tests/testthat/test-classConceptSetExpression.R

In omopgenerics: Methods and Classes for the OMOP Common Data Model

test_that("simple examples of concept set", {
  asthma_cs <- list(
    "asthma_narrow" = dplyr::tibble(
      "concept_id" = 1,
      "excluded" = FALSE,
      "descendants" = TRUE,
      "mapped" = FALSE
    ),
    "asthma_broad" = dplyr::tibble(
      "concept_id" = c(1, 2),
      "excluded" = FALSE,
      "descendants" = TRUE,
      "mapped" = FALSE
    )
  )
  expect_no_error(asthma_cs <- newConceptSetExpression(asthma_cs))

  # no error if extra columns
  asthma_cs <- list(
    "asthma_narrow" = dplyr::tibble(
      "concept_id" = 1,
      "concept_name" = "asthma",
      "excluded" = FALSE,
      "descendants" = TRUE,
      "mapped" = FALSE
    ),
    "asthma_broad" = dplyr::tibble(
      "concept_id" = c(1, 2),
      "concept_name" = "asthma",
      "excluded" = FALSE,
      "descendants" = TRUE,
      "mapped" = FALSE
    )
  )

  expect_no_error(asthma_cs <- newConceptSetExpression(asthma_cs))

  # expected errors
  expect_error(newConceptSetExpression(list(
    "asthma_narrow" = dplyr::tibble(
      "concept_id" = 1,
      "excluded" = FALSE,
      "descendants" = TRUE,
      "mapped" = FALSE
    ),
    dplyr::tibble( # no name
      "concept_id" = 2,
      "excluded" = FALSE,
      "descendants" = TRUE,
      "mapped" = FALSE
    )
  )))

  expect_error(newConceptSetExpression(list(
    "asthma_narrow" = dplyr::tibble(
      "concept_id" = 1,
      "excluded" = FALSE,
      "descendants" = TRUE,
      "mapped" = FALSE
    ),
    "asthma_broad" = dplyr::tibble(
      "concept_id" = "not a id",
      "excluded" = FALSE,
      "descendants" = TRUE,
      "mapped" = FALSE
    )
  )))

  expect_error(newConceptSetExpression(list(
    "asthma_narrow" = dplyr::tibble(
      "concept_id" = 1,
      "excluded" = FALSE,
      "descendants" = TRUE,
      "mapped" = FALSE
    ),
    "asthma_broad" = dplyr::tibble(
      "concept_id" = 2,
      "excluded" = "not logical",
      "descendants" = TRUE,
      "mapped" = FALSE
    )
  )))

  expect_error(newConceptSetExpression(list(
    "asthma_narrow" = dplyr::tibble(
      "concept_id" = 1,
      "excluded" = FALSE,
      "descendants" = TRUE,
      "mapped" = FALSE
    ),
    "asthma_broad" = dplyr::tibble(
      "concept_id" = 2,
      "excluded" = TRUE,
      "descendants" = "not logical",
      "mapped" = FALSE
    )
  )))

  expect_error(newConceptSetExpression(list(
    "asthma_narrow" = dplyr::tibble(
      "concept_id" = 1,
      "excluded" = FALSE,
      "descendants" = TRUE,
      "mapped" = FALSE
    ),
    "asthma_broad" = dplyr::tibble(
      "concept_id" = 2,
      "excluded" = TRUE,
      "descendants" = TRUE,
      "mapped" = "not logical"
    )
  )))

  expect_error(newConceptSetExpression(list(
    "diabetes" = dplyr::tibble(
      "concept_id" = c(201820, NA),
      "excluded" = c(FALSE, FALSE),
      "descendants" = c(TRUE, FALSE),
      "mapped" = c(FALSE, FALSE)
    ),
    "asthma" = dplyr::tibble(
      "concept_id" = 317009,
      "excluded" = FALSE,
      "descendants" = FALSE,
      "mapped" = FALSE
    )
  )))
})