From f633b6abca1a30fa7115bda38e4305215b41a1ce Mon Sep 17 00:00:00 2001
From: Anthony Sena <asena5@its.jnj.com>
Date: Wed, 1 May 2024 12:01:23 -0400
Subject: [PATCH] Enforce unique cohorts before generating - fixes #130

---
 R/CohortConstruction.R                        |  6 +++++
 R/NegativeControlCohorts.R                    |  7 +++++
 .../test-CohortConstructionAndStats.R         | 26 +++++++++++++++++++
 tests/testthat/test-NegativeControlCohorts.R  | 24 +++++++++++++++++
 4 files changed, 63 insertions(+)

diff --git a/R/CohortConstruction.R b/R/CohortConstruction.R
index d29953b..0706287 100644
--- a/R/CohortConstruction.R
+++ b/R/CohortConstruction.R
@@ -76,6 +76,12 @@ generateCohortSet <- function(connectionDetails = NULL,
       "sql"
     )
   )
+  # Verify that cohort IDs are not repeated in the cohort definition
+  # set before generating
+  if (length(unique(cohortDefinitionSet$cohortId)) != length(cohortDefinitionSet$cohortId)) {
+    duplicatedCohortIds <- cohortDefinitionSet$cohortId[duplicated(cohortDefinitionSet$cohortId)]
+    stop("Cannot generate! Duplicate cohort IDs found in your cohortDefinitionSet: ", paste(duplicatedCohortIds, sep=","), ". Please fix your cohortDefinitionSet and try again.")
+  } 
   if (is.null(connection) && is.null(connectionDetails)) {
     stop("You must provide either a database connection or the connection details.")
   }
diff --git a/R/NegativeControlCohorts.R b/R/NegativeControlCohorts.R
index fc634f7..bef2695 100644
--- a/R/NegativeControlCohorts.R
+++ b/R/NegativeControlCohorts.R
@@ -118,6 +118,13 @@ generateNegativeControlOutcomeCohorts <- function(connectionDetails = NULL,
     min.rows = 1
   )
 
+  # Verify that cohort IDs are not repeated in the negative control
+  # cohort definition set before generating
+  if (length(unique(negativeControlOutcomeCohortSet$cohortId)) != length(negativeControlOutcomeCohortSet$cohortId)) {
+    duplicatedCohortIds <- negativeControlOutcomeCohortSet$cohortId[duplicated(negativeControlOutcomeCohortSet$cohortId)]
+    stop("Cannot generate! Duplicate cohort IDs found in your negativeControlOutcomeCohortSet: ", paste(duplicatedCohortIds, sep=","), ". Please fix your negativeControlOutcomeCohortSet and try again.")
+  } 
+  
   if (incremental) {
     if (is.null(incrementalFolder)) {
       stop("Must specify incrementalFolder when incremental = TRUE")
diff --git a/tests/testthat/test-CohortConstructionAndStats.R b/tests/testthat/test-CohortConstructionAndStats.R
index 0088390..18956b4 100644
--- a/tests/testthat/test-CohortConstructionAndStats.R
+++ b/tests/testthat/test-CohortConstructionAndStats.R
@@ -19,6 +19,32 @@ test_that("Call generateCohortSet with default parameters", {
   )
 })
 
+test_that("Call generateCohortSet with cohortDefinitionSet containing duplicate IDs", {
+  cohortDefinitionSet <- data.frame(
+    cohortId = 1,
+    cohortName = "duplicate #1",
+    sql = "",
+    json = ""
+  )
+  cohortDefinitionSet <- rbind(
+    cohortDefinitionSet,
+    data.frame(
+      cohortId = 1,
+      cohortName = "duplicate #2",
+      sql = "",
+      json = ""
+    )
+  )
+  expect_error(
+    generateCohortSet(
+      connectionDetails = connectionDetails,
+      cohortDefinitionSet = cohortDefinitionSet
+    ),
+    message = "(Cannot generate! Duplicate cohort IDs found in your cohortDefinitionSet)"
+  )
+})
+
+
 test_that("Call instatiateCohortSet with malformed cohortDefinitionSet parameter", {
   expect_error(
     generateCohortSet(
diff --git a/tests/testthat/test-NegativeControlCohorts.R b/tests/testthat/test-NegativeControlCohorts.R
index 1064644..19c4d02 100644
--- a/tests/testthat/test-NegativeControlCohorts.R
+++ b/tests/testthat/test-NegativeControlCohorts.R
@@ -12,6 +12,30 @@ test_that("Call generateNegativeControlOutcomeCohorts without connection or conn
   expect_error(generateNegativeControlOutcomeCohorts())
 })
 
+test_that("Call generateNegativeControlOutcomeCohorts with negativeControlOutcomeCohortSet containing duplicate IDs", {
+  negativeControlOutcomeCohortSet <- data.frame(
+    cohortId = 1,
+    cohortName = "duplicate #1",
+    outcomeConceptId = 1
+  )
+  negativeControlOutcomeCohortSet <- rbind(
+    negativeControlOutcomeCohortSet,
+    data.frame(
+      cohortId = 1,
+      cohortName = "duplicate #2",
+      outcomeConceptId = 1
+    )
+  )
+  expect_error(
+    generateNegativeControlOutcomeCohorts(
+      connectionDetails = connectionDetails,
+      cdmDatabaseSchema = "main",
+      negativeControlOutcomeCohortSet = negativeControlOutcomeCohortSet
+    ),
+    message = "(Cannot generate! Duplicate cohort IDs found in your negativeControlOutcomeCohortSet)"
+  )
+})
+
 test_that("Call generateNegativeControlOutcomeCohorts before creating cohort table fails", {
   cohortTableNames <- getCohortTableNames(cohortTable = "missing_cohort_table")
   ncSet <- getNegativeControlOutcomeCohortsForTest()