Fix #136 (#139)

DESCRIPTION

@@ -45,6 +45,6 @@ License: Apache License
 VignetteBuilder: knitr
 URL: https://ohdsi.github.io/CohortGenerator/, https://github.com/OHDSI/CohortGenerator
 BugReports: https://github.com/OHDSI/CohortGenerator/issues
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 Language: en-US

R/CohortCount.R

@@ -27,7 +27,10 @@
 #' @template CohortTable
 #'
 #' @param cohortIds            The cohort Id(s) used to reference the cohort in the cohort
-#'                             table. If left empty, all cohorts in the table will be included.
+#'                             table. If left empty and no `cohortDefinitionSet` argument is
+#'                             specified, all cohorts in the table will be included. If
+#'                             you specify the `cohortIds` AND `cohortDefinitionSet`, the counts will
+#'                             reflect the `cohortIds` from the `cohortDefinitionSet`.
 #'
 #' @template CohortDefinitionSet
 #'
@@ -67,6 +70,12 @@ getCohortCounts <- function(connectionDetails = NULL,
     delta <- Sys.time() - start
     ParallelLogger::logInfo(paste("Counting cohorts took", signif(delta, 3), attr(delta, "units")))
     if (!is.null(cohortDefinitionSet)) {
+      # If the user has NOT specified a list of cohortIds
+      # to use to filter the cohortDefinitionSet, then
+      # extract the unique cohortIds
+      if (length(cohortIds) == 0) {
+        cohortIds <- cohortDefinitionSet$cohortId
+      }
       counts <- merge(
         x = counts,
         y = cohortDefinitionSet[cohortDefinitionSet$cohortId %in% cohortIds, ],

tests/testthat/test-CohortCount.R

@@ -119,5 +119,31 @@ test_that("Call getCohortCounts with a cohortDefinitionSet returns 0 counts for
   expect_true(testCohortCounts[testCohortCounts$cohortId == 100, "cohortSubjects"] == 0)
 })
 
+test_that("Call getCohortCounts with no cohortId specified and cohortDefinitionSet returns 0 counts for cohortId not in cohort table", {
+  cohortDefinitionSet <- getCohortDefinitionSet(
+    settingsFileName = "testdata/id/Cohorts.csv",
+    jsonFolder = "testdata/id/cohorts",
+    sqlFolder = "testdata/id/sql/sql_server",
+    packageName = "CohortGenerator",
+    verbose = TRUE
+  )
+
+  cohortDefinitionSet <- rbind(
+    cohortDefinitionSet,
+    cohortDefinitionSet[1, ] |> transform(atlasId = 100, cohortId = 100, cohortName = "not in cohort table", logicDescription = "not in cohort table")
+  )
+
+  testCohortCounts <- getCohortCounts(
+    connectionDetails = connectionDetails,
+    cohortDatabaseSchema = "main",
+    cohortTable = "cohort",
+    cohortDefinitionSet = cohortDefinitionSet
+  )
+
+  expect_true(nrow(testCohortCounts) == 4)
+  expect_true(testCohortCounts[testCohortCounts$cohortId == 100, "cohortEntries"] == 0)
+  expect_true(testCohortCounts[testCohortCounts$cohortId == 100, "cohortSubjects"] == 0)
+})
+
 # Cleanup ------
 rm(cohortCounts)