test_that("check working example with defaults", { db <- mockDrugExposure() cdmCheck <- inherits(db, "cdm_reference") expect_true(cdmCheck) expect_true(nrow(db$drug_exposure %>% dplyr::collect()) >= 1) expect_true(nrow(db$concept %>% dplyr::collect()) >= 1) expect_true(nrow(db$concept_ancestor %>% dplyr::collect()) >= 1) expect_true(nrow(db$drug_strength %>% dplyr::collect()) >= 1) ancestor_conceptDbNames <- c( "ancestor_concept_id", "descendant_concept_id", "min_levels_of_separation", "max_levels_of_separation" ) ancestor_conceptNamesCheck <- all(ancestor_conceptDbNames %in% names(db$concept_ancestor %>% utils::head(1) %>% dplyr::collect() %>% dplyr::rename_with(tolower))) drugstrengthNames <- c( "drug_concept_id", "ingredient_concept_id", "amount_value", "amount_unit_concept_id", "numerator_value", "numerator_unit_concept_id", "denominator_value", "denominator_unit_concept_id", "valid_start_date", "valid_end_date", "invalid_reason" ) drugstrengthNamesCheck <- all(drugstrengthNames %in% names(db$drug_strength %>% utils::head(1) %>% dplyr::collect() %>% dplyr::rename_with(tolower))) expect_true(drugstrengthNamesCheck) conceptNames <- c( "concept_id", "concept_name", "domain_id", "vocabulary_id", "concept_class_id", "standard_concept", "concept_code", "valid_start_date", "valid_end_date", "invalid_reason" ) conceptNamesCheck <- all(conceptNames %in% names(db$concept %>% utils::head(1) %>% dplyr::collect() %>% dplyr::rename_with(tolower))) expect_true(conceptNamesCheck) drug_exposureNames <- c( "drug_exposure_id", "person_id", "drug_concept_id", "drug_exposure_start_date", "drug_exposure_end_date", "drug_type_concept_id ", "stop_reason", "refills", "quantity", "days_supply", "sig", "route_concept_id", "lot_number", "provider_id", "visit_occurrence_id", "drug_source_value", "drug_source_concept_id", "route_source_value", "dose_unit_source_value" ) drug_exposureNamesCheck <- all(drug_exposureNames %in% names(db$drug_exposure %>% utils::head(1) %>% dplyr::collect() %>% dplyr::rename_with(tolower))) expect_true(conceptNamesCheck) DBI::dbDisconnect(attr(db, "dbcon"), shutdown = TRUE) }) test_that("check working example with drug_strength", { drug_strength <- tibble::tibble( drug_concept_id = "1", ingredient_concept_id = "1", valid_start_date = c( as.Date("2010-02-05") ), valid_end_date = c( as.Date("2010-02-05") ) ) db <- mockDrugExposure(drug_strength = drug_strength) expect_true(nrow(db$drug_strength %>% dplyr::collect()) == 1) drug_strengthDbNames <- c( "drug_concept_id", "ingredient_concept_id", "ingredient_concept_id", "valid_start_date" ) drug_strengthCheck <- all(drug_strengthDbNames %in% names(db$drug_strength %>% utils::head(1) %>% dplyr::collect() %>% dplyr::rename_with(tolower))) expect_true(drug_strengthCheck) DBI::dbDisconnect(attr(db, "dbcon"), shutdown = TRUE) }) test_that("check working example with drug drug_exposure", { drug_exposure <- tibble::tibble( drug_exposure_id = "1", person_id = c("1"), drug_concept_id = c("1"), drug_type_concept_id = c("1"), drug_exposure_start_date = c( as.Date("2010-02-05") ), drug_exposure_end_date = c( as.Date("2010-02-05") ) ) db <- mockDrugExposure(drug_exposure = drug_exposure) expect_true(nrow(db$drug_exposure %>% dplyr::collect()) == 1) drug_exposureDbNames <- c( "drug_exposure_id", "drug_exposure_start_date", "drug_exposure_end_date" ) drug_exposureCheck <- all(drug_exposureDbNames %in% names(db$drug_exposure %>% utils::head(1) %>% dplyr::collect() %>% dplyr::rename_with(tolower))) expect_true(drug_exposureCheck) DBI::dbDisconnect(attr(db, "dbcon"), shutdown = TRUE) }) test_that("check working example with drug_exposure options", { db <- mockDrugExposure(drug_exposure_size = 1, patient_size = 1) expect_true(nrow(db$drug_exposure %>% dplyr::collect()) == 1) DBI::dbDisconnect(attr(db, "dbcon"), shutdown = TRUE) db <- mockDrugExposure(drug_exposure_size = 2, patient_size = 1) expect_true(nrow(db$drug_exposure %>% dplyr::collect()) == 2) DBI::dbDisconnect(attr(db, "dbcon"), shutdown = TRUE) }) test_that("check working example with drug_strength default options", { db <- mockDrugExposure( drug_exposure_size = 20, patient_size = 10, amount_val = c(100, 200), denom_unit = NA, num_unit = NA ) expect_true(nrow(db$drug_strength %>% dplyr::select("amount_value") %>% dplyr::distinct() %>% dplyr::collect()) == 2) expect_true(nrow(db$drug_strength %>% dplyr::select("denominator_value") %>% dplyr::distinct() %>% dplyr::collect()) == 1) expect_true(nrow(db$drug_strength %>% dplyr::select("numerator_value") %>% dplyr::distinct() %>% dplyr::collect()) == 1) DBI::dbDisconnect(attr(db, "dbcon"), shutdown = TRUE) }) test_that("check working example with drug_strength num_denom only", { db <- mockDrugExposure(amount_val = NA, amount_unit = NA) expect_true(nrow(db$drug_strength %>% dplyr::select("amount_value") %>% dplyr::distinct() %>% dplyr::collect()) == 1) expect_true(nrow(db$drug_strength %>% dplyr::select("denominator_value") %>% dplyr::distinct() %>% dplyr::collect()) == 1) expect_true(nrow(db$drug_strength %>% dplyr::select("numerator_value") %>% dplyr::distinct() %>% dplyr::collect()) == 1) DBI::dbDisconnect(attr(db, "dbcon"), shutdown = TRUE) }) test_that("check expected errors", { testthat::expect_error( mockDrugExposure(drug_exposure_size = "x") ) testthat::expect_error( mockDrugExposure(patient_size = "x") ) testthat::expect_error( mockDrugExposure(den_val = "x") ) testthat::expect_error( mockDrugExposure(patient_size = -1) ) })