api.utils

Module Contents

Classes

RemoteEntity

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

RemoteSpacyDoc

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

SimpleFilters

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

Functions

call_remote_model_service(service_url, text)

Call the remote MedCAT service API to process text.

remove_annotations(document, project[, partial])

add_annotations(spacy_doc, user, project, document, ...)

Add annotations from spacy_doc to the database.

clear_cdb_cnf_addons(cdb, cdb_id)

get_create_cdb_infos(cdb, concept, cui, cui_info_prop, ...)

create_annotation(source_val, ...)

train_medcat(cat, project, document)

prep_docs(project_id, doc_ids, user_id)

save_project_anno(sender, instance, **kwargs)

env_str_to_bool(var, default)

Attributes

logger

api.utils.logger
class api.utils.RemoteEntity(entity_data, text)

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

__init__(entity_data, text)
get_addon_data(key)

Mimic get_addon_data for meta_cat_meta_anns.

class api.utils.RemoteSpacyDoc(linked_ents)

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

__init__(linked_ents)
api.utils.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

api.utils.remove_annotations(document, project, partial=False)
class api.utils.SimpleFilters(cuis=None, cuis_exclude=None)

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

__init__(cuis=None, cuis_exclude=None)
api.utils.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)

api.utils.clear_cdb_cnf_addons(cdb, cdb_id)
Parameters:

  • cdb (medcat.cdb.CDB) –

  • cdb_id (str | int) –

api.utils.get_create_cdb_infos(cdb, concept, cui, cui_info_prop, code_prop, desc_prop, model_clazz)
api.utils.create_annotation(source_val, selection_occurrence_index, cui, user, project, document)
Parameters:
api.utils.train_medcat(cat, project, document)
api.utils.prep_docs(project_id, doc_ids, user_id)
Parameters:

  • project_id (List[int]) –

  • doc_ids (List[int]) –

  • user_id (int) –

api.utils.save_project_anno(sender, instance, **kwargs)
api.utils.env_str_to_bool(var, default)
Parameters:

  • var (str) –

  • default (bool) –