From b2b15e25963fd14e3f31981b317e95b02bff1b9d Mon Sep 17 00:00:00 2001
From: Anthony Sena <asena5@its.jnj.com>
Date: Mon, 19 Aug 2024 09:32:01 -0400
Subject: [PATCH 1/2] Make negative control outcomes optional - fixes #153

---
 R/Module-StrategusModule.R | 58 ++++++++++++++++++--------------------
 1 file changed, 27 insertions(+), 31 deletions(-)

diff --git a/R/Module-StrategusModule.R b/R/Module-StrategusModule.R
index a9d783cd..4f206999 100644
--- a/R/Module-StrategusModule.R
+++ b/R/Module-StrategusModule.R
@@ -241,45 +241,41 @@ StrategusModule <- R6::R6Class(
 
       return(cohortDefinitionSet)
     },
-    .jobContextHasNegativeControlOutcomeSharedResource = function() {
-      jobContext <- private$jobContext
-      ncSharedResource <- private$.getSharedResourceByClassName(
-        sharedResources = jobContext$sharedResources,
-        className = "NegativeControlOutcomeSharedResources"
-      )
-      hasNegativeControlOutcomeSharedResource <- !is.null(ncSharedResource)
-      invisible(hasNegativeControlOutcomeSharedResource)
-    },
     .createNegativeControlOutcomeSettingsFromJobContext = function() {
       jobContext <- private$jobContext
       negativeControlSharedResource <- private$.getSharedResourceByClassName(
         sharedResources = jobContext$sharedResources,
         className = "NegativeControlOutcomeSharedResources"
       )
-      if (is.null(negativeControlSharedResource)) {
-        stop("Negative control outcome shared resource not found!")
-      }
-      negativeControlOutcomes <- negativeControlSharedResource$negativeControlOutcomes$negativeControlOutcomeCohortSet
-      if (length(negativeControlOutcomes) <= 0) {
-        stop("No negative control outcomes found")
-      }
-      negativeControlOutcomeCohortSet <- CohortGenerator::createEmptyNegativeControlOutcomeCohortSet()
-      for (i in 1:length(negativeControlOutcomes)) {
-        nc <- negativeControlOutcomes[[i]]
-        negativeControlOutcomeCohortSet <- rbind(
-          negativeControlOutcomeCohortSet,
-          data.frame(
-            cohortId = as.numeric(nc$cohortId),
-            cohortName = nc$cohortName,
-            outcomeConceptId = as.numeric(nc$outcomeConceptId)
+      if (!is.null(negativeControlSharedResource)) {
+        negativeControlOutcomes <- negativeControlSharedResource$negativeControlOutcomes$negativeControlOutcomeCohortSet
+        if (length(negativeControlOutcomes) <= 0) {
+          stop("Negative control outcome shared resource found but no negative control outcomes were provided.")
+        }
+        negativeControlOutcomeCohortSet <- CohortGenerator::createEmptyNegativeControlOutcomeCohortSet()
+        for (i in 1:length(negativeControlOutcomes)) {
+          nc <- negativeControlOutcomes[[i]]
+          negativeControlOutcomeCohortSet <- rbind(
+            negativeControlOutcomeCohortSet,
+            data.frame(
+              cohortId = as.numeric(nc$cohortId),
+              cohortName = nc$cohortName,
+              outcomeConceptId = as.numeric(nc$outcomeConceptId)
+            )
           )
-        )
+        }
+        invisible(list(
+          cohortSet = negativeControlOutcomeCohortSet,
+          occurrenceType = negativeControlSharedResource$negativeControlOutcomes$occurrenceType,
+          detectOnDescendants = negativeControlSharedResource$negativeControlOutcomes$detectOnDescendants
+        ))
+      } else {
+        invisible(list(
+          cohortSet = NULL,
+          occurrenceType = "all",
+          detectOnDescendants = FALSE
+        ))
       }
-      invisible(list(
-        cohortSet = negativeControlOutcomeCohortSet,
-        occurrenceType = negativeControlSharedResource$negativeControlOutcomes$occurrenceType,
-        detectOnDescendants = negativeControlSharedResource$negativeControlOutcomes$detectOnDescendants
-      ))
     }
   )
 )

From 81e2d9c543b5b112d2e2f497db670f693913c352 Mon Sep 17 00:00:00 2001
From: Anthony Sena <asena5@its.jnj.com>
Date: Mon, 19 Aug 2024 09:52:06 -0400
Subject: [PATCH 2/2] Add test case

---
 tests/testthat/test-Execution.R | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/tests/testthat/test-Execution.R b/tests/testthat/test-Execution.R
index 2404b711..64da5c65 100644
--- a/tests/testthat/test-Execution.R
+++ b/tests/testthat/test-Execution.R
@@ -179,3 +179,35 @@ test_that("Execute on Oracle stops if table names exceed length limit", {
     )
   )
 })
+
+test_that("Negative control outcomes are optional", {
+  analysisSpecifications <- ParallelLogger::loadSettingsFromJson(
+    fileName = system.file("testdata/cdmModulesAnalysisSpecifications.json",
+                           package = "Strategus"
+    )
+  )
+
+  # Remove the nco section
+  analysisSpecifications$sharedResources <- list(analysisSpecifications$sharedResources[[1]])
+
+  # Remove all but CG
+  analysisSpecifications$moduleSpecifications <- list(analysisSpecifications$moduleSpecifications[[3]])
+
+  executionSettings <- createCdmExecutionSettings(
+    workDatabaseSchema = workDatabaseSchema,
+    cdmDatabaseSchema = cdmDatabaseSchema,
+    cohortTableNames = CohortGenerator::getCohortTableNames(cohortTable = "unit_test"),
+    workFolder = file.path(tempDir, "work_folder"),
+    resultsFolder = file.path(tempDir, "results_folder")
+  )
+
+  expect_output(
+    Strategus::execute(
+      connectionDetails = connectionDetails,
+      analysisSpecifications = analysisSpecifications,
+      executionSettings = executionSettings
+    ),
+    "Generating cohort set",
+    ignore.case = TRUE
+  )
+})