Add unit test for min cell count

tests/testthat/test-RunCohortGeneration.R

@@ -74,3 +74,63 @@ test_that("Call runCohortGeneration happy path", {
     expect_true(all(data$databaseId == expectedDatabaseId))
   }
 })
+
+test_that("Call runCohortGeneration and verify censoring of minimum cell counts", {
+  testOutputFolder1 <- file.path(outputFolder, "minCellCountRun1")
+  testOutputFolder2 <- file.path(outputFolder, "minCellCountRun2")
+  on.exit(expr = {
+    unlink(testOutputFolder1, recursive = TRUE)
+    unlink(testOutputFolder2, recursive = TRUE)
+  })
+  minCellCountForTest <- 500
+  cohortsWithStats <- getCohortsForTest(cohorts, generateStats = TRUE)
+  ncSet <- getNegativeControlOutcomeCohortsForTest()
+  expectedDatabaseId <- "db1"
+
+  runCohortGeneration(
+    connectionDetails = connectionDetails,
+    cdmDatabaseSchema = "main",
+    cohortDatabaseSchema = "main",
+    cohortTableNames = CohortGenerator::getCohortTableNames("runCG"),
+    cohortDefinitionSet = cohortsWithStats,
+    negativeControlOutcomeCohortSet = ncSet,
+    occurrenceType = "all",
+    detectOnDescendants = TRUE,
+    stopOnError = FALSE,
+    outputFolder = testOutputFolder1,
+    databaseId = expectedDatabaseId,
+    minCellCount = 0,
+    incremental = F
+  )
+
+  runCohortGeneration(
+    connectionDetails = connectionDetails,
+    cdmDatabaseSchema = "main",
+    cohortDatabaseSchema = "main",
+    cohortTableNames = CohortGenerator::getCohortTableNames("runCG"),
+    cohortDefinitionSet = cohortsWithStats,
+    negativeControlOutcomeCohortSet = ncSet,
+    occurrenceType = "all",
+    detectOnDescendants = TRUE,
+    stopOnError = FALSE,
+    outputFolder = testOutputFolder2,
+    databaseId = expectedDatabaseId,
+    minCellCount = minCellCountForTest,
+    incremental = F
+  )
+
+
+  # Verify that values below the minCellCountForTest are censored properly
+  spec <- CohortGenerator::readCsv(
+    file = system.file("csv", "resultsDataModelSpecification.csv", package = "CohortGenerator")
+  ) %>%
+    dplyr::filter(tolower(.data$minCellCount) == "yes") %>%
+    dplyr::arrange(.data$tableName, .data$columnName)
+
+  for (i in 1:nrow(spec)) {
+    data1 <- readr::read_csv(file = file.path(testOutputFolder1, paste0(spec$tableName[i], ".csv")), col_types = readr::cols(), lazy = F)
+    data2 <- readr::read_csv(file = file.path(testOutputFolder2, paste0(spec$tableName[i], ".csv")), col_types = readr::cols(), lazy = F)
+    rowsBelowMinCellCount <- which(data1[[spec$columnName[i]]] < minCellCountForTest)
+    expect_true(all(data2[rowsBelowMinCellCount, spec$columnName[i]] == -minCellCountForTest))
+  }
+})