medcat.tokenizing.spacy_impl.tokens
===================================

.. py:module:: medcat.tokenizing.spacy_impl.tokens


Attributes
----------

.. autoapisummary::

   medcat.tokenizing.spacy_impl.tokens.logger


Exceptions
----------

.. autoapisummary::

   medcat.tokenizing.spacy_impl.tokens.UnregisteredDataPathException


Classes
-------

.. autoapisummary::

   medcat.tokenizing.spacy_impl.tokens.BaseToken
   medcat.tokenizing.spacy_impl.tokens.MutableToken
   medcat.tokenizing.spacy_impl.tokens.BaseEntity
   medcat.tokenizing.spacy_impl.tokens.MutableEntity
   medcat.tokenizing.spacy_impl.tokens.BaseDocument
   medcat.tokenizing.spacy_impl.tokens.Token
   medcat.tokenizing.spacy_impl.tokens.Entity
   medcat.tokenizing.spacy_impl.tokens.Document


Module Contents
---------------

.. py:class:: BaseToken

   Bases: :py:obj:`Protocol`


   Base token protocol.

   This represents the static (unchangeable) parts of a token.


   .. py:property:: text
      :type: str


      The text represented by this token.


   .. py:property:: lower
      :type: str


      The lower case text representation.


   .. py:property:: text_versions
      :type: list[str]


      The different versions of text (e.g normalised and lower)


   .. py:property:: is_upper
      :type: bool


      Whether the text is upper case.


   .. py:property:: is_stop
      :type: bool


      Whether the token represents a stop token.


   .. py:property:: char_index
      :type: int


      The character index of the start of this token


   .. py:property:: index
      :type: int


      The index (in terms of tokens) of this token in the document.


   .. py:property:: text_with_ws
      :type: str


      The text with tailing whitespace (where applicable).


   .. py:property:: is_digit
      :type: bool


      Whether the token represents a digit.


   .. py:attribute:: __slots__
      :value: ()



   .. py:attribute:: _is_protocol
      :value: True



   .. py:attribute:: _is_runtime_protocol
      :value: False



   .. py:method:: __init_subclass__(*args, **kwargs)
      :classmethod:



   .. py:method:: __class_getitem__(params)
      :classmethod:



.. py:class:: MutableToken

   Bases: :py:obj:`Protocol`


   The mutable part of a token.

   This protocol describes all the parts of a token that could be expected to
   change.


   .. py:property:: base
      :type: BaseToken


      The base portion of the token.


   .. py:property:: is_punctuation
      :type: bool


      Whether the token represents punctuation.


   .. py:property:: to_skip
      :type: bool


      Whether the token should be skipped.


   .. py:property:: lemma
      :type: str


      The lemmatised version of the text.


   .. py:property:: tag
      :type: Optional[str]


      Optional tag (e.g) for normalization.


   .. py:property:: norm
      :type: str


      The normalised text.


   .. py:attribute:: __slots__
      :value: ()



   .. py:attribute:: _is_protocol
      :value: True



   .. py:attribute:: _is_runtime_protocol
      :value: False



   .. py:method:: __init_subclass__(*args, **kwargs)
      :classmethod:



   .. py:method:: __class_getitem__(params)
      :classmethod:



.. py:class:: BaseEntity

   Bases: :py:obj:`Protocol`


   Base entity protocol.

   This describes the static (unchangeable) parts of an entity or
   sequence of tokens.


   .. py:property:: start_index
      :type: int


      The index of the first token in the entity.


   .. py:property:: end_index
      :type: int


      The index of the last token in the entity.


   .. py:property:: start_char_index
      :type: int


      The character index of the first token.


   .. py:property:: end_char_index
      :type: int


      The character index of the last token.


   .. py:property:: label
      :type: int


      seems unused).

      :type: The label of the entity (NOTE


   .. py:property:: text
      :type: str


      The text of the entire entity.


   .. py:method:: __iter__()


   .. py:method:: __len__()


   .. py:attribute:: __slots__
      :value: ()



   .. py:attribute:: _is_protocol
      :value: True



   .. py:attribute:: _is_runtime_protocol
      :value: False



   .. py:method:: __init_subclass__(*args, **kwargs)
      :classmethod:



   .. py:method:: __class_getitem__(params)
      :classmethod:



.. py:class:: MutableEntity

   Bases: :py:obj:`Protocol`


   The mutable part of an entity.

   This represent the changeable part of an entnity. That is, parts
   that should be changed by the various components.


   .. py:property:: base
      :type: BaseEntity


      The base / static entity part.


   .. py:property:: detected_name
      :type: str


      The detected name (if any) for this entity.

      This should be set by the NER component.


   .. py:method:: set_addon_data(path, val)

      Used to add arbitrary data to the entity.

      This is generally used by addons to keep track of their data.

      NB! The path used needs to be registered using the
      `register_addon_path` class method.

      :param path: The data ID / path.
      :type path: str
      :param val: The value to be added.
      :type val: Any



   .. py:method:: has_addon_data(path)

      Checks whether the addon data for a specific path has been set.

      :param path: The path to check.
      :type path: str

      :Returns: **bool** -- Whether the addon data had been set.



   .. py:method:: get_addon_data(path)

      Get data added to the entity.

      See `add_data` for details.

      :param path: The data ID / path.
      :type path: str

      :Returns: **Any** -- The stored value.



   .. py:method:: get_available_addon_paths()

      Gets the available addon data paths for this entity.

      This will only include paths that have values set.

      :Returns: **list[str]** -- List of available addon data paths.



   .. py:property:: link_candidates
      :type: list[str]


      The candidates for the detected name (if any) for this entity.

      This should be set by the NER component.


   .. py:property:: context_similarity
      :type: float


      The context similarity of the lnked entity.

      This should be set by the linker component.


   .. py:property:: confidence
      :type: float


      The confidence for the lnked entity.

      NOTE: This seems to be unused!


   .. py:property:: cui
      :type: str


      The CUI of the lnked entity.

      This should be set by the linker component.


   .. py:property:: id
      :type: int


      The ID of the entity within the document.

      This counts all the entities recognised, not just ones that
      were successfully linked.

      This should be set by the NER.


   .. py:method:: register_addon_path(path, def_val = None, force = True)
      :classmethod:


      Register a custom/arbitrary data path.

      This can be used to store arbitrary data along with the entity for
      use in an addon (e.g MetaCAT).

      PS: If using this, it is important to use paths namespaced to the
      component you're using in order to avoid conflicts.

      :param path: The path to be used. Should be prefixed by component
                   name (e.g `meta_cat_id` for an ID tied to the `meta_cat` addon)
      :type path: str
      :param def_val: Default value. Defaults to `None`.
      :type def_val: Any
      :param force: Whether to forcefully add the value.
                    Defaults to True.
      :type force: bool



   .. py:method:: __iter__()


   .. py:method:: __len__()


   .. py:attribute:: __slots__
      :value: ()



   .. py:attribute:: _is_protocol
      :value: True



   .. py:attribute:: _is_runtime_protocol
      :value: False



   .. py:method:: __init_subclass__(*args, **kwargs)
      :classmethod:



   .. py:method:: __class_getitem__(params)
      :classmethod:



.. py:class:: BaseDocument

   Bases: :py:obj:`Protocol`


   The base document protocol.

   Represents the unchangeable parts of the whole document.


   .. py:property:: text
      :type: str


      The document raw text.


   .. py:method:: __getitem__(index: int) -> BaseToken
                  __getitem__(index: slice) -> BaseEntity


   .. py:method:: __iter__()


   .. py:method:: isupper()

      Whether the entire document is upper case.



   .. py:attribute:: __slots__
      :value: ()



   .. py:attribute:: _is_protocol
      :value: True



   .. py:attribute:: _is_runtime_protocol
      :value: False



   .. py:method:: __init_subclass__(*args, **kwargs)
      :classmethod:



   .. py:method:: __class_getitem__(params)
      :classmethod:



.. py:exception:: UnregisteredDataPathException(cls, path)

   Bases: :py:obj:`ValueError`


   Inappropriate argument value (of correct type).


   .. py:method:: __init__(cls, path)

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



   .. py:attribute:: cls


   .. py:attribute:: path


   .. py:class:: __cause__

      exception cause



   .. py:class:: __context__

      exception context



   .. py:method:: __delattr__()

      Implement delattr(self, name).



   .. py:method:: __dir__()

      Default dir() implementation.



   .. py:method:: __eq__()

      Return self==value.



   .. py:method:: __format__()

      Default object formatter.



   .. py:method:: __ge__()

      Return self>=value.



   .. py:method:: __getattribute__()

      Return getattr(self, name).



   .. py:method:: __gt__()

      Return self>value.



   .. py:method:: __hash__()

      Return hash(self).



   .. py:method:: __le__()

      Return self<=value.



   .. py:method:: __lt__()

      Return self<value.



   .. py:method:: __ne__()

      Return self!=value.



   .. py:method:: __new__()

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



   .. py:method:: __reduce__()


   .. py:method:: __reduce_ex__()

      Helper for pickle.



   .. py:method:: __repr__()

      Return repr(self).



   .. py:method:: __setattr__()

      Implement setattr(self, name, value).



   .. py:method:: __setstate__()


   .. py:method:: __sizeof__()

      Size of object in memory, in bytes.



   .. py:method:: __str__()

      Return str(self).



   .. py:method:: __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).



   .. py:class:: __suppress_context__


   .. py:class:: __traceback__


   .. py:class:: args


   .. py:method:: with_traceback()

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



.. py:data:: logger

.. py:class:: Token(delegate)

   .. py:method:: __init__(delegate)


   .. py:attribute:: _delegate


   .. py:property:: is_punctuation
      :type: bool



   .. py:property:: to_skip
      :type: bool



   .. py:property:: norm
      :type: str



   .. py:property:: base
      :type: medcat.tokenizing.tokens.BaseToken



   .. py:property:: text
      :type: str



   .. py:property:: text_versions
      :type: list[str]



   .. py:property:: lower
      :type: str



   .. py:property:: is_stop
      :type: bool



   .. py:property:: is_digit
      :type: bool



   .. py:property:: is_upper
      :type: bool



   .. py:property:: tag
      :type: Optional[str]



   .. py:property:: lemma
      :type: str



   .. py:property:: text_with_ws
      :type: str



   .. py:property:: char_index
      :type: int



   .. py:property:: index
      :type: int



   .. py:method:: __str__()


   .. py:method:: __repr__()


   .. py:method:: __hash__()


   .. py:method:: __eq__(value)


.. py:class:: Entity(delegate)

   .. py:attribute:: _addon_extension_paths
      :type:  set[str]


   .. py:method:: __init__(delegate)


   .. py:attribute:: _delegate


   .. py:attribute:: link_candidates
      :type:  list[str]
      :value: []



   .. py:attribute:: context_similarity
      :type:  float
      :value: 0.0



   .. py:attribute:: confidence
      :type:  float
      :value: 0.0



   .. py:attribute:: cui
      :value: ''



   .. py:attribute:: id
      :value: -1



   .. py:attribute:: detected_name
      :value: ''



   .. py:property:: base
      :type: medcat.tokenizing.tokens.BaseEntity



   .. py:method:: set_addon_data(path, val)


   .. py:method:: has_addon_data(path)


   .. py:method:: get_addon_data(path)


   .. py:method:: get_available_addon_paths()


   .. py:method:: register_addon_path(path, def_val = None, force = True)
      :classmethod:



   .. py:property:: text
      :type: str



   .. py:property:: label
      :type: int



   .. py:property:: start_index
      :type: int



   .. py:property:: end_index
      :type: int



   .. py:property:: start_char_index
      :type: int



   .. py:property:: end_char_index
      :type: int



   .. py:method:: __iter__()


   .. py:method:: __len__()


   .. py:method:: __str__()


   .. py:method:: __repr__()


.. py:class:: Document(delegate)

   .. py:attribute:: _addon_extension_paths
      :type:  set[str]


   .. py:method:: __init__(delegate)


   .. py:attribute:: _delegate


   .. py:attribute:: ner_ents
      :type:  list[medcat.tokenizing.tokens.MutableEntity]
      :value: []



   .. py:attribute:: linked_ents
      :type:  list[medcat.tokenizing.tokens.MutableEntity]
      :value: []



   .. py:property:: base
      :type: medcat.tokenizing.tokens.BaseDocument



   .. py:property:: text
      :type: str



   .. py:method:: __getitem__(index: int) -> medcat.tokenizing.tokens.MutableToken
                  __getitem__(index: slice) -> medcat.tokenizing.tokens.MutableEntity


   .. py:method:: __len__()


   .. py:method:: get_tokens(start_index, end_index)


   .. py:method:: set_addon_data(path, val)


   .. py:method:: has_addon_data(path)


   .. py:method:: get_addon_data(path)


   .. py:method:: get_available_addon_paths()


   .. py:method:: register_addon_path(path, def_val = None, force = True)
      :classmethod:



   .. py:method:: __iter__()


   .. py:method:: isupper()


   .. py:method:: __str__()


   .. py:method:: __repr__()