test_that("test with synthea on sql server", { skip_if(Sys.getenv("darwinDbDatabaseServer") == "") db <-DBI::dbConnect(odbc::odbc(), Driver = Sys.getenv("SQL_SERVER_DRIVER"), # Driver = "ODBC Driver 17 for SQL Server", #asdf Server = Sys.getenv("CDM5_SQL_SERVER_SERVER"), Database = Sys.getenv("CDM5_SQL_SERVER_CDM_DATABASE"), UID = Sys.getenv("CDM5_SQL_SERVER_USER"), PWD = Sys.getenv("CDM5_SQL_SERVER_PASSWORD"), TrustServerCertificate="yes", Port = Sys.getenv("CDM5_SQL_SERVER_PORT")) cdm <- CDMConnector::cdm_from_con( con = db, cdm_schema = strsplit(Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA"), "\\.")[[1]], write_schema = strsplit(Sys.getenv("CDM5_SQL_SERVER_SCRATCH_SCHEMA"), "\\.")[[1]]) 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) })