Fix bug where list attributes were lost

R/StrategusModule.R

@@ -317,7 +317,7 @@ StrategusModule <- R6::R6Class(
   checkmate::assertClass(executionSettings, "ExecutionSettings", add = errorMessages)
   checkmate::reportAssertions(collection = errorMessages)
 
-  .replaceAttributes <- function(s) {
+  .replaceProperties <- function(s) {
     if (inherits(s, "covariateSettings") && "fun" %in% names(attributes(s))) {
       if (attr(s, "fun") == "getDbCohortBasedCovariatesData") {
         # Set the covariateCohortDatabaseSchema & covariateCohortTable values
@@ -329,10 +329,10 @@ StrategusModule <- R6::R6Class(
   }
   if (is.null(names(covariateSettings))) {
     # List of lists
-    modifiedCovariateSettings <- lapply(covariateSettings, .replaceAttributes)
+    modifiedCovariateSettings <- lapply(covariateSettings, .replaceProperties)
   } else {
     # Plain list
-    modifiedCovariateSettings <- .replaceAttributes(covariateSettings)
+    modifiedCovariateSettings <- .replaceProperties(covariateSettings)
   }
   return(modifiedCovariateSettings)
 }
@@ -351,7 +351,12 @@ StrategusModule <- R6::R6Class(
       return(.replaceCovariateSettingsCohortTableNames(x, executionSettings))
     } else if (is.list(x)) {
       # If the element is a list, recurse on each element
-      return(lapply(x, replaceHelper))
+      # Keep the original attributes by saving them before modification
+      attrs <- attributes(x)
+      newList <- lapply(x, replaceHelper)
+      # Restore attributes to the new list
+      attributes(newList) <- attrs
+      return(newList)
     } else {
       # If the element is not a list or "covariateSettings", return it as is
       return(x)

tests/testthat/test-Settings.R

@@ -414,6 +414,13 @@ test_that("Test internal function for modifying covariate settings", {
   # 1) covariate settings that do not contain cohort table settings
   # 2) covariate settings that contain cohort table settings
   # 3) a list of covariate setting that has 1 & 2 above
+  # 4) Something other than a covariate setting object
+  esModuleSettingsCreator <- EvidenceSynthesisModule$new()
+  evidenceSynthesisSourceCmGrid <- esModuleSettingsCreator$createEvidenceSynthesisSource(
+    sourceMethod = "CohortMethod",
+    likelihoodApproximation = "adaptive grid"
+  )
+
   cov1 <- FeatureExtraction::createDefaultCovariateSettings()
   cov2 <- FeatureExtraction::createCohortBasedCovariateSettings(
     analysisId = 999,
@@ -430,7 +437,8 @@ test_that("Test internal function for modifying covariate settings", {
         nested1 = cov1,
         nested2 = cov2,
         nested3 = covariateSettings
-      )
+      ),
+      esSettings = evidenceSynthesisSourceCmGrid
     )
   )
   workDatabaseSchema <- "foo"
@@ -444,6 +452,9 @@ test_that("Test internal function for modifying covariate settings", {
   )
 
   testReplacedModuleSettings <- .replaceCovariateSettings(moduleSettings, executionSettings)
+  # For visual inspection
+  #ParallelLogger::saveSettingsToJson(moduleSettings, "before_unit_test.json")
+  #ParallelLogger::saveSettingsToJson(testReplacedModuleSettings, "after_unit_test.json")
   expect_equal(testReplacedModuleSettings$analysis$something[[1]]$covariateCohortDatabaseSchema, NULL)
   expect_equal(testReplacedModuleSettings$analysis$something[[1]]$covariateCohortTable, NULL)
   expect_equal(testReplacedModuleSettings$analysis$something[[2]]$covariateCohortDatabaseSchema, workDatabaseSchema)
@@ -459,4 +470,5 @@ test_that("Test internal function for modifying covariate settings", {
   expect_equal(testReplacedModuleSettings$analysis$somethingElse$nested3[[1]]$covariateCohortTable, NULL)
   expect_equal(testReplacedModuleSettings$analysis$somethingElse$nested3[[2]]$covariateCohortDatabaseSchema, workDatabaseSchema)
   expect_equal(testReplacedModuleSettings$analysis$somethingElse$nested3[[2]]$covariateCohortTable, cohortTableNames$cohortTable)
+  expect_equal(class(testReplacedModuleSettings$analysis$esSettings), class(moduleSettings$analysis$esSettings))
 })