add tests, use use_grs param instead

scripts/uploads/merge_and_uncode_rca_uploads.R

@@ -323,16 +323,17 @@ merge_mappings <- function(primarys, secondarys, debug = F) {
 #' @param dd Matrix with two columns, first containing a label and
 #' second columns a mapping string.  
 #' @param grs Another mapping matrix that is used secondarily
-#' if the label is not found in the primary mapping matrix. Optional.
+#' if the label is not found in the primary mapping matrix.
+#' @param use_grs Whether we are using grs or not
 #' @return Data frame of uncoded data.
 #' @example
 #' map_code_to_value(data = my_data, dd = dd, grs = grs)
-uncode_data <- function(df_coded, dd, grs = NULL) {
+uncode_data <- function(df_coded, dd, grs, use_grs) {
 
   df_uncoded <- df_coded
 
   # merge reference mappings
-  if(!is.null(grs)){
+  if(use_grs){
     mappings_primary <- parse_mappings(strs = grs[,config$column_name$variable_mapping], 
                                       labels = grs[,config$column_name$variable_name])
     mappings_secondary <- parse_mappings(strs = dd[[config$column_name$variable_mapping]], 
@@ -597,9 +598,10 @@ get_data_dictionary <- function(cohort) {
   return(dd)
 }
 
-#' Retrieves the Global Response Set (grs)
+#' Retrieves the Global Response Set (grs) depending 
+#' on value of use_grs. If not using grs, returns NULL
 #' 
-#' @param use_grs Whether to retrieve it or not
+#' @param use_grs Whether to use grs or not
 #' @return grs
 get_global_response_set <- function(use_grs){
   if(use_grs){
@@ -744,7 +746,7 @@ main <- function(){
     make_option(c("--comment"), type = "character",
               help="Comment for new table snapshot version. This must be unique and is tied to the cohort run."),
     make_option(c("--use_grs"), type="logical", default = FALSE,
-              help="Whether to use GRS / DD or just DD for mapping")
+              help="Whether to use grs as primary mapping (dd as secondary) or not (using dd only).")
   )
   opt <- parse_args(OptionParser(option_list=option_list))
 
@@ -817,7 +819,8 @@ main <- function(){
     # uncode
     uncoded <- uncode_data(df_coded = coded, 
                           dd = dd,
-                          grs = grs)
+                          grs = grs,
+                          use_grs = opt$use_grs)
 
     if (debug) {
       print(glue("{now(timeOnly = T)}: Formatting uncoded data..."))

scripts/uploads/tests/test_merge_and_uncode_rca_uploads.R

@@ -1,3 +1,4 @@
+library(mockery)
 library(testthat)
 
 source(testthat::test_path("..", "merge_and_uncode_rca_uploads.R"))
@@ -8,18 +9,78 @@ setup({
   if (!file.exists("config.yaml")) {
     workdir <- "/usr/local/src/myscripts"
   }
-  config <<- read_yaml(glue("{workdir}/config.yaml"))
+  config_path <<- read_yaml(glue("{workdir}/config.yaml"))
+
+  # Mock config
+  config <<- list(
+    synapse = list(
+      prissmm = list(id = "mock_prissmm_id"),
+      grs = list(id = "mock_grs_id")
+    ),
+    upload = list(
+      cohort1 = list(
+        site1 = list(
+          data1 = "mock_data1_id",
+          data2 = "mock_data2_id"
+        ),
+        site2 = list(
+          data1 = "mock_data3_id",
+          data2 = "mock_data4_id"
+        )
+      )
+    )
+  )
 
 })
 
 
 test_that("get_output_folder_id gets expected id when environment is production", {
-    folder_id <- get_output_folder_id(config, environment = "production")
+    folder_id <- get_output_folder_id(config_path, environment = "production")
     expect_equal(folder_id, "syn23286928")
 })
 
 
 test_that("get_output_folder_id gets expected id when environment is staging", {
-    folder_id <- get_output_folder_id(config, environment = "staging")
+    folder_id <- get_output_folder_id(config_path, environment = "staging")
     expect_equal(folder_id, "syn63887337")
-})
+})
+
+
+test_that("get_global_response_set returns NULL when use_grs is FALSE", {
+  result <- get_global_response_set(use_grs = FALSE)
+  expect_null(result)
+})
+
+
+test_that("get_global_response_set calls read.csv and returns data when use_grs is TRUE", {
+  mock_read_csv <- mock(data.frame(a = 1:3, b = 4:6))  # Example mock data frame
+  stub(get_global_response_set, "read.csv", mock_read_csv)
+
+  mock_synGet <- mock(list(path = "mock_path"))
+  stub(get_global_response_set, "synGet", mock_synGet)
+
+  result <- get_global_response_set(use_grs = TRUE)
+
+  # Verify the function returns the mocked data frame
+  expect_equal(result, data.frame(a = 1:3, b = 4:6))
+})
+
+
+test_that("get_prov_used returns correct prov when use_grs is FALSE", {
+  # Mock the `get_bpc_synid_prissmm` function
+  mock_get_bpc_synid_prissmm <- mock("mock_synid_dd")
+  stub(get_prov_used, "get_bpc_synid_prissmm", mock_get_bpc_synid_prissmm)
+
+  result <- get_prov_used(cohort = "cohort1", use_grs = FALSE)
+  expect_equal(result, c("mock_data1_id", "mock_data2_id", "mock_data3_id", "mock_data4_id", "mock_synid_dd"))
+})
+
+test_that("get_prov_used returns correct prov when use_grs is TRUE", {
+  # Mock the `get_bpc_synid_prissmm` function
+  mock_get_bpc_synid_prissmm <- mock("mock_synid_dd")
+  stub(get_prov_used, "get_bpc_synid_prissmm", mock_get_bpc_synid_prissmm)
+
+  result <- get_prov_used(cohort = "cohort1", use_grs = TRUE)
+  print(result)
+  expect_equal(result, c("mock_data1_id", "mock_data2_id", "mock_data3_id", "mock_data4_id", "mock_synid_dd", "mock_grs_id"))
+})