prepare_cdm <- function(con, write_schema) { # eunomia cdm eunomia_con <- DBI::dbConnect(duckdb::duckdb(eunomiaDir())) eunomia_cdm <- cdmFromCon(eunomia_con, cdmName = "eunomia", cdmSchema = "main", writeSchema = "main") %>% cdmSelect("person", "observation_period") cdm <- copyCdmTo(con = con, cdm = eunomia_cdm, schema = write_schema, overwrite = TRUE) DBI::dbDisconnect(eunomia_con, shutdown = TRUE) return(cdm) } check_counts <- function(cdm) { nm <- cdm$person %>% dplyr::count() %>% dplyr::collect() %>% colnames() expect_true("n" %in% nm) nm <- cdm$person %>% dplyr::group_by(.data$gender_concept_id, .data$month_of_birth) %>% dplyr::count() %>% dplyr::collect() %>% colnames() expect_true(all(c("gender_concept_id", "month_of_birth", "n") %in% nm)) } check_mutate <- function(cdm) { expect_true(unique(cdm$person %>% dplyr::mutate(new_var = 1L) %>% dplyr::pull("new_var")) == 1L) expect_true(unique(cdm$person %>% dplyr::mutate(new_var = 1.55) %>% dplyr::pull("new_var")) == 1.55) expect_true(all(c("F","M") %in% unique(cdm$person %>% dplyr::mutate(new_var = dplyr::if_else(gender_concept_id == 8532, "F", "M")) %>% dplyr::pull("new_var")))) expect_no_error(cdm$observation_period %>% dplyr::mutate(observation_period_start_date = as.Date(observation_period_start_date), new_date = as.Date("2000-01-01"), missing_date = as.Date(NA))) expect_no_error({ cdm$person %>% dplyr::mutate(gender_concept_id = as.integer(gender_concept_id)) }) # expect_no_error(cdm$person %>% # dplyr::mutate(year_1 = as.integer(1990), # month_1 = as.integer(01), # day_1 = as.integer(01)) %>% # dplyr::mutate(date_1=!!asDate(paste0( # year_1, "/", month_1, "/", day_1))) %>% # dplyr::select(date_1)) } check_summarise_dplyr <- function(cdm) { expect_true(all(c("min", "mean", "max") %in% colnames(cdm$person %>% dplyr::summarise(min = min(year_of_birth, na.rm = TRUE), mean = mean(year_of_birth, na.rm = TRUE), max = max(year_of_birth, na.rm = TRUE), .groups = "drop") %>% dplyr::collect()))) nms <- cdm$person %>% dplyr::group_by(gender_concept_id, month_of_birth) %>% dplyr::summarise(min = min(year_of_birth, na.rm = TRUE), mean = mean(year_of_birth, na.rm = TRUE), max = max(year_of_birth, na.rm = TRUE), .groups = "drop") %>% dplyr::ungroup() %>% dplyr::collect() %>% colnames() expect_true(all(c("gender_concept_id", "month_of_birth", "min", "mean", "max") %in% nms)) } check_summarise_quantiles <- function(cdm){ expect_true(all(c("p0_quant","p20_quant","p40_quant","p50_quant", "p60_quant","p80_quant","p100_quant") %in% colnames( cdm$person %>% summariseQuantile(year_of_birth, probs = c(0, 0.2, 0.4, 0.5, 0.6, 0.8, 1), nameSuffix = "quant") %>% dplyr::collect()))) expect_true(all(c("gender_concept_id", "month_of_birth", "p0_quant","p20_quant","p40_quant","p50_quant", "p60_quant","p80_quant","p100_quant") %in% colnames( cdm$person %>% dplyr::group_by(gender_concept_id, month_of_birth) %>% summariseQuantile(year_of_birth, probs = c(0, 0.2, 0.4, 0.5, 0.6, 0.8, 1), nameSuffix = "quant") %>% dplyr::collect()))) } check_joins <- function(cdm){ expect_no_error(cdm$person %>% dplyr::left_join(cdm$observation_period, by = "person_id" )) expect_no_error(cdm$person %>% dplyr::inner_join(cdm$observation_period, by = "person_id")) expect_no_error( cdm$person %>% dplyr::full_join(cdm$observation_period, by = "person_id")) expect_no_error(cdm$person %>% dplyr::anti_join(cdm$observation_period, by = "person_id")) } check_dates <- function(cdm){ d1 <- cdm$observation_period %>% dplyr::mutate(date_var = !!dateadd("observation_period_start_date", 1, interval = "year" )) %>% dplyr::pull("date_var") expect_true(inherits(d1, c("Date", "POSIXt"))) d2 <- cdm$observation_period %>% dplyr::mutate(date_var = !!dateadd("observation_period_start_date", 1, interval = "day" )) %>% dplyr::pull("date_var") expect_true(inherits(d2, c("Date", "POSIXt"))) d3 <- cdm$observation_period %>% dplyr::mutate(date_var = !!datediff("observation_period_start_date", "observation_period_end_date" )) %>% dplyr::pull("date_var") expect_true(is.integer(d3) || is.numeric(d3)) d4 <- cdm$observation_period %>% dplyr::mutate(year = !!datepart("observation_period_start_date", "year"), month = !!datepart("observation_period_start_date", "month"), day = !!datepart("observation_period_start_date", "day")) %>% dplyr::collect() expect_true(is.integer(d4$year) || is.numeric(d3)) expect_true(is.integer(d4$month) || is.numeric(d3)) expect_true(is.integer(d4$day) || is.numeric(d3)) } check_row_number <- function(cdm){ expect_no_error(cdm$person %>% dplyr::filter(row_number() == 1)) expect_no_error(cdm$person %>% dplyr::group_by(person_id) %>% dplyr::filter(row_number() == 1)) expect_no_error(cdm$observation_period %>% dbplyr::window_order(observation_period_start_date) %>% dplyr::filter(row_number() == 1)) expect_no_error(cdm$observation_period %>% dplyr::group_by(person_id) %>% dbplyr::window_order(observation_period_start_date) %>% dplyr::filter(row_number() == 1)) } checks <- list() for (dbtype in dbToTest) { if (dbtype == "bigquery") next test_that(glue::glue("{dbtype} - checking common usage"), { if (dbtype != "duckdb") skip_on_cran() else skip_if_not_installed("duckdb") con <- get_connection(dbtype) cdm_schema <- get_cdm_schema(dbtype) write_prefix <- paste0("test", as.integer(Sys.time()), "_") write_schema <- get_write_schema(dbtype, prefix = write_prefix) skip_if(any(write_schema == "") || any(cdm_schema == "") || is.null(con)) skip_if_not_installed("duckdb") # prepare_cdm require duckdb cdm <- prepare_cdm(con, write_schema) check_counts(cdm) check_mutate(cdm) check_summarise_dplyr(cdm) check_summarise_quantiles(cdm) check_joins(cdm) check_dates(cdm) check_row_number(cdm) checks[[dbtype]] <<- dplyr::tibble(dbtype = dbtype, "dplyr::count" = 1, "dplyr::tally" = 1, "dplyr::mutate(as.integer(x))" = 1, "dplyr::mutate(as.Date(x))" = 1, # "CDMConnector::asDate" = 0, "dplyr::if_else" = 1, "dplyr::summaise(min(x))" = 1, "dplyr::summaise(mean(x))" = 1, "dplyr::summaise(max(x))" = 1, "CDMConnector::summariseQuantile" = 1, "dplyr::left_join" = 1, "dplyr::right_join" = 1, "dplyr::inner_join" = 1, "dplyr::anti_join" = 1, "CDMConnector::dateadd" = 0, "CDMConnector::datediff" = 0, "CDMConnector::datepart" = 0, "dplyr::row_number" = 1) rm(cdm) # clean up cdm <- cdmFromCon(con, cdmName = "test", cdmSchema = cdm_schema, writeSchema = write_schema) expect_s3_class(cdm, "cdm_reference") dropTable(cdm, dplyr::contains(write_prefix)) disconnect(con) }) } # checks <- dplyr::bind_rows(checks) # plot_levels <- rev(colnames(checks)) # plot <- checks %>% # tidyr::pivot_longer( # cols = !dbtype, # names_to = "check", # values_to = "value", # cols_vary = 'slowest', # ) %>% # dplyr::mutate(check=factor(check, # levels = plot_levels)) %>% # ggplot2::ggplot(ggplot2::aes(x = dbtype, # y = check, # fill = as.character(value))) + # ggplot2::geom_tile(colour="grey", alpha=0.8, width=1) + # ggplot2::xlab(label = "Sample")+ # ggplot2::theme_bw() + # ggplot2::theme(legend.position="none") + # ggplot2::scale_x_discrete(expand=c(0,0))+ # ggplot2::scale_y_discrete(expand=c(0,0)) + # ggplot2::scale_fill_manual(values = c("red", "green"))+ # ggplot2::xlab("DBMS")+ # ggplot2::ylab("")+ # ggplot2::ggtitle("Analytic functionality checked in continuous integration") # ggplot2::ggsave("dbms_coverage/tests.png", plot)