Sanitize NULL values for search result processing (#18)

Added unit test coverage for null handling scenario.

R/bdc.R

@@ -143,6 +143,12 @@ initializeGenomicAnnotations <- function(session) {
 
 # Maps the search results to a more user friendly format, which is valid to be turned into a data frame
 projectAndFilterResults = function(results, scopes, showAll) {
+  # Replace NULL values with an empty string for string fields
+  sanitize <- function(value) {
+    if (is.null(value)) return("")
+    return(value)
+  }
+
   scopes = if (is.null(scopes)) c() else stringr::str_replace_all(scopes[str_detect(scopes, "^\\\\")], "\\\\", "")
   in_scope = function(study) Reduce(function(acc, scope) (acc | stringr::str_detect(study, fixed(scope))), scopes, init=FALSE)
 
@@ -158,21 +164,21 @@ projectAndFilterResults = function(results, scopes, showAll) {
 
     paths <- c(paths, resultMetadata$columnmeta_HPDS_PATH)
     results[[index]] <- list(
-      name = resultMetadata$columnmeta_HPDS_PATH,
-      var_id = resultMetadata$derived_var_id,
-      var_name = resultMetadata$derived_var_name,
-      var_description = resultMetadata$derived_var_description,
-      data_type = resultMetadata$columnmeta_data_type,
-      group_id = resultMetadata$derived_group_id,
-      group_name = resultMetadata$derived_group_name,
-      group_description = resultMetadata$derived_group_description,
-      study_id = resultMetadata$derived_study_id,
-      study_description = resultMetadata$derived_study_description,
-      is_stigmatized = resultMetadata$is_stigmatized,
+      name = sanitize(resultMetadata$columnmeta_HPDS_PATH),
+      var_id = sanitize(resultMetadata$derived_var_id),
+      var_name = sanitize(resultMetadata$derived_var_name),
+      var_description = sanitize(resultMetadata$derived_var_description),
+      data_type = sanitize(resultMetadata$columnmeta_data_type),
+      group_id = sanitize(resultMetadata$derived_group_id),
+      group_name = sanitize(resultMetadata$derived_group_name),
+      group_description = sanitize(resultMetadata$derived_group_description),
+      study_id = sanitize(resultMetadata$derived_study_id),
+      study_description = sanitize(resultMetadata$derived_study_description),
+      is_stigmatized = sanitize(resultMetadata$is_stigmatized),
       min = if (categorical) NA else as.numeric(resultMetadata$columnmeta_min),
       max = if (categorical) NA else as.numeric(resultMetadata$columnmeta_max),
       categorical = categorical,
-      values = toString(results[[index]]$result$values)
+      values = sanitize(toString(results[[index]]$result$values))
     )
     include_list <- c(include_list, index)
   }

tests/testthat/test-bdc.R

@@ -0,0 +1,70 @@
+source("../../R/bdc.R", chdir = TRUE)
+library(testthat)
+
+test_that("projectAndFilterResults handles nulls and in-scope results correctly", {
+  # Mock input data
+  mockResults <- list(
+    list(result = list(
+      metadata = list(
+        columnmeta_HPDS_PATH = "\\phs000001\\unit_test\\test_categorical_variable\\",
+        derived_var_id = "var1",
+        derived_var_name = NULL,  # Should be converted to ""
+        derived_var_description = NULL,  # Should be converted to ""
+        columnmeta_data_type = "categorical",
+        derived_group_id = "group1",
+        derived_group_name = NULL,  # Should be converted to ""
+        derived_group_description = "desc1",
+        derived_study_id = "study1",
+        derived_study_description = NULL,  # Should be converted to ""
+        is_stigmatized = NULL,  # Should be converted to ""
+        columnmeta_min = NULL,
+        columnmeta_max = NULL
+      ),
+      is_categorical = TRUE,
+      values = NULL  # Should be converted to ""
+    )),
+    list(result = list(
+      metadata = list(
+        columnmeta_HPDS_PATH = "\\phs000001\\unit_test\\test_continuous_variable\\",
+        derived_var_id = "var2",
+        derived_var_name = "Test Continuous Variable",
+        derived_var_description = "A test continuous variable",
+        columnmeta_data_type = "continuous",
+        derived_group_id = "group2",
+        derived_group_name = "Test Group",
+        derived_group_description = "A description for group 2",
+        derived_study_id = "study2",
+        derived_study_description = "Study 2 Description",
+        is_stigmatized = "false",
+        columnmeta_min = "1.1",
+        columnmeta_max = "42"
+      ),
+      is_categorical = FALSE,
+      values = ""  # Should remain unchanged
+    ))
+  )
+
+  mockScopes <- c("phs000001")
+  mockShowAll <- TRUE
+
+  # Run the function
+  result <- projectAndFilterResults(mockResults, mockScopes, mockShowAll)
+
+  expect_true(length(result$results) > 0, info = "No results returned; check input data or filtering logic.")
+
+  # Verify results structure
+  expect_true(is.list(result))
+  expect_named(result, c("results", "paths"))
+
+  # Verify paths
+  expect_equal(result$paths, c("\\phs000001\\unit_test\\test_categorical_variable\\", "\\phs000001\\unit_test\\test_continuous_variable\\"))
+
+  expect_equal(result$results[[1]]$var_name, "")  # NULL replaced with ""
+  expect_equal(result$results[[1]]$min, NA)  # Categorical, so NA
+  expect_equal(result$results[[1]]$categorical, TRUE)
+
+  expect_equal(result$results[[2]]$name, "\\phs000001\\unit_test\\test_continuous_variable\\")
+  expect_equal(result$results[[2]]$min, 1.1)  # Converted to numeric
+  expect_equal(result$results[[2]]$max, 42)  # Converted to numeric
+  expect_equal(result$results[[2]]$categorical, FALSE)
+})