From ae31ddbf2c7511b389d234a0797ac7375906251b Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Fri, 14 Jul 2023 15:31:44 +0200
Subject: [PATCH] update ram_yaml

---
 .../helper_functions/read_and_merge_yaml.R    | 56 ++++++++++++-------
 1 file changed, 35 insertions(+), 21 deletions(-)

diff --git a/src/common/helper_functions/read_and_merge_yaml.R b/src/common/helper_functions/read_and_merge_yaml.R
index 2bc9a14ecb..932d3feb92 100644
--- a/src/common/helper_functions/read_and_merge_yaml.R
+++ b/src/common/helper_functions/read_and_merge_yaml.R
@@ -12,7 +12,7 @@ read_and_merge_yaml <- function(path, project_path = .ram_find_project(path)) {
   }, error = function(e) {
     stop("Could not read ", path, ". Error: ", e)
   })
-  .ram_process_merge(data, path, project_path)
+  .ram_process_merge(data, data, path, project_path)
 }
 
 .ram_find_project <- function(path) {
@@ -31,41 +31,51 @@ read_and_merge_yaml <- function(path, project_path = .ram_find_project(path)) {
   is.null(obj) || (is.list(obj) && (length(obj) == 0 || !is.null(names(obj))))
 }
 
-.ram_process_merge <- function(data, path, project_path) {
+.ram_process_merge <- function(data, root_data, path, project_path) {
   if (.ram_is_named_list(data)) {
     # check whether children have `__merge__` entries
     processed_data <- lapply(data, function(dat) {
-      .ram_process_merge(dat, path, project_path)
+      .ram_process_merge(dat, root_data, path, project_path)
+    })
+    processed_data <- lapply(names(data), function(nm) {
+      dat <- data[[nm]]
+      .ram_process_merge(dat, root_data, path, project_path)
     })
     names(processed_data) <- names(data)
 
     # if current element has __merge__, read list2 yaml and combine with data
     new_data <-
-      if ("__merge__" %in% names(processed_data)) {
+      if ("__merge__" %in% names(processed_data) && !.ram_is_named_list(processed_data$`__merge__`)) {
         new_data_path <- .ram_resolve_path(
           path = processed_data$`__merge__`,
           project_path = project_path,
           parent_path = dirname(path)
         )
         read_and_merge_yaml(new_data_path, project_path)
-      } else if ("$ref" %in% names(processed_data)) {
+      } else if ("$ref" %in% names(processed_data) && !.ram_is_named_list(processed_data$`$ref`)) {
         ref_parts <- strsplit(processed_data$`$ref`, "#")[[1]]
 
         # resolve the path in $ref
-        new_data_path <- .ram_resolve_path(
-          path = ref_parts[[1]],
-          project_path = project_path,
-          parent_path = dirname(path)
-        )
-        new_data_path <- normalizePath(new_data_path, mustWork = FALSE)
-
-        # read in the new data
         x <-
-          tryCatch({
-            suppressWarnings(yaml::read_yaml(new_data_path))
-          }, error = function(e) {
-            stop("Could not read ", new_data_path, ". Error: ", e)
-          })
+          if (ref_parts[[1]] == "") {
+            root_data
+          } else {
+            new_data_path <- .ram_resolve_path(
+              path = ref_parts[[1]],
+              project_path = project_path,
+              parent_path = dirname(path)
+            )
+            new_data_path <- normalizePath(new_data_path, mustWork = FALSE)
+
+            # read in the new data
+            tryCatch({
+              suppressWarnings(yaml::read_yaml(new_data_path))
+            }, error = function(e) {
+              stop("Could not read ", new_data_path, ". Error: ", e)
+            })
+          }
+        x_root <- x
+        
 
         # Navigate the path and retrieve the referenced data
         ref_path_parts <- unlist(strsplit(ref_parts[[2]], "/"))
@@ -75,12 +85,16 @@ read_and_merge_yaml <- function(path, project_path = .ram_find_project(path)) {
           } else if (part %in% names(x)) {
             x <- x[[part]]
           } else {
-            stop("Could not find ", part, " in ", new_data_path, "#", ref_parts[[2]])
+            stop("Could not find ", processed_data$`$ref`, " in ", path)
           }
         }
 
         # postprocess the new data
-        .ram_process_merge(x, new_data_path, project_path)
+        if (ref_parts[[1]] == "") {
+          x
+        } else {
+          .ram_process_merge(x, x_root, new_data_path, project_path)
+        }
       } else {
         list()
       }
@@ -88,7 +102,7 @@ read_and_merge_yaml <- function(path, project_path = .ram_find_project(path)) {
     .ram_deep_merge(new_data, processed_data)
   } else if (is.list(data)) {
     lapply(data, function(dat) {
-      .ram_process_merge(dat, path, project_path)
+      .ram_process_merge(dat, root_data, path, project_path)
     })
   } else {
     data