test_that("test with synthea on sql server", { skip_if(Sys.getenv("darwinDbDatabaseServer") == "") db <- DBI::dbConnect(odbc::odbc(), Driver = "ODBC Driver 11 for SQL Server", Server = Sys.getenv("darwinDbDatabaseServer"), Database = Sys.getenv("darwinDbDatabase"), UID = Sys.getenv("darwinDbUser"), PWD = Sys.getenv("darwinDbPassword"), Port = Sys.getenv("darwinDbDatabasePort") ) cdm <- CDMConnector::cdm_from_con( con = db, cdm_schema = "cdm_synthea_100k", cdm_tables = tidyselect::all_of(c( "concept", "concept_relationship", "concept_ancestor", "concept_synonym", "vocabulary" )) ) vocabVersion <- getVocabVersion(cdm = cdm) expect_true(length(vocabVersion) == 1) expect_true(is.character(vocabVersion)) # search in database asthma <- getCandidateCodes( cdm = cdm, keywords = "asthma", domains = "Condition" ) expect_true(all(c( "concept_id", "concept_name", "domain_id", "vocabulary_id" ) %in% names(asthma))) expect_true(nrow(asthma) > 0) asthmaIcdMappings <- getMappings( cdm = cdm, candidateCodelist = asthma, nonStandardVocabularies = "ICD10CM" ) 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(asthmaIcdMappings))) expect_true(nrow(asthmaIcdMappings) > 0) dbDisconnect(db) })