tests/testthat/test-importCodelist.R

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

test_that("import codelist json", {
  skip_if_not_installed("jsonlite")

  dir.create(cs_path <- file.path(tempdir(), uniqueTableName()))

  codes <- newCodelist(list(
    "disease X" = c(1L, 2L, 3L),
    "disease Y" = c(4L, 5L)
  ))

  expect_no_error(exportCodelist(x = codes, path = cs_path))
  expect_true("disease X.json" %in% list.files(cs_path))
  expect_true("disease Y.json" %in% list.files(cs_path))

  codes_imported <- importCodelist(path = cs_path)
  expect_identical(codes, codes_imported)

  # we get an error if descendants set to TRUE
  expect_warning(
    x <- importCodelist(path = system.file(
      package = "omopgenerics",
      "concepts_for_mock"
    ))
  )
  expect_true(length(x) == 1)

  unlink(cs_path, recursive = TRUE)
})

test_that("import codelist from codelist with details json", {
  skip_if_not_installed("jsonlite")

  dir.create(cs_path <- file.path(tempdir(), uniqueTableName()))

  codes <- newCodelistWithDetails(list(
    "disease X" = dplyr::tibble(
      concept_id = c(1L, 2L, 3L),
      concept_name = c("one", "two", "three"),
      domain_id = "Condition"
    ),
    "disease Y" = dplyr::tibble(
      concept_id = c(4L, 5L),
      concept_name = c("four", "five"),
      domain_id = "Drug"
    )
  ))

  expect_no_error(exportCodelistWithDetails(x = codes, path = cs_path))
  codes_imported <- importCodelist(path = cs_path)
  expect_identical(codes_imported, validateConceptSetArgument(codes))

  unlink(cs_path, recursive = TRUE)
})

test_that("import codelist from concept set expression json", {
  skip_if_not_installed("jsonlite")

  dir.create(cs_path <- file.path(tempdir(), uniqueTableName()))
  asthma_cs <- newConceptSetExpression(list(
    "asthma_narrow" = dplyr::tibble(
      concept_id = c(1L, 2L),
      excluded = FALSE,
      descendants = FALSE,
      mapped = FALSE
    )
  ))

  expect_no_error(exportConceptSetExpression(x = asthma_cs, path = cs_path))
  codes_imported <- importCodelist(path = cs_path)
  expect_identical(
    codes_imported,
    newCodelist(list("asthma_narrow" = c(1L, 2L)))
  )

  unlink(cs_path, recursive = TRUE)

  dir.create(cs_path <- file.path(tempdir(), uniqueTableName()))
  asthma_cs <- newConceptSetExpression(list(
    "asthma_narrow" = dplyr::tibble(
      concept_id = 1L,
      excluded = FALSE,
      descendants = TRUE,
      mapped = FALSE
    )
  ))

  expect_no_error(exportConceptSetExpression(x = asthma_cs, path = cs_path))
  expect_warning(codes_imported <- importCodelist(path = cs_path))
  expect_identical(codes_imported, emptyCodelist())

  unlink(cs_path, recursive = TRUE)
})

test_that("import codelist csv", {
  dir.create(cs_path <- file.path(tempdir(), uniqueTableName()))

  codes <- newCodelist(list(
    "disease X" = c(1L, 2L, 3L), "disease Y" = c(4L, 5L)
  ))

  expect_no_error(exportCodelist(x = codes, path = cs_path, type = "csv"))
  expect_true("disease X.csv" %in% list.files(cs_path))
  expect_true("disease Y.csv" %in% list.files(cs_path))

  codes_imported <- importCodelist(path = cs_path, type = "csv")
  expect_identical(codes, codes_imported)

  unlink(cs_path, recursive = TRUE)
})

test_that("import codelist discovers csv and json by default", {
  skip_if_not_installed("jsonlite")

  dir.create(cs_path <- file.path(tempdir(), uniqueTableName()))
  json_codes <- newCodelist(list("json disease" = c(1L, 2L)))
  csv_codes <- newCodelist(list("csv disease" = c(3L, 4L)))

  expect_no_error(exportCodelist(x = json_codes, path = cs_path))
  expect_no_error(exportCodelist(x = csv_codes, path = cs_path, type = "csv"))

  codes_imported <- importCodelist(path = cs_path)
  expect_identical(
    codes_imported,
    newCodelist(list(
      "csv disease" = c(3L, 4L),
      "json disease" = c(1L, 2L)
    ))
  )

  unlink(cs_path, recursive = TRUE)
})

test_that("import codelist from codelist with details csv", {
  dir.create(cs_path <- file.path(tempdir(), uniqueTableName()))

  codes <- newCodelistWithDetails(list(
    "disease X" = dplyr::tibble(
      concept_id = c(1L, 2L, 3L),
      concept_name = c("one", "two", "three"),
      domain_id = "Condition"
    ),
    "disease Y" = dplyr::tibble(
      concept_id = c(4L, 5L),
      concept_name = c("four", "five"),
      domain_id = "Drug"
    )
  ))

  expect_no_error(exportCodelistWithDetails(x = codes, path = cs_path, type = "csv"))
  codes_imported <- importCodelist(path = cs_path, type = "csv")
  expect_identical(codes_imported, validateConceptSetArgument(codes))

  unlink(cs_path, recursive = TRUE)
})

test_that("import codelist from concept set expression csv", {
  dir.create(cs_path <- file.path(tempdir(), uniqueTableName()))
  asthma_cs <- newConceptSetExpression(list(
    "asthma_narrow" = dplyr::tibble(
      concept_id = c(1L, 2L),
      excluded = FALSE,
      descendants = FALSE,
      mapped = FALSE
    )
  ))

  expect_no_error(exportConceptSetExpression(x = asthma_cs, path = cs_path, type = "csv"))
  codes_imported <- importCodelist(path = cs_path, type = "csv")
  expect_identical(
    codes_imported,
    newCodelist(list("asthma_narrow" = c(1L, 2L)))
  )

  unlink(cs_path, recursive = TRUE)

  dir.create(cs_path <- file.path(tempdir(), uniqueTableName()))
  asthma_cs <- newConceptSetExpression(list(
    "asthma_narrow" = dplyr::tibble(
      concept_id = 1L,
      excluded = FALSE,
      descendants = TRUE,
      mapped = FALSE
    )
  ))

  expect_no_error(exportConceptSetExpression(x = asthma_cs, path = cs_path, type = "csv"))
  expect_warning(codes_imported <- importCodelist(path = cs_path, type = "csv"))
  expect_identical(codes_imported, emptyCodelist())

  unlink(cs_path, recursive = TRUE)
})