getstate__()

Return type:

dict[Any, Any]

__setstate__(state)

Parameters:

state (dict[Any, Any])

Return type:

None

__eq__(other)

Parameters:

other (Any)

Return type:

bool

classmethod __init_subclass__(**kwargs)

This signature is included purely to help type-checkers check arguments to class declaration, which provides a way to conveniently set model_config key/value pairs.

```py from pydantic import BaseModel

class MyModel(BaseModel, extra=’allow’): … ```

However, this may be deceiving, since the _actual_ calls to __init_subclass__ will not receive any of the config arguments, and will only receive any keyword arguments passed during class initialization that are _not_ expected keys in ConfigDict. (This is due to the way ModelMetaclass.__new__ works.)

Parameters:

**kwargs (typing_extensions.Unpack[pydantic.config.ConfigDict]) – Keyword arguments passed to the class definition, which set model_config

Note

You may want to override __pydantic_init_subclass__ instead, which behaves similarly but is called after the class is fully initialized.

__iter__()

So dict(model) works.

Return type:

TupleGenerator

__repr__()

Return type:

str

__repr_args__()

Return type:

pydantic._internal._repr.ReprArgs

__repr_name__

__repr_str__

__pretty__

__rich_repr__

__str__()

Return type:

str

property __fields__: dict[str, pydantic.fields.FieldInfo]

Return type:

dict[str, pydantic.fields.FieldInfo]

property __fields_set__: set[str]

Return type:

set[str]

dict(*, include=None, exclude=None, by_alias=False, exclude_unset=False, exclude_defaults=False, exclude_none=False)

Parameters:

• include (IncEx | None)

• exclude (IncEx | None)

• by_alias (bool)

• exclude_unset (bool)

• exclude_defaults (bool)

• exclude_none (bool)

Return type:

Dict[str, Any]

classmethod parse_obj(obj)

Parameters:

obj (Any)

Return type:

typing_extensions.Self

classmethod parse_raw(b, *, content_type=None, encoding='utf8', proto=None, allow_pickle=False)

Parameters:

• b (str | bytes)

• content_type (str | None)

• encoding (str)

• proto (pydantic.deprecated.parse.Protocol | None)

• allow_pickle (bool)

Return type:

typing_extensions.Self

classmethod parse_file(path, *, content_type=None, encoding='utf8', proto=None, allow_pickle=False)

Parameters:

• path (str | pathlib.Path)

• content_type (str | None)

• encoding (str)

• proto (pydantic.deprecated.parse.Protocol | None)

• allow_pickle (bool)

Return type:

typing_extensions.Self

classmethod from_orm(obj)

Parameters:

obj (Any)

Return type:

typing_extensions.Self

classmethod construct(_fields_set=None, **values)

Parameters:

• _fields_set (set[str] | None)

• values (Any)

Return type:

typing_extensions.Self

copy(*, include=None, exclude=None, update=None, deep=False)

Returns a copy of the model.

!!! warning “Deprecated”

This method is now deprecated; use model_copy instead.

If you need include or exclude, use:

`py data = self.model_dump(include=include, exclude=exclude, round_trip=True) data = {**data, **(update or {})} copied = self.model_validate(data) `

Parameters:

• include (pydantic._internal._utils.AbstractSetIntStr | pydantic._internal._utils.MappingIntStrAny | None) – Optional set or mapping specifying which fields to include in the copied model.

• exclude (pydantic._internal._utils.AbstractSetIntStr | pydantic._internal._utils.MappingIntStrAny | None) – Optional set or mapping specifying which fields to exclude in the copied model.

• update (Dict[str, Any] | None) – Optional dictionary of field-value pairs to override field values in the copied model.

• deep (bool) – If True, the values of fields that are Pydantic models will be deep-copied.

Returns:

A copy of the model with included, excluded and updated fields as specified.

Return type:

typing_extensions.Self

classmethod schema(by_alias=True, ref_template=DEFAULT_REF_TEMPLATE)

Parameters:

• by_alias (bool)

• ref_template (str)

Return type:

Dict[str, Any]

classmethod schema_json(*, by_alias=True, ref_template=DEFAULT_REF_TEMPLATE, **dumps_kwargs)

Parameters:

• by_alias (bool)

• ref_template (str)

• dumps_kwargs (Any)

Return type:

str

classmethod validate(value)

Parameters:

value (Any)

Return type:

typing_extensions.Self

classmethod update_forward_refs(**localns)

Parameters:

localns (Any)

Return type:

None

_iter(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

_copy_and_set_values(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

classmethod _get_value(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

_calculate_keys(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

class medcat.utils.regression.results.ResultDescriptor(/, **data)

Bases: SingleResultDescriptor

The overarching result descriptor that handles multiple phrases.

This class keeps track of the results on a per-phrase basis and can be used to get the overall report and/or iterate over examples.

Parameters:

data (Any)

per_phrase_results: dict[str, SingleResultDescriptor]

report(target, finding)

Report a test case and its successfulness

Parameters:

• target (FinalTarget) – The final targe configuration

• finding (tuple[Finding, Optional[str]]) – To what extent the concept was recognised

Return type:

None

iter_examples(strictness_threshold)

Iterate suitable examples.

The strictness threshold at which to include examples.

Any finding that is assumed to be “correct enough” according to the strictness matrix for this threshold will be withheld from examples.

In simpler terms, if the finding is NOT in the strictness matrix for this strictness, the example is recorded.

NOTE: To disable example keeping, set the threshold to

Strictness.ANYTHING.

Parameters:

strictness_threshold (Strictness) – The strictness threshold.

Yields:

Iterable[tuple[FinalTarget, tuple[Finding, Optional[str]]]] – The placeholder, phrase, finding, CUI, and name.

Return type:

Iterable[tuple[medcat.utils.regression.targeting.FinalTarget, tuple[Finding, Optional[str]]]]

get_report(phrases_separately=False)

Get the report associated with this descriptor

Parameters:

phrases_separately (bool) – Whether to output descriptor for each phrase separately

Returns:

str – The report string

Return type:

str

model_dump(**kwargs)

Usage docs: https://docs.pydantic.dev/2.9/concepts/serialization/#modelmodel_dump

Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

Parameters:

• mode – The mode in which to_python should run. If mode is ‘json’, the output will only contain JSON serializable types. If mode is ‘python’, the output may contain non-JSON-serializable Python objects.

• include – A set of fields to include in the output.

• exclude – A set of fields to exclude from the output.

• context – Additional context to pass to the serializer.

• by_alias – Whether to use the field’s alias in the dictionary key if defined.

• exclude_unset – Whether to exclude fields that have not been explicitly set.

• exclude_defaults – Whether to exclude fields that are set to their default value.

• exclude_none – Whether to exclude fields that have a value of None.

• round_trip – If True, dumped values should be valid as input for non-idempotent types such as Json[T].

• warnings – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].

• serialize_as_any – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A dictionary representation of the model.

Return type:

dict

name: str

The name of the part that was checked

findings: dict[Finding, int]

The description of failures

examples: list[tuple[medcat.utils.regression.targeting.FinalTarget, tuple[Finding, str | None]]] = []

The examples of non-perfect alignment.

report_success(target, found)

Report a test case and its successfulness.

Parameters:

• target (FinalTarget) – The target configuration

• found (tuple[Finding, Optional[str]]) – Whether or not the check was successful

Return type:

None

json(**kwargs)

Return type:

str

model_config: ClassVar[pydantic.config.ConfigDict]

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[Dict[str, pydantic.fields.FieldInfo]]

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

model_computed_fields: ClassVar[Dict[str, pydantic.fields.ComputedFieldInfo]]

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

__class_vars__: ClassVar[set[str]]

The names of the class variables defined on the model.

__private_attributes__: ClassVar[Dict[str, pydantic.fields.ModelPrivateAttr]]

Metadata about the private attributes of the model.

__signature__: ClassVar[inspect.Signature]

The synthesized __init__ [Signature][inspect.Signature] of the model.

__pydantic_complete__: ClassVar[bool] = False

Whether model building is completed, or if there are still undefined fields.

__pydantic_core_schema__: ClassVar[pydantic_core.CoreSchema]

The core schema of the model.

__pydantic_custom_init__: ClassVar[bool]

Whether the model has a custom __init__ method.

__pydantic_decorators__: ClassVar[pydantic._internal._decorators.DecoratorInfos]

Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.

__pydantic_generic_metadata__: ClassVar[pydantic._internal._generics.PydanticGenericMetadata]

Metadata for generic models; contains data used for a similar purpose to __args__, __origin__, __parameters__ in typing-module generics. May eventually be replaced by these.

__pydantic_parent_namespace__: ClassVar[Dict[str, Any] | None] = None

Parent namespace of the model, used for automatic rebuilding of models.

__pydantic_post_init__: ClassVar[None | Literal['model_post_init']]

The name of the post-init method for the model, if defined.

__pydantic_root_model__: ClassVar[bool] = False

Whether the model is a [RootModel][pydantic.root_model.RootModel].

__pydantic_serializer__: ClassVar[pydantic_core.SchemaSerializer]

The pydantic-core SchemaSerializer used to dump instances of the model.

__pydantic_validator__: ClassVar[pydantic_core.SchemaValidator | pydantic.plugin._schema_validator.PluggableSchemaValidator]

The pydantic-core SchemaValidator used to validate instances of the model.

__pydantic_extra__: dict[str, Any] | None

A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.

__pydantic_fields_set__: set[str]

The names of fields explicitly set during instantiation.

__pydantic_private__: dict[str, Any] | None

Values of private attributes set on the model instance.

__slots__ = ('__dict__', '__pydantic_fields_set__', '__pydantic_extra__', '__pydantic_private__')

__init__(/, **data)

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Parameters:

data (Any)

Return type:

None

property model_extra: dict[str, Any] | None

Get extra fields set during validation.

Returns:

A dictionary of extra fields, or `None` if `config.extra` is not set to `”allow”`.

Return type:

dict[str, Any] | None

property model_fields_set: set[str]

Returns the set of fields that have been explicitly set on this model instance.

Returns:

A set of strings representing the fields that have been set, – i.e. that were not filled from defaults.

Return type:

set[str]

classmethod model_construct(_fields_set=None, **values)

Creates a new instance of the Model class with validated data.

Creates a new model setting __dict__ and __pydantic_fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed.

!!! note

model_construct() generally respects the model_config.extra setting on the provided model. That is, if model_config.extra == ‘allow’, then all extra passed values are added to the model instance’s __dict__ and __pydantic_extra__ fields. If model_config.extra == ‘ignore’ (the default), then all extra passed values are ignored. Because no validation is performed with a call to model_construct(), having model_config.extra == ‘forbid’ does not result in an error if extra values are passed, but they will be ignored.

Parameters:

• _fields_set (set[str] | None) – A set of field names that were originally explicitly set during instantiation. If provided, this is directly used for the [model_fields_set][pydantic.BaseModel.model_fields_set] attribute. Otherwise, the field names from the values argument will be used.

• values (Any) – Trusted or pre-validated data dictionary.

Returns:

A new instance of the `Model` class with validated data.

Return type:

typing_extensions.Self

model_copy(*, update=None, deep=False)

Usage docs: https://docs.pydantic.dev/2.9/concepts/serialization/#model_copy

Returns a copy of the model.

Parameters:

• update (dict[str, Any] | None) – Values to change/add in the new model. Note: the data is not validated before creating the new model. You should trust this data.

• deep (bool) – Set to True to make a deep copy of the model.

Returns:

New model instance.

Return type:

typing_extensions.Self

model_dump_json(*, indent=None, include=None, exclude=None, context=None, by_alias=False, exclude_unset=False, exclude_defaults=False, exclude_none=False, round_trip=False, warnings=True, serialize_as_any=False)

Usage docs: https://docs.pydantic.dev/2.9/concepts/serialization/#modelmodel_dump_json

Generates a JSON representation of the model using Pydantic’s to_json method.

Parameters:

• indent (int | None) – Indentation to use in the JSON output. If None is passed, the output will be compact.

• include (IncEx | None) – Field(s) to include in the JSON output.

• exclude (IncEx | None) – Field(s) to exclude from the JSON output.

• context (Any | None) – Additional context to pass to the serializer.

• by_alias (bool) – Whether to serialize using field aliases.

• exclude_unset (bool) – Whether to exclude fields that have not been explicitly set.

• exclude_defaults (bool) – Whether to exclude fields that are set to their default value.

• exclude_none (bool) – Whether to exclude fields that have a value of None.

• round_trip (bool) – If True, dumped values should be valid as input for non-idempotent types such as Json[T].

• warnings (bool | Literal['none', 'warn', 'error']) – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].

• serialize_as_any (bool) – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A JSON string representation of the model.

Return type:

str

classmethod model_json_schema(by_alias=True, ref_template=DEFAULT_REF_TEMPLATE, schema_generator=GenerateJsonSchema, mode='validation')

Generates a JSON schema for a model class.

Parameters:

• by_alias (bool) – Whether to use attribute aliases or not.

• ref_template (str) – The reference template.

• schema_generator (type[pydantic.json_schema.GenerateJsonSchema]) – To override the logic used to generate the JSON schema, as a subclass of GenerateJsonSchema with your desired modifications

• mode (pydantic.json_schema.JsonSchemaMode) – The mode in which to generate the schema.

Returns:

The JSON schema for the given model class.

Return type:

dict[str, Any]

classmethod model_parametrized_name(params)

Compute the class name for parametrizations of generic classes.

This method can be overridden to achieve a custom naming scheme for generic BaseModels.

Parameters:

params (tuple[type[Any], Ellipsis]) – Tuple of types of the class. Given a generic class Model with 2 type variables and a concrete model Model[str, int], the value (str, int) would be passed to params.

Returns:

String representing the new class where `params` are passed to `cls` as type variables.

Raises:

TypeError – Raised when trying to generate concrete names for non-generic models.

Return type:

str

model_post_init(__context)

Override this method to perform additional initialization after __init__ and model_construct. This is useful if you want to do some validation that requires the entire model to be initialized.

Parameters:

__context (Any)

Return type:

None

classmethod model_rebuild(*, force=False, raise_errors=True, _parent_namespace_depth=2, _types_namespace=None)

Try to rebuild the pydantic-core schema for the model.

This may be necessary when one of the annotations is a ForwardRef which could not be resolved during the initial attempt to build the schema, and automatic rebuilding fails.

Parameters:

• force (bool) – Whether to force the rebuilding of the model schema, defaults to False.

• raise_errors (bool) – Whether to raise errors, defaults to True.

• _parent_namespace_depth (int) – The depth level of the parent namespace, defaults to 2.

• _types_namespace (dict[str, Any] | None) – The types namespace, defaults to None.

Returns:

• Returns `None` if the schema is already “complete” and rebuilding was not required.

• If rebuilding _was_ required, returns `True` if rebuilding was successful, otherwise `False`.

Return type:

bool | None

classmethod model_validate(obj, *, strict=None, from_attributes=None, context=None)

Validate a pydantic model instance.

Parameters:

• obj (Any) – The object to validate.

• strict (bool | None) – Whether to enforce types strictly.

• from_attributes (bool | None) – Whether to extract data from object attributes.

• context (Any | None) – Additional context to pass to the validator.

Raises:

ValidationError – If the object could not be validated.

Returns:

The validated model instance.

Return type:

typing_extensions.Self

classmethod model_validate_json(json_data, *, strict=None, context=None)

Usage docs: https://docs.pydantic.dev/2.9/concepts/json/#json-parsing

Validate the given JSON data against the Pydantic model.

Parameters:

• json_data (str | bytes | bytearray) – The JSON data to validate.

• strict (bool | None) – Whether to enforce types strictly.

• context (Any | None) – Extra variables to pass to the validator.

Returns:

The validated Pydantic model.

Raises:

ValidationError – If json_data is not a JSON string or the object could not be validated.

Return type:

typing_extensions.Self

classmethod model_validate_strings(obj, *, strict=None, context=None)

Validate the given object with string data against the Pydantic model.

Parameters:

• obj (Any) – The object containing string data to validate.

• strict (bool | None) – Whether to enforce types strictly.

• context (Any | None) – Extra variables to pass to the validator.

Returns:

The validated Pydantic model.

Return type:

typing_extensions.Self

classmethod __get_pydantic_core_schema__(source, handler, /)

Hook into generating the model’s CoreSchema.

Parameters:

• source (type[BaseModel]) – The class we are generating a schema for. This will generally be the same as the cls argument if this is a classmethod.

• handler (pydantic.annotated_handlers.GetCoreSchemaHandler) – A callable that calls into Pydantic’s internal CoreSchema generation logic.

Returns:

A `pydantic-core` `CoreSchema`.

Return type:

pydantic_core.CoreSchema

classmethod __get_pydantic_json_schema__(core_schema, handler, /)

Hook into generating the model’s JSON schema.

Parameters:

• core_schema (pydantic_core.CoreSchema) – A pydantic-core CoreSchema. You can ignore this argument and call the handler with a new CoreSchema, wrap this CoreSchema ({‘type’: ‘nullable’, ‘schema’: current_schema}), or just call the handler with the original schema.

• handler (pydantic.annotated_handlers.GetJsonSchemaHandler) – Call into Pydantic’s internal JSON schema generation. This will raise a pydantic.errors.PydanticInvalidForJsonSchema if JSON schema generation fails. Since this gets called by BaseModel.model_json_schema you can override the schema_generator argument to that function to change JSON schema generation globally for a type.

Returns:

A JSON schema, as a Python object.

Return type:

pydantic.json_schema.JsonSchemaValue

classmethod __pydantic_init_subclass__(**kwargs)

This is intended to behave just like __init_subclass__, but is called by ModelMetaclass only after the class is actually fully initialized. In particular, attributes like model_fields will be present when this is called.

This is necessary because __init_subclass__ will always be called by type.__new__, and it would require a prohibitively large refactor to the ModelMetaclass to ensure that type.__new__ was called in such a manner that the class would already be sufficiently initialized.

This will receive the same kwargs that would be passed to the standard __init_subclass__, namely, any kwargs passed to the class definition that aren’t used internally by pydantic.

Parameters:

**kwargs (Any) – Any keyword arguments passed to the class definition that aren’t used internally by pydantic.

Return type:

None

classmethod __class_getitem__(typevar_values)

Parameters:

typevar_values (type[Any] | tuple[type[Any], Ellipsis])

Return type:

type[BaseModel] | pydantic._internal._forward_ref.PydanticRecursiveRef

__copy__()

Returns a shallow copy of the model.

Return type:

typing_extensions.Self

__deepcopy__(memo=None)

Returns a deep copy of the model.

Parameters:

memo (dict[int, Any] | None)

Return type:

typing_extensions.Self

__getattr__(item)

Parameters:

item (str)

Return type:

Any

_check_frozen(name, value)

Parameters:

• name (str)

• value (Any)

Return type:

None

__getstate__()

Return type:

dict[Any, Any]

__setstate__(state)

Parameters:

state (dict[Any, Any])

Return type:

None

__eq__(other)

Parameters:

other (Any)

Return type:

bool

classmethod __init_subclass__(**kwargs)

This signature is included purely to help type-checkers check arguments to class declaration, which provides a way to conveniently set model_config key/value pairs.

```py from pydantic import BaseModel

class MyModel(BaseModel, extra=’allow’): … ```

However, this may be deceiving, since the _actual_ calls to __init_subclass__ will not receive any of the config arguments, and will only receive any keyword arguments passed during class initialization that are _not_ expected keys in ConfigDict. (This is due to the way ModelMetaclass.__new__ works.)

Parameters:

**kwargs (typing_extensions.Unpack[pydantic.config.ConfigDict]) – Keyword arguments passed to the class definition, which set model_config

Note

You may want to override __pydantic_init_subclass__ instead, which behaves similarly but is called after the class is fully initialized.

__iter__()

So dict(model) works.

Return type:

TupleGenerator

__repr__()

Return type:

str

__repr_args__()

Return type:

pydantic._internal._repr.ReprArgs

__repr_name__

__repr_str__

__pretty__

__rich_repr__

__str__()

Return type:

str

property __fields__: dict[str, pydantic.fields.FieldInfo]

Return type:

dict[str, pydantic.fields.FieldInfo]

property __fields_set__: set[str]

Return type:

set[str]

dict(*, include=None, exclude=None, by_alias=False, exclude_unset=False, exclude_defaults=False, exclude_none=False)

Parameters:

• include (IncEx | None)

• exclude (IncEx | None)

• by_alias (bool)

• exclude_unset (bool)

• exclude_defaults (bool)

• exclude_none (bool)

Return type:

Dict[str, Any]

classmethod parse_obj(obj)

Parameters:

obj (Any)

Return type:

typing_extensions.Self

classmethod parse_raw(b, *, content_type=None, encoding='utf8', proto=None, allow_pickle=False)

Parameters:

• b (str | bytes)

• content_type (str | None)

• encoding (str)

• proto (pydantic.deprecated.parse.Protocol | None)

• allow_pickle (bool)

Return type:

typing_extensions.Self

classmethod parse_file(path, *, content_type=None, encoding='utf8', proto=None, allow_pickle=False)

Parameters:

• path (str | pathlib.Path)

• content_type (str | None)

• encoding (str)

• proto (pydantic.deprecated.parse.Protocol | None)

• allow_pickle (bool)

Return type:

typing_extensions.Self

classmethod from_orm(obj)

Parameters:

obj (Any)

Return type:

typing_extensions.Self

classmethod construct(_fields_set=None, **values)

Parameters:

• _fields_set (set[str] | None)

• values (Any)

Return type:

typing_extensions.Self

copy(*, include=None, exclude=None, update=None, deep=False)

Returns a copy of the model.

!!! warning “Deprecated”

This method is now deprecated; use model_copy instead.

If you need include or exclude, use:

`py data = self.model_dump(include=include, exclude=exclude, round_trip=True) data = {**data, **(update or {})} copied = self.model_validate(data) `

Parameters:

• include (pydantic._internal._utils.AbstractSetIntStr | pydantic._internal._utils.MappingIntStrAny | None) – Optional set or mapping specifying which fields to include in the copied model.

• exclude (pydantic._internal._utils.AbstractSetIntStr | pydantic._internal._utils.MappingIntStrAny | None) – Optional set or mapping specifying which fields to exclude in the copied model.

• update (Dict[str, Any] | None) – Optional dictionary of field-value pairs to override field values in the copied model.

• deep (bool) – If True, the values of fields that are Pydantic models will be deep-copied.

Returns:

A copy of the model with included, excluded and updated fields as specified.

Return type:

typing_extensions.Self

classmethod schema(by_alias=True, ref_template=DEFAULT_REF_TEMPLATE)

Parameters:

• by_alias (bool)

• ref_template (str)

Return type:

Dict[str, Any]

classmethod schema_json(*, by_alias=True, ref_template=DEFAULT_REF_TEMPLATE, **dumps_kwargs)

Parameters:

• by_alias (bool)

• ref_template (str)

• dumps_kwargs (Any)

Return type:

str

classmethod validate(value)

Parameters:

value (Any)

Return type:

typing_extensions.Self

classmethod update_forward_refs(**localns)

Parameters:

localns (Any)

Return type:

None

_iter(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

_copy_and_set_values(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

classmethod _get_value(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

_calculate_keys(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

class medcat.utils.regression.results.MultiDescriptor(/, **data)

Bases: pydantic.BaseModel

The descriptor of results over multiple different results (parts).

The idea is that this would likely be used with a regression suite and it would incorporate all the different regression cases it describes.

Parameters:

data (Any)

name: str

The name of the collection being checked

parts: list[ResultDescriptor] = []

The parts kept track of

property findings: dict[Finding, int]

The total findings.

Returns:

dict[Finding, int] – The total number of successes.

Return type:

dict[Finding, int]

iter_examples(strictness_threshold)

Iterate over all relevant examples.

Only examples that are not in the strictness matrix for the specified threshold will be used.

Parameters:

strictness_threshold (Strictness) – The threshold of avoidance.

Yields:

Iterable[tuple[FinalTarget, tuple[Finding, Optional[str]]]] – The examples

Return type:

Iterable[tuple[medcat.utils.regression.targeting.FinalTarget, tuple[Finding, Optional[str]]]]

_get_part_report(part, allowed_findings, total_findings, hide_empty, examples_strictness, phrases_separately, phrase_max_len)

Parameters:

• part (ResultDescriptor)

• allowed_findings (set[Finding])

• total_findings (dict[Finding, int])

• hide_empty (bool)

• examples_strictness (Optional[Strictness])

• phrases_separately (bool)

• phrase_max_len (int)

Return type:

tuple[str, int, int, int]

calculate_report(phrases_separately=False, hide_empty=False, examples_strictness=Strictness.STRICTEST, strictness=Strictness.NORMAL, phrase_max_len=80)

Calculate some of the major parts of the report.

Parameters:

• phrases_separately (bool) – Whether to include per-phrase information

• hide_empty (bool) – Whether to hide empty cases

• examples_strictness (Optional[Strictness.STRICTEST]) – What level of strictness to show for examples. Set to None to disable examples. Defaults to Strictness.STRICTEST.

• strictness (Strictness) – The strictness of the success / fail overview. Defaults to Strictness.NORMAL.

• phrase_max_len (int) – The maximum length of the phrase in examples. Defaults to 80.

Returns:

tuple[int, int, int, int, str] – The total number of examples, the total successes, the total failures, the delegated part, and the number of empty

Return type:

tuple[int, int, int, str, int]

get_report(phrases_separately, hide_empty=False, examples_strictness=Strictness.STRICTEST, strictness=Strictness.NORMAL, phrase_max_len=80)

Get the report associated with this descriptor

Parameters:

• phrases_separately (bool) – Whether to include per-phrase information

• hide_empty (bool) – Whether to hide empty cases

• examples_strictness (Optional[Strictness.STRICTEST]) – What level of strictness to show for examples. Set to None to disable examples. Defaults to Strictness.STRICTEST.

• strictness (Strictness) – The strictness of the success / fail overview. Defaults to Strictness.NORMAL.

• phrase_max_len (int) – The maximum length of the phrase in examples. Defaults to 80.

Returns:

str – The report string

Return type:

str

model_dump(**kwargs)

Usage docs: https://docs.pydantic.dev/2.9/concepts/serialization/#modelmodel_dump

Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

Parameters:

• mode – The mode in which to_python should run. If mode is ‘json’, the output will only contain JSON serializable types. If mode is ‘python’, the output may contain non-JSON-serializable Python objects.

• include – A set of fields to include in the output.

• exclude – A set of fields to exclude from the output.

• context – Additional context to pass to the serializer.

• by_alias – Whether to use the field’s alias in the dictionary key if defined.

• exclude_unset – Whether to exclude fields that have not been explicitly set.

• exclude_defaults – Whether to exclude fields that are set to their default value.

• exclude_none – Whether to exclude fields that have a value of None.

• round_trip – If True, dumped values should be valid as input for non-idempotent types such as Json[T].

• warnings – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].

• serialize_as_any – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A dictionary representation of the model.

Return type:

dict

model_config: ClassVar[pydantic.config.ConfigDict]

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[Dict[str, pydantic.fields.FieldInfo]]

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo] objects.

This replaces Model.__fields__ from Pydantic V1.

model_computed_fields: ClassVar[Dict[str, pydantic.fields.ComputedFieldInfo]]

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

__class_vars__: ClassVar[set[str]]

The names of the class variables defined on the model.

__private_attributes__: ClassVar[Dict[str, pydantic.fields.ModelPrivateAttr]]

Metadata about the private attributes of the model.

__signature__: ClassVar[inspect.Signature]

The synthesized __init__ [Signature][inspect.Signature] of the model.

__pydantic_complete__: ClassVar[bool] = False

Whether model building is completed, or if there are still undefined fields.

__pydantic_core_schema__: ClassVar[pydantic_core.CoreSchema]

The core schema of the model.

__pydantic_custom_init__: ClassVar[bool]

Whether the model has a custom __init__ method.

__pydantic_decorators__: ClassVar[pydantic._internal._decorators.DecoratorInfos]

Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.

__pydantic_generic_metadata__: ClassVar[pydantic._internal._generics.PydanticGenericMetadata]

Metadata for generic models; contains data used for a similar purpose to __args__, __origin__, __parameters__ in typing-module generics. May eventually be replaced by these.

__pydantic_parent_namespace__: ClassVar[Dict[str, Any] | None] = None

Parent namespace of the model, used for automatic rebuilding of models.

__pydantic_post_init__: ClassVar[None | Literal['model_post_init']]

The name of the post-init method for the model, if defined.

__pydantic_root_model__: ClassVar[bool] = False

Whether the model is a [RootModel][pydantic.root_model.RootModel].

__pydantic_serializer__: ClassVar[pydantic_core.SchemaSerializer]

The pydantic-core SchemaSerializer used to dump instances of the model.

__pydantic_validator__: ClassVar[pydantic_core.SchemaValidator | pydantic.plugin._schema_validator.PluggableSchemaValidator]

The pydantic-core SchemaValidator used to validate instances of the model.

__pydantic_extra__: dict[str, Any] | None

A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.

__pydantic_fields_set__: set[str]

The names of fields explicitly set during instantiation.

__pydantic_private__: dict[str, Any] | None

Values of private attributes set on the model instance.

__slots__ = ('__dict__', '__pydantic_fields_set__', '__pydantic_extra__', '__pydantic_private__')

__init__(/, **data)

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Parameters:

data (Any)

Return type:

None

property model_extra: dict[str, Any] | None

Get extra fields set during validation.

Returns:

A dictionary of extra fields, or `None` if `config.extra` is not set to `”allow”`.

Return type:

dict[str, Any] | None

property model_fields_set: set[str]

Returns the set of fields that have been explicitly set on this model instance.

Returns:

A set of strings representing the fields that have been set, – i.e. that were not filled from defaults.

Return type:

set[str]

classmethod model_construct(_fields_set=None, **values)

Creates a new instance of the Model class with validated data.

Creates a new model setting __dict__ and __pydantic_fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed.

!!! note

model_construct() generally respects the model_config.extra setting on the provided model. That is, if model_config.extra == ‘allow’, then all extra passed values are added to the model instance’s __dict__ and __pydantic_extra__ fields. If model_config.extra == ‘ignore’ (the default), then all extra passed values are ignored. Because no validation is performed with a call to model_construct(), having model_config.extra == ‘forbid’ does not result in an error if extra values are passed, but they will be ignored.

Parameters:

• _fields_set (set[str] | None) – A set of field names that were originally explicitly set during instantiation. If provided, this is directly used for the [model_fields_set][pydantic.BaseModel.model_fields_set] attribute. Otherwise, the field names from the values argument will be used.

• values (Any) – Trusted or pre-validated data dictionary.

Returns:

A new instance of the `Model` class with validated data.

Return type:

typing_extensions.Self

model_copy(*, update=None, deep=False)

Usage docs: https://docs.pydantic.dev/2.9/concepts/serialization/#model_copy

Returns a copy of the model.

Parameters:

• update (dict[str, Any] | None) – Values to change/add in the new model. Note: the data is not validated before creating the new model. You should trust this data.

• deep (bool) – Set to True to make a deep copy of the model.

Returns:

New model instance.

Return type:

typing_extensions.Self

model_dump_json(*, indent=None, include=None, exclude=None, context=None, by_alias=False, exclude_unset=False, exclude_defaults=False, exclude_none=False, round_trip=False, warnings=True, serialize_as_any=False)

Usage docs: https://docs.pydantic.dev/2.9/concepts/serialization/#modelmodel_dump_json

Generates a JSON representation of the model using Pydantic’s to_json method.

Parameters:

• indent (int | None) – Indentation to use in the JSON output. If None is passed, the output will be compact.

• include (IncEx | None) – Field(s) to include in the JSON output.

• exclude (IncEx | None) – Field(s) to exclude from the JSON output.

• context (Any | None) – Additional context to pass to the serializer.

• by_alias (bool) – Whether to serialize using field aliases.

• exclude_unset (bool) – Whether to exclude fields that have not been explicitly set.

• exclude_defaults (bool) – Whether to exclude fields that are set to their default value.

• exclude_none (bool) – Whether to exclude fields that have a value of None.

• round_trip (bool) – If True, dumped values should be valid as input for non-idempotent types such as Json[T].

• warnings (bool | Literal['none', 'warn', 'error']) – How to handle serialization errors. False/”none” ignores them, True/”warn” logs errors, “error” raises a [PydanticSerializationError][pydantic_core.PydanticSerializationError].

• serialize_as_any (bool) – Whether to serialize fields with duck-typing serialization behavior.

Returns:

A JSON string representation of the model.

Return type:

str

classmethod model_json_schema(by_alias=True, ref_template=DEFAULT_REF_TEMPLATE, schema_generator=GenerateJsonSchema, mode='validation')

Generates a JSON schema for a model class.

Parameters:

• by_alias (bool) – Whether to use attribute aliases or not.

• ref_template (str) – The reference template.

• schema_generator (type[pydantic.json_schema.GenerateJsonSchema]) – To override the logic used to generate the JSON schema, as a subclass of GenerateJsonSchema with your desired modifications

• mode (pydantic.json_schema.JsonSchemaMode) – The mode in which to generate the schema.

Returns:

The JSON schema for the given model class.

Return type:

dict[str, Any]

classmethod model_parametrized_name(params)

Compute the class name for parametrizations of generic classes.

This method can be overridden to achieve a custom naming scheme for generic BaseModels.

Parameters:

params (tuple[type[Any], Ellipsis]) – Tuple of types of the class. Given a generic class Model with 2 type variables and a concrete model Model[str, int], the value (str, int) would be passed to params.

Returns:

String representing the new class where `params` are passed to `cls` as type variables.

Raises:

TypeError – Raised when trying to generate concrete names for non-generic models.

Return type:

str

model_post_init(__context)

Override this method to perform additional initialization after __init__ and model_construct. This is useful if you want to do some validation that requires the entire model to be initialized.

Parameters:

__context (Any)

Return type:

None

classmethod model_rebuild(*, force=False, raise_errors=True, _parent_namespace_depth=2, _types_namespace=None)

Try to rebuild the pydantic-core schema for the model.

This may be necessary when one of the annotations is a ForwardRef which could not be resolved during the initial attempt to build the schema, and automatic rebuilding fails.

Parameters:

• force (bool) – Whether to force the rebuilding of the model schema, defaults to False.

• raise_errors (bool) – Whether to raise errors, defaults to True.

• _parent_namespace_depth (int) – The depth level of the parent namespace, defaults to 2.

• _types_namespace (dict[str, Any] | None) – The types namespace, defaults to None.

Returns:

• Returns `None` if the schema is already “complete” and rebuilding was not required.

• If rebuilding _was_ required, returns `True` if rebuilding was successful, otherwise `False`.

Return type:

bool | None

classmethod model_validate(obj, *, strict=None, from_attributes=None, context=None)

Validate a pydantic model instance.

Parameters:

• obj (Any) – The object to validate.

• strict (bool | None) – Whether to enforce types strictly.

• from_attributes (bool | None) – Whether to extract data from object attributes.

• context (Any | None) – Additional context to pass to the validator.

Raises:

ValidationError – If the object could not be validated.

Returns:

The validated model instance.

Return type:

typing_extensions.Self

classmethod model_validate_json(json_data, *, strict=None, context=None)

Usage docs: https://docs.pydantic.dev/2.9/concepts/json/#json-parsing

Validate the given JSON data against the Pydantic model.

Parameters:

• json_data (str | bytes | bytearray) – The JSON data to validate.

• strict (bool | None) – Whether to enforce types strictly.

• context (Any | None) – Extra variables to pass to the validator.

Returns:

The validated Pydantic model.

Raises:

ValidationError – If json_data is not a JSON string or the object could not be validated.

Return type:

typing_extensions.Self

classmethod model_validate_strings(obj, *, strict=None, context=None)

Validate the given object with string data against the Pydantic model.

Parameters:

• obj (Any) – The object containing string data to validate.

• strict (bool | None) – Whether to enforce types strictly.

• context (Any | None) – Extra variables to pass to the validator.

Returns:

The validated Pydantic model.

Return type:

typing_extensions.Self

classmethod __get_pydantic_core_schema__(source, handler, /)

Hook into generating the model’s CoreSchema.

Parameters:

• source (type[BaseModel]) – The class we are generating a schema for. This will generally be the same as the cls argument if this is a classmethod.

• handler (pydantic.annotated_handlers.GetCoreSchemaHandler) – A callable that calls into Pydantic’s internal CoreSchema generation logic.

Returns:

A `pydantic-core` `CoreSchema`.

Return type:

pydantic_core.CoreSchema

classmethod __get_pydantic_json_schema__(core_schema, handler, /)

Hook into generating the model’s JSON schema.

Parameters:

• core_schema (pydantic_core.CoreSchema) – A pydantic-core CoreSchema. You can ignore this argument and call the handler with a new CoreSchema, wrap this CoreSchema ({‘type’: ‘nullable’, ‘schema’: current_schema}), or just call the handler with the original schema.

• handler (pydantic.annotated_handlers.GetJsonSchemaHandler) – Call into Pydantic’s internal JSON schema generation. This will raise a pydantic.errors.PydanticInvalidForJsonSchema if JSON schema generation fails. Since this gets called by BaseModel.model_json_schema you can override the schema_generator argument to that function to change JSON schema generation globally for a type.

Returns:

A JSON schema, as a Python object.

Return type:

pydantic.json_schema.JsonSchemaValue

classmethod __pydantic_init_subclass__(**kwargs)

This is intended to behave just like __init_subclass__, but is called by ModelMetaclass only after the class is actually fully initialized. In particular, attributes like model_fields will be present when this is called.

This is necessary because __init_subclass__ will always be called by type.__new__, and it would require a prohibitively large refactor to the ModelMetaclass to ensure that type.__new__ was called in such a manner that the class would already be sufficiently initialized.

This will receive the same kwargs that would be passed to the standard __init_subclass__, namely, any kwargs passed to the class definition that aren’t used internally by pydantic.

Parameters:

**kwargs (Any) – Any keyword arguments passed to the class definition that aren’t used internally by pydantic.

Return type:

None

classmethod __class_getitem__(typevar_values)

Parameters:

typevar_values (type[Any] | tuple[type[Any], Ellipsis])

Return type:

type[BaseModel] | pydantic._internal._forward_ref.PydanticRecursiveRef

__copy__()

Returns a shallow copy of the model.

Return type:

typing_extensions.Self

__deepcopy__(memo=None)

Returns a deep copy of the model.

Parameters:

memo (dict[int, Any] | None)

Return type:

typing_extensions.Self

__getattr__(item)

Parameters:

item (str)

Return type:

Any

_check_frozen(name, value)

Parameters:

• name (str)

• value (Any)

Return type:

None

__getstate__()

Return type:

dict[Any, Any]

__setstate__(state)

Parameters:

state (dict[Any, Any])

Return type:

None

__eq__(other)

Parameters:

other (Any)

Return type:

bool

classmethod __init_subclass__(**kwargs)

This signature is included purely to help type-checkers check arguments to class declaration, which provides a way to conveniently set model_config key/value pairs.

```py from pydantic import BaseModel

class MyModel(BaseModel, extra=’allow’): … ```

However, this may be deceiving, since the _actual_ calls to __init_subclass__ will not receive any of the config arguments, and will only receive any keyword arguments passed during class initialization that are _not_ expected keys in ConfigDict. (This is due to the way ModelMetaclass.__new__ works.)

Parameters:

**kwargs (typing_extensions.Unpack[pydantic.config.ConfigDict]) – Keyword arguments passed to the class definition, which set model_config

Note

You may want to override __pydantic_init_subclass__ instead, which behaves similarly but is called after the class is fully initialized.

__iter__()

So dict(model) works.

Return type:

TupleGenerator

__repr__()

Return type:

str

__repr_args__()

Return type:

pydantic._internal._repr.ReprArgs

__repr_name__

__repr_str__

__pretty__

__rich_repr__

__str__()

Return type:

str

property __fields__: dict[str, pydantic.fields.FieldInfo]

Return type:

dict[str, pydantic.fields.FieldInfo]

property __fields_set__: set[str]

Return type:

set[str]

dict(*, include=None, exclude=None, by_alias=False, exclude_unset=False, exclude_defaults=False, exclude_none=False)

Parameters:

• include (IncEx | None)

• exclude (IncEx | None)

• by_alias (bool)

• exclude_unset (bool)

• exclude_defaults (bool)

• exclude_none (bool)

Return type:

Dict[str, Any]

json(*, include=None, exclude=None, by_alias=False, exclude_unset=False, exclude_defaults=False, exclude_none=False, encoder=PydanticUndefined, models_as_dict=PydanticUndefined, **dumps_kwargs)

Parameters:

• include (IncEx | None)

• exclude (IncEx | None)

• by_alias (bool)

• exclude_unset (bool)

• exclude_defaults (bool)

• exclude_none (bool)

• encoder (Callable[[Any], Any] | None)

• models_as_dict (bool)

• dumps_kwargs (Any)

Return type:

str

classmethod parse_obj(obj)

Parameters:

obj (Any)

Return type:

typing_extensions.Self

classmethod parse_raw(b, *, content_type=None, encoding='utf8', proto=None, allow_pickle=False)

Parameters:

• b (str | bytes)

• content_type (str | None)

• encoding (str)

• proto (pydantic.deprecated.parse.Protocol | None)

• allow_pickle (bool)

Return type:

typing_extensions.Self

classmethod parse_file(path, *, content_type=None, encoding='utf8', proto=None, allow_pickle=False)

Parameters:

• path (str | pathlib.Path)

• content_type (str | None)

• encoding (str)

• proto (pydantic.deprecated.parse.Protocol | None)

• allow_pickle (bool)

Return type:

typing_extensions.Self

classmethod from_orm(obj)

Parameters:

obj (Any)

Return type:

typing_extensions.Self

classmethod construct(_fields_set=None, **values)

Parameters:

• _fields_set (set[str] | None)

• values (Any)

Return type:

typing_extensions.Self

copy(*, include=None, exclude=None, update=None, deep=False)

Returns a copy of the model.

!!! warning “Deprecated”

This method is now deprecated; use model_copy instead.

If you need include or exclude, use:

`py data = self.model_dump(include=include, exclude=exclude, round_trip=True) data = {**data, **(update or {})} copied = self.model_validate(data) `

Parameters:

• include (pydantic._internal._utils.AbstractSetIntStr | pydantic._internal._utils.MappingIntStrAny | None) – Optional set or mapping specifying which fields to include in the copied model.

• exclude (pydantic._internal._utils.AbstractSetIntStr | pydantic._internal._utils.MappingIntStrAny | None) – Optional set or mapping specifying which fields to exclude in the copied model.

• update (Dict[str, Any] | None) – Optional dictionary of field-value pairs to override field values in the copied model.

• deep (bool) – If True, the values of fields that are Pydantic models will be deep-copied.

Returns:

A copy of the model with included, excluded and updated fields as specified.

Return type:

typing_extensions.Self

classmethod schema(by_alias=True, ref_template=DEFAULT_REF_TEMPLATE)

Parameters:

• by_alias (bool)

• ref_template (str)

Return type:

Dict[str, Any]

classmethod schema_json(*, by_alias=True, ref_template=DEFAULT_REF_TEMPLATE, **dumps_kwargs)

Parameters:

• by_alias (bool)

• ref_template (str)

• dumps_kwargs (Any)

Return type:

str

classmethod validate(value)

Parameters:

value (Any)

Return type:

typing_extensions.Self

classmethod update_forward_refs(**localns)

Parameters:

localns (Any)

Return type:

None

_iter(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

_copy_and_set_values(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

classmethod _get_value(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

_calculate_keys(*args, **kwargs)

Parameters:

• args (Any)

• kwargs (Any)

Return type:

Any

exception medcat.utils.regression.results.MalformedFinding(*args)

Bases: ValueError

Inappropriate argument value (of correct type).

Parameters:

args (object)

__init__(*args)

Initialize self. See help(type(self)) for accurate signature.

Parameters:

args (object)

Return type:

None

class __cause__

exception cause

class __context__

exception context

__delattr__()

Implement delattr(self, name).

__dir__()

Default dir() implementation.

__eq__()

Return self==value.

__format__()

Default object formatter.

__ge__()

Return self>=value.

__getattribute__()

Return getattr(self, name).

__gt__()

Return self>value.

__hash__()

Return hash(self).

__le__()

Return self<=value.

__lt__()

Return self<value.

__ne__()

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

__reduce_ex__()

Helper for pickle.

__repr__()

Return repr(self).

__setattr__()

Implement setattr(self, name, value).

__setstate__()

__sizeof__()

Size of object in memory, in bytes.

__str__()

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

class __suppress_context__

class __traceback__

class args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.