Nothing
test_that("tests with mock db", {
# mock db
cdm <- mockVocabRef("database")
codes <- getCandidateCodes(
cdm = cdm,
keywords = "Musculoskeletal disorder",
domains = "Condition",
includeDescendants = FALSE
)
orphan_codes <- summariseOrphanCodes(x = list("msk" = codes$concept_id),
cdm = cdm)
# we should pick up knee osteoarthritis from our achilles tables
expect_true(all(stringr::str_detect(orphan_codes %>%
dplyr::pull("variable_level"), c("4", "5"))))
expect_equal(orphan_codes %>%
dplyr::pull("estimate_value"),
c("400", "200"))
settings <- omopgenerics::settings(orphan_codes)
expect_true(all(settings$result_type == "orphan_code_use"))
# with phoebe present
cdm <- omopgenerics::insertTable(cdm,
name = "concept_recommended",
table = data.frame(concept_id_1 = 1,
concept_id_2 = 9,
relationship_id = "from phoebe"),
overwrite = TRUE,
temporary = FALSE)
orphan_codes <- summariseOrphanCodes(x = list("msk" = codes$concept_id),
cdm = cdm)
expect_true(9 %in% orphan_codes$variable_level)
cdm <- omopgenerics::insertTable(cdm,
name = "concept_recommended",
table = data.frame(concept_id_1 = 8,
concept_id_2 = 9,
relationship_id = "from phoebe"),
overwrite = TRUE,
temporary = FALSE)
orphan_codes <- summariseOrphanCodes(x = list("msk" = codes$concept_id),
cdm = cdm)
expect_true(!9 %in% orphan_codes$variable_level)
#expected error
expect_error(summariseOrphanCodes(x = "a", cdm = cdm))
expect_error(summariseOrphanCodes(x = list("msk" = codes$concept_id),
cdm = "a"))
# requires achilles
cdm$achilles_results <- NULL
expect_error(summariseOrphanCodes(x = list("msk" = codes$concept_id),
cdm = cdm))
CDMConnector::cdm_disconnect(cdm)
})
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