tests/testthat/test-readCohortSet.R

In CDMConnector: Connect to an OMOP Common Data Model

test_that("From csv camelCase", {
  pathCsv <- system.file(package = "CDMConnector", "cohorts1")
  data <- readCohortSet(pathCsv)

  expect_in(
    data$cohort_definition_id,
    c(1, 2)
  )

  expect_in(
    data$cohort_name,
    c("cerebral_venous_sinus_thrombosis_01", "deep_vein_thrombosis_01")
  )

  expect_identical(nrow(data), 2L)
  expect_identical(ncol(data), 5L)
})

test_that("From csv snake_case", {
  pathCsv <- system.file(package = "CDMConnector", "cohorts1")
  data <- readCohortSet(pathCsv)

  expect_in(
    data$cohort_definition_id,
    c(1, 2)
  )

  expect_in(
    data$cohort_name,
    c("cerebral_venous_sinus_thrombosis_01", "deep_vein_thrombosis_01")
  )

  expect_identical(nrow(data), 2L)
  expect_identical(ncol(data), 5L)
})

test_that("From json camelCase", {
  pathJson <- system.file(package = "CDMConnector", "cohorts2")
  data <- readCohortSet(pathJson)

  expect_in(
    data$cohort_definition_id,
    c(1L, 2L, 3L)
  )

  # Unsure what dictates the order
  # expect_equal(
  #   sort(data$cohort_name),
  #   sort(c("cerebralVenousSinusThrombosis01", "deepVeinThrombosis01", "GIBleed_male"))
  # )

  expect_equal(
    sort(data$cohort_name_snakecase),
    sort(c("cerebral_venous_sinus_thrombosis_01", "deep_vein_thrombosis_01", "gibleed_male"))
  )

  expect_identical(nrow(data), 3L)
  expect_identical(ncol(data), 5L)
})

test_that("From json snake_case", {
  pathJson <- system.file(package = "CDMConnector", "cohorts2")
  data <- readCohortSet(pathJson)

  expect_in(
    data$cohort_definition_id,
    c(1L, 2L, 3L)
  )

  # expect_in(
  #   data$cohort_name,
  #   c("cerebralVenousSinusThrombosis1", "deepVeinThrombosis1", "GIBleed_male")
  # )

  expect_identical(nrow(data), 3L)
  expect_identical(ncol(data), 5L)
})


test_that("cohort json file names with numbers", {
  df <- readCohortSet(system.file("cohorts4", package = "CDMConnector"))
  expect_equal(df$cohort_definition_id, 100)
  expect_equal(df$cohort_name, "cohort_100")
})