test_that("tests with mock", { backends <- c("database") for (i in seq_along(backends)) { # mock db cdm <- mockVocabRef(backends[[i]]) # tests codes <- getCandidateCodes( cdm = cdm, keywords = "Musculoskeletal disorder", domains = "Condition", includeDescendants = TRUE ) mappings <- getMappings( cdm = cdm, candidateCodelist = codes, nonStandardVocabularies = "READ" ) expect_true( any(mappings$standard_concept_name %in% "Osteoarthrosis") ) expect_true( any(mappings$non_standard_concept_name %in% "Degenerative arthropathy") ) expect_true( any(mappings$standard_concept_name %in% "Osteoarthritis of knee") ) expect_true( any(mappings$non_standard_concept_name %in% "Knee osteoarthritis") ) expect_true(all(c( "standard_concept_id", "standard_concept_name", "standard_vocabulary_id", "non_standard_concept_id", "non_standard_concept_name", "non_standard_concept_code", "non_standard_vocabulary_id" ) %in% names(mappings))) # expect error if not a cdm reference expect_error(getMappings( cdm = "Not a cdm", candidateCodelist = codes, nonStandardVocabularies = "READ" )) # expect error if nonStandardVocabularies does not exist # expect works mappings <- getMappings( cdm = cdm, candidateCodelist = codes, nonStandardVocabularies = "READ" ) # expect error expect_error(getMappings( cdm = cdm, candidateCodelist = codes, nonStandardVocabularies = "READX" )) expect_error(getMappings( cdm = cdm, candidateCodelist = codes, nonStandardVocabularies = c("Read", "READX") )) if (backends[[i]] == "database") { CDMConnector::cdm_disconnect(cdm) } } })