test_that("test methods against sql test server", { testthat::skip_on_ci() server <- Sys.getenv("SERVER") database <- Sys.getenv("DATABASE") user <- Sys.getenv("USER") password <- Sys.getenv("PW") port <- Sys.getenv("PORT") driver <- Sys.getenv("DRIVER") dbName <- Sys.getenv("DBNAME") db <- DBI::dbConnect(odbc::odbc(), Driver = driver, Server = server, Database = database, UID = user, PWD = password, Port = port ) cdm <- CDMConnector::cdm_from_con(db, cdm_schema = "cdm_synthea_1M", write_schema = "mdu", cohort_tables = c("cohort", "cohort1") ) # add age and add sex cdm$condition_occurrence <- cdm$condition_occurrence |> addAge(indexDate = "condition_start_date") |> addSex() expect_true(all(c("sex", "age") %in% colnames(cdm$condition_occurrence))) cdm$condition_occurrence |> PatientProfiles::addDemographics( age = TRUE, ageName = "age", ageGroup = NULL, sex = TRUE, sexName = "sex", priorHistory = FALSE, priorHistoryName = "prior_history", futureObservation = FALSE, indexDate = "condition_start_date" ) # add demographics expect_true(all(c("sex", "age") %in% colnames(cdm$condition_occurrence))) # add cohort intersect cohort <- cdm$cohort |> addIntersect( tableName = "cohort1", window = list(c(-Inf, 0)), value = "date" ) expect_true(all(c("all_0_to_inf") %in% colnames(cohort))) # add cohort occurrences cohort <- cdm$cohort |> addCohortIntersectCount(targetCohortTable = "cohort1") |> dplyr::arrange(subject_id, cohort_start_date) expect_true(all(c("all_0_to_inf") %in% colnames(cohort))) # countflag cohort <- cdm$cohort |> addCohortIntersectFlag(targetCohortTable = "cohort1") |> dplyr::arrange(subject_id, cohort_start_date) expect_true(all(c("all_0_to_inf") %in% colnames(cohort))) # time to cohort cohort <- cdm$cohort |> addCohortIntersectTime(targetCohortTable = "cohort1") |> dplyr::arrange(subject_id, cohort_start_date) expect_true(all(c("all_0_to_inf") %in% colnames(cohort))) # dateOfCohort cohort <- cdm$cohort |> addCohortIntersectDate(targetCohortTable = "cohort1") |> dplyr::arrange(subject_id, cohort_start_date) expect_true(all(c("all_0_to_inf") %in% colnames(cohort))) })