:py:mod:`api.utils`
===================

.. py:module:: api.utils


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

Classes
~~~~~~~

.. autoapisummary::

   api.utils.RemoteEntity
   api.utils.RemoteSpacyDoc
   api.utils.SimpleFilters



Functions
~~~~~~~~~

.. autoapisummary::

   api.utils.call_remote_model_service
   api.utils.remove_annotations
   api.utils.add_annotations
   api.utils.clear_cdb_cnf_addons
   api.utils.get_create_cdb_infos
   api.utils.create_annotation
   api.utils.train_medcat
   api.utils.prep_docs
   api.utils.save_project_anno
   api.utils.env_str_to_bool



Attributes
~~~~~~~~~~

.. autoapisummary::

   api.utils.logger


.. py:data:: logger

   

.. py:class:: RemoteEntity(entity_data, text)


   A simple class to mimic spaCy entity structure for remote API responses.

   .. py:method:: __init__(entity_data, text)


   .. py:method:: get_addon_data(key)

      Mimic get_addon_data for meta_cat_meta_anns.



.. py:class:: RemoteSpacyDoc(linked_ents)


   A simple class to mimic spaCy document structure for remote API responses.

   .. py:method:: __init__(linked_ents)



.. py:function:: call_remote_model_service(service_url, text)

   Call the remote MedCAT service API to process text.

   Args:
       service_url: Base URL of the remote service (e.g., http://medcat-service:8000)
       text: Text to process

   Returns:
       RemoteSpacyDoc object with linked_ents


.. py:function:: remove_annotations(document, project, partial=False)


.. py:class:: SimpleFilters(cuis=None, cuis_exclude=None)


   Simple filter object for remote service when cat is not available.

   .. py:method:: __init__(cuis=None, cuis_exclude=None)



.. py:function:: add_annotations(spacy_doc, user, project, document, existing_annotations, cat=None, filters=None, similarity_threshold=0.3)

   Add annotations from spacy_doc to the database.

   Args:
       spacy_doc: spaCy document with linked_ents or RemoteSpacyDoc
       user: User object
       project: ProjectAnnotateEntities object
       document: Document object
       existing_annotations: List of existing AnnotatedEntity objects
       cat: CAT object (optional, required if filters not provided)
       filters: SimpleFilters object (optional, used when cat is None)
       similarity_threshold: float (optional, default 0.3, used when cat is None)


.. py:function:: clear_cdb_cnf_addons(cdb, cdb_id)


.. py:function:: get_create_cdb_infos(cdb, concept, cui, cui_info_prop, code_prop, desc_prop, model_clazz)


.. py:function:: create_annotation(source_val, selection_occurrence_index, cui, user, project, document)


.. py:function:: train_medcat(cat, project, document)


.. py:function:: prep_docs(project_id, doc_ids, user_id)


.. py:function:: save_project_anno(sender, instance, **kwargs)


.. py:function:: env_str_to_bool(var, default)