Assert that tables exist in a cdm object — assert

A cdm object is a list of references to a subset of tables in the OMOP Common Data Model. If you write a function that accepts a cdm object as a parameter assert_tables/assertTables will help you check that the tables you need are in the cdm object, have the correct columns/fields, and (optionally) are not empty.

Usage

assert_tables(cdm, tables, empty.ok = FALSE, add = NULL)

assertTables(cdm, tables, empty.ok = FALSE, add = NULL)

Arguments

cdm: A cdm object
tables: A character vector of table names to check.
empty.ok: Should an empty table (0 rows) be considered an error? TRUE or FALSE (default)
add: An optional AssertCollection created by checkmate::makeAssertCollection() that errors should be added to.

Value

Invisibly returns the cdm object

Examples

if (FALSE) { # \dontrun{
# Use assertTables inside a function to check that tables exist
countDrugsByGender <- function(cdm) {
  assertTables(cdm, tables = c("person", "drug_era"), empty.ok = FALSE)

  cdm$person %>%
    dplyr::inner_join(cdm$drug_era, by = "person_id") %>%
    dplyr::count(.data$gender_concept_id, .data$drug_concept_id) %>%
    dplyr::collect()
}

library(CDMConnector)
con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
cdm <- cdm_from_con(con)

countDrugsByGender(cdm)

DBI::dbDisconnect(con, shutdown = TRUE)

} # }