# Store all input data as a list ------------------------------------------------ source_data <- list( ds = datacutr_ds, dm = datacutr_dm, ae = datacutr_ae, sc = datacutr_sc, lb = datacutr_lb, ts = datacutr_ts ) # Create dcut dataset ---------------------------------------------------------- dcut <- tibble::tribble( ~USUBJID, ~DCUTDTC, ~DCUTDTM, ~DCUTDESC, "AB12345-001", "2022-06-04", as.POSIXct("2022-06-04 23:59:59"), "Clinical Cutoff Date", "AB12345-002", "2022-06-04", as.POSIXct("2022-06-04 23:59:59"), "Clinical Cutoff Date", "AB12345-003", "2022-06-04", as.POSIXct("2022-06-04 23:59:59"), "Clinical Cutoff Date", "AB12345-004", "2022-06-04", as.POSIXct("2022-06-04 23:59:59"), "Clinical Cutoff Date", ) # Expected final data --------- ------------------------------------------------ ds_cut <- tibble::tribble( ~USUBJID, ~DSDECOD, ~DSSTDTC, "AB12345-001", "RANDOMIZATION", "2022-06-01", "AB12345-002", "RANDOMIZATION", "2022-06-02", "AB12345-003", "RANDOMIZATION", "2022-06-03", "AB12345-004", "RANDOMIZATION", "2022-06-04", ) dm_cut <- tibble::tribble( ~USUBJID, ~DTHFL, ~DTHDTC, "AB12345-001", "Y", "2022-06-01", "AB12345-002", "", "", "AB12345-003", "", "", "AB12345-004", "", "", ) ae_cut <- tibble::tribble( ~USUBJID, ~AETERM, ~AESTDTC, "AB12345-001", "AE1", "2022-06-01", "AB12345-004", "AE4", "2022-05-04", ) sc_cut <- tibble::tribble( ~USUBJID, ~SCORRES, "AB12345-001", "A", "AB12345-002", "B", "AB12345-003", "C", "AB12345-004", "D", ) lb_cut <- tibble::tribble( ~USUBJID, ~LBORRES, ~LBDTC, "AB12345-001", 1, "2022-06-01", "AB12345-004", 4, "2022-05-04", ) ts_cut <- tibble::tribble( ~USUBJID, ~TSVAL, "AB12345-001", 1, "AB12345-002", 2, "AB12345-003", 3, "AB12345-004", 4, "AB12345-005", 5, ) # Store all expected data as a list expected <- list( dcut = dcut, dm = dm_cut, sc = sc_cut, ds = ds_cut, ae = ae_cut, lb = lb_cut, ts = ts_cut ) # Test that every type of datacut gives the expected result, when special_dm=TRUE ----------- test_that("Test that every type of datacut gives the expected result, when special_dm=TRUE", { expect_equal( process_cut( source_sdtm_data = source_data, patient_cut_v = c("sc", "ds"), date_cut_m = rbind( c("ae", "AESTDTC"), c("lb", "LBDTC") ), no_cut_v = c("ts"), dataset_cut = dcut, cut_var = DCUTDTM, special_dm = TRUE ), expected ) }) # Test that process_cut() errors when a source SDTM dataset is not referenced # in any input list test_that("Test that process_cut() errors when a source SDTM dataset is not referenced in any input list", { expect_error( process_cut( source_sdtm_data = source_data, patient_cut_v = c("ds"), date_cut_m = rbind( c("ae", "AESTDTC"), c("lb", "LBDTC") ), no_cut_v = c("ts"), dataset_cut = dcut, cut_var = DCUTDTM, special_dm = TRUE ), regexp = "sc exists in source_sdtm_data but no cut method has been assigned" ) }) # Test that process_cut() errors when an input list includes a source SDTMv # dataset that does not exist test_that("Test that process_cut() errors when an input list includes a source SDTMv dataset that does not exist in the source SDTMv data", { expect_error( process_cut( source_sdtm_data = source_data, patient_cut_v = c("sc", "ds", "vs"), date_cut_m = rbind( c("ae", "AESTDTC"), c("lb", "LBDTC") ), no_cut_v = c("ts"), dataset_cut = dcut, cut_var = DCUTDTM, special_dm = TRUE ), regexp = "Cut types have been assigned for vs which does not exist in source_sdtm_data" ) }) # Test that process_cut() errors when a source SDTMv dataset is referenced in # more than one input list test_that("Test that process_cut() errors when a source SDTMv dataset is referenced in more than one input list", { expect_error( process_cut( source_sdtm_data = source_data, patient_cut_v = c("sc", "ds", "ae"), date_cut_m = rbind( c("ae", "AESTDTC"), c("lb", "LBDTC") ), no_cut_v = c("ts"), dataset_cut = dcut, cut_var = DCUTDTM, special_dm = TRUE ), regexp = "Multiple cut types have been assigned for ae" ) }) # Test that process_cut() errors when special_dm = TRUE and dm is also referenced # in an input list test_that("Test that process_cut() errors when special_dm = TRUE and dm is also referenced in an input list", { expect_error( process_cut( source_sdtm_data = source_data, patient_cut_v = c("sc", "ds", "dm"), date_cut_m = rbind( c("ae", "AESTDTC"), c("lb", "LBDTC") ), no_cut_v = c("ts"), dataset_cut = dcut, cut_var = DCUTDTM, special_dm = TRUE ), regexp = "Multiple cut types have been assigned for dm" ) }) # Test Read-out file ------------- # Test that read-out file is ran successfully when special_dm = TRUE test_that("Test that Correct .Rmd file is ran successfully when read_out = TRUE", { process_cut( source_sdtm_data = source_data, patient_cut_v = c("sc", "ds"), date_cut_m = rbind( c("ae", "AESTDTC"), c("lb", "LBDTC") ), no_cut_v = c("ts"), dataset_cut = dcut, cut_var = DCUTDTM, special_dm = TRUE, read_out = TRUE, out_path = "~/dummyfile" ) expect_true(dir.exists("~/dummyfile") & (length(list.files("~/dummyfile")) > 0)) unlink("~/dummyfile", recursive = TRUE) }) # Test that every type of datacut gives the expected result, when special_dm=FALSE ----------- # Remove dm from the source data list and expected data list source_data["dm"] <- NULL expected["dm"] <- NULL test_that("Test that every type of datacut gives the expected result, when special_dm=FALSE", { expect_equal( process_cut( source_sdtm_data = source_data, patient_cut_v = c("sc", "ds"), date_cut_m = rbind( c("ae", "AESTDTC"), c("lb", "LBDTC") ), no_cut_v = c("ts"), dataset_cut = dcut, cut_var = DCUTDTM, special_dm = FALSE ), expected ) }) # Test that Read-out file is ran successfully when special_dm = FALSE test_that("Test that Correct .Rmd file is ran successfully when read_out = TRUE", { process_cut( source_sdtm_data = source_data, patient_cut_v = c("sc", "ds"), date_cut_m = rbind( c("ae", "AESTDTC"), c("lb", "LBDTC") ), no_cut_v = c("ts"), dataset_cut = dcut, cut_var = DCUTDTM, special_dm = FALSE, read_out = TRUE, out_path = "~/dummyfile" ) expect_true(dir.exists("~/dummyfile") & (length(list.files("~/dummyfile")) > 0)) unlink("~/dummyfile", recursive = TRUE) })