save_query: Save Search Query

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

Save Search Query

Description

Saves the search query. The query consists of keywords/UMLS concept unique identifiers (CUI's), boolean elements and other operators ('AND', 'OR', '!', '(', or ')').

Usage

save_query(
  uri_fun,
  user,
  password,
  host,
  replica_set,
  port,
  database,
  search_query,
  use_negation,
  hide_duplicates,
  skip_after_event,
  tag_query = NA,
  date_min = NA,
  date_max = NA
)

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.
search_query	Medical corpus query containg keywords/CUI's, boolean elements and other operators ('AND', 'OR', '!', '(', or ')').
use_negation	Should negated items be ignored in the keyword/concept search?
hide_duplicates	Should duplicated sentences be removed for search results?
skip_after_event	Should sentences occurring after recorded clinical event be skipped?
tag_query	List with 2 sublists, namely "include" and "exclude", indicating matching strings for metadata tag parameters.
date_min	Minimum date for NLP processing and text search.
date_max	Maximum date for NLP processing and text search.

Value

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

Examples

## Not run: 
save_query(uri_fun = mongo_uri_standard, user = 'John', password = 'db_password_1234',
host = 'server1234', port = NA, database = 'TEST_PROJECT', search_query = 'thrombosis AND venous',
use_negation = TRUE, hide_duplicates = TRUE, skip_after_event = TRUE,
tag_query = list(exact = FALSE, nlp_apply = FALSE, include = list(text_tag_1 = c("admission"),
text_tag_2 = c("impression", "plan")), exclude = NA))

## End(Not run)

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