get_wrapper: Wrap the get_data() Function

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

Wrap the get_data() Function

Description

Obtain one sentence and related info from MongoDB. Uses DB credentials pre-loaded in the main environment. For use with Shiny or REST GET (latter yet to be implemented).

Usage

get_wrapper(
  database,
  end_user,
  end_user_password,
  html = TRUE,
  position,
  patient_id = NA,
  ldap = FALSE
)

Arguments

database	MongoDB database.
end_user	CEDARS end user name..
end_user_password	CEDARS end user password.
html	Should output keywords/concepts be highlighted with HTML markup? Default is TRUE.
position	Sentence position within the sequence of selected sentences for a given patient.
patient_id	Used if a specific patient record is requested, instead of a search for next record to annotate.
ldap	Is LDAP authentication being used? If so, password will not be checked and access will be granted automatically.

Value

A list with patient-specific information and a dataframe with selected sentences along with sentence-specific data.

Examples

## Not run: 
get_wrapper(database = 'TEST_PROJECT', end_user = 'John', end_user_password = 'db_password_1234',
html = TRUE, position = NA)

## End(Not run)

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