[annotation] Integration test of base+delta generation.

Author: ml-ebs-ext

R/review_structures.R

@@ -502,9 +502,10 @@ RS_append <- function(path, contents){
   close(f)
 }
 
-# NOTE: The contents of the following conditional are a WIP of the annotation feature.
-#       They are parked until user requirements and technical blockers are clarified.
-# TODO? Repurpose as test/performance test/"live documentation"
+# NOTE: The contents of the following conditional are a WIP of the review feature.
+#       They may be useful for performance testing, but maybe a higher-level approach,
+#       such as that on `tests/testthat/test-review.R`, is enough and we don't need
+#       to call the `RS_*` functions directly.
 if(FALSE){
   describe_and_time <- function(description, expr){
     t0 <- Sys.time()

tests/testthat/test-review.R

@@ -0,0 +1,57 @@
+local({
+  folder_contents <- NULL
+  fs_callbacks <- list(
+    attach = function(arg) NULL, list = function(arg) NULL, read = function(arg) NULL, write = function(arg) NULL,
+    append = function(arg) NULL, execute_IO_plan = function(arg) NULL,
+    read_folder = function(arg) folder_contents <<- arg
+  )
+  
+  store_path <- file.path(tempdir(), "data_checks")
+  dir.create(store_path)
+  on.exit(unlink(store_path, recursive = TRUE), add = TRUE, after = FALSE)
+  
+  fs_client <- fs_init(callbacks = fs_callbacks, store_path)
+  fs_client[["read_folder"]](subfolder_candidates = "dataset_list")
+  
+  # Review folder contents is initialized here
+  review = list(
+    datasets = list(
+      ae = list(
+        id_vars = c("USUBJID", "AESEQ"), 
+        tracked_vars = c(
+          "AESEV", "AETERM", "AEHLGT", "AEHLT", "AELLT", 
+          "AEDECOD", "AESOC", "AESTDTC", "AEENDTC", "AESTDY","AEOUT", "AEACN", "AEREL"
+        )
+      )
+    ),
+    choices = c("choiceA", "choiceB"),
+    roles = c("roleA", "roleB")
+  )
+  
+  dataset_lists <- list(
+    dataset_list = list(
+      ae = safetyData::sdtm_ae[1:2,]
+    )
+  )
+  
+  info <- REV_load_annotation_info(folder_contents, review, dataset_lists)
+  expect_length(info[["error"]], 0)
+  fs_client[["execute_IO_plan"]](IO_plan = info[["folder_IO_plan"]], is_init = TRUE)
+  fs_client[["read_folder"]](subfolder_candidates = "dataset_list")
+  
+  test_that("Detect modification of previously known row and output new delta file", {
+    dataset_lists2 <- dataset_lists
+    dataset_lists2[["dataset_list"]][["ae"]][["AESEV"]][[1]] <- "SEVERE"
+    
+    info <- REV_load_annotation_info(folder_contents, review, dataset_lists2)
+    expect_length(info[["error"]], 0)
+    expect_length(info[["folder_IO_plan"]], 1)
+    folder_op <- info[["folder_IO_plan"]][[1]]
+    expect_equal(folder_op[["type"]], "write_file")
+    expect_equal(folder_op[["fname"]], "ae_001.delta")
+    
+    delta <- RS_parse_delta(info[["folder_IO_plan"]][[1]][["contents"]], 13)
+    
+    expect_equal(delta[["modified_row_indices"]], c(1L))
+  })
+})