initialize_annotations: Initialize Annotations Deletes all NLP annotations and...

In simon-hans/CEDARS: Simple and Efficient Pipeline for Electronic Health Record Annotation

Initialize Annotations Deletes all NLP annotations and patient-specific information, including clinical event dates.New, empty 'ANNOTATIONS' and 'PATIENTS' collections are created. Dictionaries and original patient notes are preserved.

Description

Initialize Annotations Deletes all NLP annotations and patient-specific information, including clinical event dates.New, empty 'ANNOTATIONS' and 'PATIENTS' collections are created. Dictionaries and original patient notes are preserved.

Usage

initialize_annotations(
  uri_fun,
  user,
  password,
  host,
  replica_set,
  port,
  database,
  override = FALSE
)

Arguments

uri_fun	Uniform resource identifier (URI) string generating function for MongoDB credentials.
user	MongoDB user name.
password	MongoDB user password.
host	MongoDB host server.
replica_set	MongoDB replica set, if indicated.
port	MongoDB port.
database	MongoDB database name.
override	Override safety checks, move directly to initialization!

Value

Confirmation that requested operation was completed, or error message if attempt failed.

Examples

## Not run: 
initialize_annotations(uri_fun = mongo_uri_standard, user = 'John', password = 'db_password_1234',
host = 'server1234', port = NA, database = 'TEST_PROJECT')

## End(Not run)

simon-hans/CEDARS documentation built on Feb. 14, 2024, 3:16 a.m.