upload_notes: Upload Notes to Database

In CEDARS: Simple and Efficient Pipeline for Electronic Health Record Annotation

Description

Allows user to populate notes in database from dataframe; could be easily inserted into wrapper batch function to serially download from other DB etc. 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

upload_notes(uri_fun, user, password, host, 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.
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)

CEDARS documentation built on Feb. 7, 2021, 5:06 p.m.