Properly remove ncos for each generation - fixes #177 (#178)

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: CohortGenerator
 Type: Package
 Title: An R Package for Cohort Generation Against the OMOP CDM
-Version: 0.10.0
+Version: 0.11.0
 Date: 2024-07-14
 Authors@R: c(
   person("Anthony", "Sena", email = "[email protected]", role = c("aut", "cre")),

NEWS.md

@@ -1,3 +1,8 @@
+CohortGenerator 0.11.0
+=======================
+Bug Fixes
+- Negative control outcome generation bug (#177)
+
 CohortGenerator 0.10.0
 =======================
 New Features

inst/sql/sql_server/NegativeControlOutcomes.sql

@@ -29,7 +29,7 @@ CREATE TABLE #Codesets (
 
 DELETE FROM @cohort_database_schema.@cohort_table
 WHERE cohort_definition_id IN (
-  SELECT DISTINCT ancestor_concept_id
+  SELECT DISTINCT cohort_definition_id
   FROM #Codesets
 )
 ;

tests/testthat/test-NegativeControlCohorts.R

@@ -1,4 +1,5 @@
 library(testthat)
+library(dplyr)
 library(CohortGenerator)
 
 # createEmptyNegativeControlOutcomeCohortSet ----------
@@ -227,6 +228,62 @@ test_that("Call generateNegativeControlOutcomeCohorts with occurrenceType == 'fi
   )
 })
 
+test_that("Call generateNegativeControlOutcomeCohorts with occurrenceType == 'first' and detectOnDescendants == FALSE multiple times to ensure there are no duplicates", {
+  cohortTableNames <- getCohortTableNames(cohortTable = "ot_first_dod_f")
+  connection <- DatabaseConnector::connect(connectionDetails = connectionDetails)
+  on.exit(DatabaseConnector::disconnect(connection))
+  createCohortTables(
+    connection = connection,
+    cohortDatabaseSchema = "main",
+    cohortTableNames = cohortTableNames
+  )
+  ncSet <- getNegativeControlOutcomeCohortsForTest()
+
+  # Set the cohort ID to something other than the concept ID
+  ncSet <- ncSet %>% 
+    mutate(cohortId = row_number())
+  expect_output(
+    generateNegativeControlOutcomeCohorts(
+      connection = connection,
+      cdmDatabaseSchema = "main",
+      cohortDatabaseSchema = "main",
+      cohortTable = cohortTableNames$cohortTable,
+      negativeControlOutcomeCohortSet = ncSet,
+      occurrenceType = "first",
+      detectOnDescendants = FALSE
+    )
+  )
+
+  # Get the cohort counts from the first run
+  counts1 <- getCohortCounts(
+    connection = connection,
+    cohortDatabaseSchema = "main",
+    cohortTable = cohortTableNames$cohortTable,
+    cohortDefinitionSet = ncSet
+  )
+
+  # Regenerate the negative control outcomes
+  expect_output(
+    generateNegativeControlOutcomeCohorts(
+      connection = connection,
+      cdmDatabaseSchema = "main",
+      cohortDatabaseSchema = "main",
+      cohortTable = cohortTableNames$cohortTable,
+      negativeControlOutcomeCohortSet = ncSet,
+      occurrenceType = "first",
+      detectOnDescendants = FALSE
+    )
+  )
+
+  counts2 <- getCohortCounts(
+    connection = connection,
+    cohortDatabaseSchema = "main",
+    cohortTable = cohortTableNames$cohortTable,
+    cohortDefinitionSet = ncSet
+  )
+
+  expect_equal(counts1,counts2)
+})
 
 test_that("incremental mode", {
   incrementalFolder <- tempfile()