test_that("runHip runs without error", { cdm <- mockPregnancyCdm() expect_s3_class(cdm, "cdm_reference") outputFolder <- file.path(tempdir(), "test_runHip") dir.create(outputFolder, recursive = TRUE, showWarnings = FALSE) logger <- PregnancyIdentifier:::makeLogger(outputFolder, outputLogToConsole = FALSE) suppressWarnings({ library(CDMConnector) library(dplyr, warn.conflicts = FALSE) }) # cdmCommentContents(cdm, 12) # person_id | observation_concept_id | start_date | end_date | type_concept_id | domain | observation_concept_name | type_concept_name # 12 | 4014295 | 2017-12-15 | NA | 32817 | condition_occurrence | Single live birth | EHR # cdm <- CDMConnector::cdmSubset(cdm, 12L) # # debugonce(initPregnancies) cdm <- initPregnancies(cdm, logger = logger) # # cdm$preg_hip_records # # debugonce(runHip) # debugonce(attachGestationAndLength) cdm <- runHip( cdm = cdm, outputFolder = outputFolder, logger = logger ) expect_true(file.exists(file.path(outputFolder, "hip_episodes.rds"))) hip <- readRDS(file.path(outputFolder, "hip_episodes.rds")) expect_true(is.data.frame(hip)) unlink(outputFolder, recursive = TRUE) cleanupCdmDb(cdm) }) test_that("runHip runs with custom parameters", { cdm <- mockPregnancyCdm() outputFolder <- file.path(tempdir(), "test_runHip_custom") dir.create(outputFolder, recursive = TRUE, showWarnings = FALSE) logger <- PregnancyIdentifier:::makeLogger(outputFolder, outputLogToConsole = FALSE) cdm <- initPregnancies(cdm, logger = logger) cdm <- runHip( cdm = cdm, outputFolder = outputFolder, startDate = as.Date("2000-01-01"), endDate = as.Date("2020-12-31"), justGestation = FALSE, logger = logger ) expect_s3_class(cdm, "cdm_reference") unlink(outputFolder, recursive = TRUE) cleanupCdmDb(cdm) })