batch_upload_notes: Upload Notes for Multiple Patients to Database

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

Upload Notes for Multiple Patients to Database

Description

Allows user to populate notes in database from dataframe. Notes dataframe must contain: 'patient_id', 'text_id' (a unique identifier for each text segment), along with 'text', 'text_date', 'doc_id' (designates unique EHR document) and ideally 'text_sequence' which indicates order of text section within document. 'doc_section_name' along 'text_tag_1' to 'text_tag_10' are optional. 'text_date' must be in format '%Y-%m-%d'!.

Usage

batch_upload_notes(
  uri_fun,
  user,
  password,
  host,
  replica_set,
  port,
  database,
  notes
)

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.
notes	Dataframe of EHR documents with metadata. The documents can consist of full notes or note subsections.

Value

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

Examples

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

## End(Not run)

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