medcat.cdb.concepts
===================

.. py:module:: medcat.cdb.concepts


Classes
-------

.. autoapisummary::

   medcat.cdb.concepts.CUIInfo
   medcat.cdb.concepts.NameInfo
   medcat.cdb.concepts.TypeInfo


Functions
---------

.. autoapisummary::

   medcat.cdb.concepts.get_new_cui_info
   medcat.cdb.concepts.reset_cui_training
   medcat.cdb.concepts.get_new_name_info


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

.. py:class:: CUIInfo

   Bases: :py:obj:`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)


   .. py:attribute:: cui
      :type:  str


   .. py:attribute:: preferred_name
      :type:  str


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


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


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


   .. py:attribute:: description
      :type:  Optional[str]


   .. py:attribute:: original_names
      :type:  Optional[set[str]]


   .. py:attribute:: tags
      :type:  Optional[list[str]]


   .. py:attribute:: group
      :type:  Optional[str]


   .. py:attribute:: in_other_ontology
      :type:  Optional[set[str]]


   .. py:attribute:: count_train
      :type:  int


   .. py:attribute:: context_vectors
      :type:  Optional[dict[str, numpy.ndarray]]


   .. py:attribute:: average_confidence
      :type:  float


   .. py:method:: __contains__()

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



   .. py:method:: __delattr__()

      Implement delattr(self, name).



   .. py:method:: __delitem__()

      Delete self[key].



   .. 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:: __getitem__()

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



   .. py:method:: __gt__()

      Return self>value.



   .. py:method:: __init__()

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



   .. py:method:: __ior__()

      Return self|=value.



   .. py:method:: __iter__()

      Implement iter(self).



   .. py:method:: __le__()

      Return self<=value.



   .. py:method:: __len__()

      Return len(self).



   .. 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:: __or__()

      Return self|value.



   .. py:method:: __reduce__()

      Helper for pickle.



   .. py:method:: __reduce_ex__()

      Helper for pickle.



   .. py:method:: __repr__()

      Return repr(self).



   .. py:method:: __reversed__()

      Return a reverse iterator over the dict keys.



   .. py:method:: __ror__()

      Return value|self.



   .. py:method:: __setattr__()

      Implement setattr(self, name, value).



   .. py:method:: __setitem__()

      Set self[key] to value.



   .. py:method:: __sizeof__()

      D.__sizeof__() -> size of D 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:method:: clear()

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



   .. py:method:: copy()

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



   .. py:method:: get()

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



   .. py:method:: items()

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



   .. py:method:: keys()

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



   .. py:method:: 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.



   .. py:method:: 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.



   .. py:method:: 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.



   .. py:method:: 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]



   .. py:method:: values()

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



.. py:function:: get_new_cui_info(cui, preferred_name, names = set(), subnames = set(), type_ids = set(), description = None, original_names = None, tags = None, group = None, in_other_ontology = None, count_train = 0, context_vectors = None, average_confidence = 0.0)

.. py:function:: reset_cui_training(cui_info)

.. py:class:: NameInfo

   Bases: :py:obj:`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)


   .. py:attribute:: name
      :type:  str


   .. py:attribute:: per_cui_status
      :type:  dict[str, str]


   .. py:attribute:: is_upper
      :type:  bool


   .. py:attribute:: count_train
      :type:  int


   .. py:method:: __contains__()

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



   .. py:method:: __delattr__()

      Implement delattr(self, name).



   .. py:method:: __delitem__()

      Delete self[key].



   .. 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:: __getitem__()

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



   .. py:method:: __gt__()

      Return self>value.



   .. py:method:: __init__()

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



   .. py:method:: __ior__()

      Return self|=value.



   .. py:method:: __iter__()

      Implement iter(self).



   .. py:method:: __le__()

      Return self<=value.



   .. py:method:: __len__()

      Return len(self).



   .. 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:: __or__()

      Return self|value.



   .. py:method:: __reduce__()

      Helper for pickle.



   .. py:method:: __reduce_ex__()

      Helper for pickle.



   .. py:method:: __repr__()

      Return repr(self).



   .. py:method:: __reversed__()

      Return a reverse iterator over the dict keys.



   .. py:method:: __ror__()

      Return value|self.



   .. py:method:: __setattr__()

      Implement setattr(self, name, value).



   .. py:method:: __setitem__()

      Set self[key] to value.



   .. py:method:: __sizeof__()

      D.__sizeof__() -> size of D 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:method:: clear()

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



   .. py:method:: copy()

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



   .. py:method:: get()

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



   .. py:method:: items()

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



   .. py:method:: keys()

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



   .. py:method:: 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.



   .. py:method:: 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.



   .. py:method:: 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.



   .. py:method:: 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]



   .. py:method:: values()

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



.. py:function:: get_new_name_info(name, per_cui_status = {}, is_upper = False, count_train = 0)

.. py:class:: TypeInfo

   Represents all the info regarding a type ID.


   .. py:attribute:: type_id
      :type:  str


   .. py:attribute:: name
      :type:  str


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