test_that("exportPregnancies runs without error", { cdm <- mockPregnancyCdm() outputFolder <- file.path(tempdir(), "test_exportPregnancies") exportFolder <- file.path(tempdir(), "test_exportPregnancies_export") dir.create(outputFolder, recursive = TRUE, showWarnings = FALSE) dir.create(exportFolder, recursive = TRUE, showWarnings = FALSE) # Run full pipeline first to create required files runPregnancyIdentifier( cdm = cdm, outputFolder = outputFolder, outputLogToConsole = FALSE ) # Now test exportPregnancies exportPregnancies( cdm = cdm, outputFolder = outputFolder, exportFolder = exportFolder ) expect_true(dir.exists(exportFolder)) expect_true(file.exists(file.path(exportFolder, "cdm_source.csv"))) unlink(outputFolder, recursive = TRUE) unlink(exportFolder, recursive = TRUE) cleanupCdmDb(cdm) }) test_that("exportPregnancies runs with custom minCellCount", { cdm <- mockPregnancyCdm() outputFolder <- file.path(tempdir(), "test_exportPregnancies_custom") exportFolder <- file.path(tempdir(), "test_exportPregnancies_export_custom") dir.create(outputFolder, recursive = TRUE, showWarnings = FALSE) dir.create(exportFolder, recursive = TRUE, showWarnings = FALSE) # Run full pipeline first runPregnancyIdentifier( cdm = cdm, outputFolder = outputFolder, outputLogToConsole = FALSE ) # Test with custom minCellCount exportPregnancies( cdm = cdm, outputFolder = outputFolder, exportFolder = exportFolder, minCellCount = 0 ) expect_true(dir.exists(exportFolder)) expect_equal(list.files(exportFolder, ".csv"), sort(c( "age_summary.csv", "age_summary_first_pregnancy.csv", "age_summary_groups.csv", "attrition.csv", "attrition_if_cleanup.csv", "cdm_source.csv", "concept_check.csv", "missing_dates.csv", "delivery_mode_summary.csv", "episode_frequency.csv", "episode_frequency_summary.csv", "esd_concept_counts.csv", "gestational_age_days_counts.csv", "gestational_age_days_per_category_summary.csv", "gestational_age_days_summary.csv", "gestational_weeks.csv", "hip_concept_counts.csv", "monthly_trend_missing.csv", "monthly_trends.csv", "pps_concept_counts.csv", "observation_period_range.csv", "outcome_categories_count.csv", "precision_days.csv", "precision_days_denominators.csv", "pregnancy_frequency.csv", "pregnancy_overlap_counts.csv", "quality_check_cleanup.csv", "swapped_dates.csv", "yearly_trend.csv", "yearly_trend_missing.csv" ))) unlink(outputFolder, recursive = TRUE) unlink(exportFolder, recursive = TRUE) cleanupCdmDb(cdm) })