tests/testthat/test-Eunomia.R

In CDMConnector: Connect to an OMOP Common Data Model

test_that("downloadEunomiaData", {
  skip("manual test")
  path <- downloadEunomiaData()
  expect_true(nchar(path) > 0)

  path <- downloadEunomiaData("GiBleed", overwrite = T)
  con <- DBI::dbConnect(duckdb::duckdb(eunomiaDir("GiBleed")))
  cdm <- cdmFromCon(con, "main", cdmName = "test")
  expect_s3_class(cdm, "cdm_reference")
  DBI::dbDisconnect(con, shutdown = TRUE)

  con <- DBI::dbConnect(duckdb::duckdb(eunomiaDir("synthea-anemia-10k")))
  cdm <- cdmFromCon(con, "main")
  expect_s3_class(cdm, "cdm_reference")
  DBI::dbDisconnect(con, shutdown = TRUE)

  path <- downloadEunomiaData("synthea-breast_cancer-10k", overwrite = T)
  con <- DBI::dbConnect(duckdb::duckdb(eunomiaDir("synthea-breast_cancer-10k")))
  cdm <- cdmFromCon(con, "main")
  expect_s3_class(cdm, "cdm_reference")
  DBI::dbDisconnect(con, shutdown = TRUE)

  path <- downloadEunomiaData("synthea-covid19-10k", overwrite = T)
  con <- DBI::dbConnect(duckdb::duckdb(eunomiaDir("synthea-covid19-10k")))
  cdm <- cdmFromCon(con, "main")
  expect_s3_class(cdm, "cdm_reference")
  DBI::dbDisconnect(con, shutdown = TRUE)

  path <- downloadEunomiaData("synthea-covid19-200k", overwrite = T)
  con <- DBI::dbConnect(duckdb::duckdb(eunomiaDir("synthea-covid19-200k")))
  cdm <- cdmFromCon(con, "main")
  expect_s3_class(cdm, "cdm_reference")
  DBI::dbDisconnect(con, shutdown = TRUE)

  expect_error(downloadEunomiaData(datasetName = NULL))
  expect_error(downloadEunomiaData(pathToData = NULL))
})

test_that("empty cdm works", {
  # skip("manual test")
  skip_if_not_installed("duckdb")
  skip_if_not(eunomiaIsAvailable("empty_cdm"))

  expect_true("empty_cdm" %in% exampleDatasets())

  expect_no_error({
    con <- DBI::dbConnect(duckdb::duckdb(eunomiaDir("empty_cdm")))
    cdm <- cdmFromCon(con, "main", "main", cdmName = "empty_cdm")
  })


  rowcounts <- purrr::map_int(cdmSelect(cdm, -tblGroup("vocab")),
                              ~dplyr::pull(dplyr::count(.), 'n'))


  expect_true(all(rowcounts == 0))
  DBI::dbDisconnect(con, shutdown = T)
})

test_that("synpuf-1k example data has achilles tables", {
  skip_on_cran()
  skip_on_ci() # datasets are large and take a while to download
  skip_if_not_installed("duckdb")

  con <- DBI::dbConnect(duckdb::duckdb(), eunomiaDir("synpuf-1k", "5.3"))
  cdm <- cdmFromCon(con, "main", "main", achillesSchema = "main")
  expect_true(all(c("achilles_analysis", "achilles_results", "achilles_results_dist") %in% names(cdm)))
  cdmDisconnect(cdm)
  expect_true(eunomiaIsAvailable("synpuf-1k", "5.3"))

  con <- DBI::dbConnect(duckdb::duckdb(), eunomiaDir("synpuf-1k", "5.4"))
  cdm <- cdmFromCon(con, "main", "main", achillesSchema = "main")
  expect_true(all(c("achilles_analysis", "achilles_results", "achilles_results_dist") %in% names(cdm)))
  cdmDisconnect(cdm)
  expect_true(eunomiaIsAvailable("synpuf-1k", "5.4"))
})

test_that("requireEunomia", {
  withr::with_envvar(list("EUNOMIA_DATA_FOLDER" = ""), {
    skip_if_not_installed("duckdb")
    expect_identical(Sys.getenv("EUNOMIA_DATA_FOLDER"), "")
    expect_no_error(requireEunomia())
    expect_true(Sys.getenv("EUNOMIA_DATA_FOLDER") != "")
    expect_no_error(con <- duckdb::dbConnect(duckdb::duckdb(), eunomiaDir()))
    duckdb::dbDisconnect(conn = con)
  })
})