medcat.data.mctexport

Attributes

MedCATTrainerExportProjectInfo

The project name, project ID, CUIs str, and TUIs str

Classes

MedCATTrainerExportAnnotationRequired	dict() -> new empty dictionary
MedCATTrainerExportAnnotation	dict() -> new empty dictionary
MedCATTrainerExportDocument	dict() -> new empty dictionary
MedCATTrainerExportProject	dict() -> new empty dictionary
MedCATTrainerExport	dict() -> new empty dictionary

Functions

iter_projects(export)	Iterate over all the projects in the trainer export.
iter_docs(export)	Iterate over all the docs in a trainer export.
iter_anns(export)	Iterate over all the annotations in a trainer export.
count_all_annotations(export)	Count the number of annotations in a trainer export.
count_all_docs(export)	Count the number of documents in a trainer export.
get_nr_of_annotations(doc)	Get the number of annotations for a tariner export document.
count_anns_per_concept(export)

Module Contents

class medcat.data.mctexport.MedCATTrainerExportAnnotationRequired

Bases: typing_extensions.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)

start: int

end: int

cui: str

value: 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.data.mctexport.MedCATTrainerExportAnnotation

Bases: MedCATTrainerExportAnnotationRequired

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)

id: str | int

validated: bool | None

start: int

end: int

cui: str

value: 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.data.mctexport.MedCATTrainerExportDocument

Bases: typing_extensions.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)

name: str

id: Any

last_modified: str

text: str

annotations: list[MedCATTrainerExportAnnotation]

__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.data.mctexport.MedCATTrainerExportProject

Bases: typing_extensions.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)

name: str

id: Any

cuis: str

tuis: str | None

documents: list[MedCATTrainerExportDocument]

__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

medcat.data.mctexport.MedCATTrainerExportProjectInfo

The project name, project ID, CUIs str, and TUIs str

class medcat.data.mctexport.MedCATTrainerExport

Bases: typing_extensions.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)

projects: list[MedCATTrainerExportProject]

__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

medcat.data.mctexport.iter_projects(export)

Iterate over all the projects in the trainer export.

Parameters:

export (MedCATTrainerExport) – The trainer export.

Yields:

Iterator[MedCATTrainerExportProject] – Project iterator.

Return type:

Iterator[MedCATTrainerExportProject]

medcat.data.mctexport.iter_docs(export)

Iterate over all the docs in a trainer export.

Parameters:

export (MedCATTrainerExport) – The trainer export.

Yields:

Iterator[tuple[MedCATTrainerExportProjectInfo,

MedCATTrainerExportDocument]]:

The project info and the document.

Return type:

Iterator[tuple[MedCATTrainerExportProjectInfo, MedCATTrainerExportDocument]]

medcat.data.mctexport.iter_anns(export)

Iterate over all the annotations in a trainer export.

Parameters:

export (MedCATTrainerExport) – The trainer export.

Yields:

Iterator[tuple[MedCATTrainerExportProjectInfo,

MedCATTrainerExportDocument, MedCATTrainerExportAnnotation]]:

The project info, the document, and the annotation.

Return type:

Iterator[tuple[MedCATTrainerExportProjectInfo, MedCATTrainerExportDocument, MedCATTrainerExportAnnotation]]

medcat.data.mctexport.count_all_annotations(export)

Count the number of annotations in a trainer export.

Parameters:

export (MedCATTrainerExport) – The trainer export.

Returns:

int – The total number of annotations.

Return type:

int

medcat.data.mctexport.count_all_docs(export)

Count the number of documents in a trainer export.

Parameters:

export (MedCATTrainerExport) – The trainer export.

Returns:

int – The total number of documents.

Return type:

int

medcat.data.mctexport.get_nr_of_annotations(doc)

Get the number of annotations for a tariner export document.

Parameters:

doc (MedCATTrainerExportDocument) – The trainer export document.

Returns:

int – The number of annotations within the document.

Return type:

int

medcat.data.mctexport.count_anns_per_concept(export)

Parameters:

export (MedCATTrainerExport)

Return type:

dict[str, int]