tests/testthat/test-codelistDiagnostics.R

In PhenotypeR: Assess Study Cohorts Using a Common Data Model

test_that("missing codelist attribute", {
  skip_on_cran()

  testthat::skip_on_cran()
  cdm_local <- omock::mockCdmReference() |>
    omock::mockPerson(nPerson = 100) |>
    omock::mockObservationPeriod() |>
    omock::mockConditionOccurrence() |>
    omock::mockDrugExposure() |>
    omock::mockCohort(name = "my_cohort_1")  |>
    omock::mockCohort(name = "my_cohort_2", numberCohorts = 2)

  db <- DBI::dbConnect(duckdb::duckdb())
  cdm <- CDMConnector::copyCdmTo(con = db, cdm = cdm_local,
                                 schema ="main", overwrite = TRUE)
  attr(cdm, "write_schema") <- "results"

  # Codelist empty
  expect_warning(result <- cdm$my_cohort_1 |>
                   codelistDiagnostics())
  expect_true("summarised_result" %in% class(result))
  expect_identical(result, omopgenerics::emptySummarisedResult())

  # No cohort codelist attribute
  attr(cdm$my_cohort_1, "cohort_codelist") <- NULL
  expect_warning(result <- cdm$my_cohort_1 |>
                   codelistDiagnostics())
  expect_true("summarised_result" %in% class(result))
  expect_identical(result, omopgenerics::emptySummarisedResult())

  # Empty cohorts
  cdm[["my_cohort_2"]] <- cdm[["my_cohort_2"]] |>
    addCodelistAttribute(codelist = list("a" = c(1L,2L)),
                         cohortName = "cohort_1") |>
    addCodelistAttribute(codelist = list("b" = c(1L,2L)),
                         cohortName = "cohort_2")

  cdm$my_cohort_2 <- cdm$my_cohort_2 |>
    CohortConstructor::requireAge(ageRange = c(201,201),
                                  name = "my_cohort_2",
                                  cohortId = c(1))
  expect_no_error(cdm$my_cohort_2 |> codelistDiagnostics())

  CDMConnector::cdmDisconnect(cdm = cdm)
})

test_that("duplicated codelists", {
  skip_on_cran()
  cdm <- omock::mockCdmFromTables(tables = list(
    cohort1 = dplyr::tibble(
      cohort_definition_id = c(1L, 2L),
      subject_id = 1L,
      cohort_start_date = as.Date("2020-01-01"),
      cohort_end_date = as.Date("2020-01-01")
    )
  )) |>
    omock::mockConditionOccurrence() |>
    omopgenerics::insertCdmTo(to = CDMConnector::dbSource(
      con = duckdb::dbConnect(duckdb::duckdb()), writeSchema = "main"
    ))
  cdm$cohort1 <- cdm$cohort1 |>
    omopgenerics::newCohortTable() |>
    addCodelistAttribute(
      codelist = list(a = c(1L, 2L, 3L)),
      cohortName = c("cohort_1")
    ) |>
    addCodelistAttribute(
      codelist = list(a = c(1L, 2L, 3L), b = 3L),
      cohortName = c("cohort_2", "cohort_2")
    )

  expect_no_error(codelistDiagnostics(cdm$cohort1))

  # now b codelist is different
  cdm$cohort1 <- cdm$cohort1 |>
    addCodelistAttribute(
      codelist = list(b = 4L),
      cohortName = c("cohort_1")
    )
  expect_error(codelistDiagnostics(cdm$cohort1))
})