pre_search: Execute Search on a Set of Records

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

Execute Search on a Set of Records

Description

Batches a keyword/CUI search for a cohort of patients. Useful to speed up the process by end users, since search results will be pre-populated. Locks each record before proceeding with search on existing NLP annotations. Patient records with no matching sentences or a known event date at or before the earliest matching sentence will be marked as reviewed. The latter assumes the query orders to skip sentences after events.

Usage

pre_search(
  patient_vect = NA,
  uri_fun,
  user,
  password,
  host,
  replica_set,
  port,
  database
)

Arguments

patient_vect	Vector of patient ID's. Default is NA, in which case all unlocked records will be searched.
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.

Value

No return value, called to execute a query in the database.

Examples

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

## End(Not run)

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