Merge pull request #37 from RMI-PACTA/multiple-inherit

Multiple inherit

R/inherit_params.R

@@ -0,0 +1,90 @@
+#' inherit_params
+#'
+#' Inherit parameters from a JSON file. This function will search for a file
+#' (in `inheritence_search_paths`) with the name of the value of the `inherit`
+#' key in the `params` list. If found, the parameters in that file will be
+#' overlaid onto the `params` list. This process will continue until no
+#' `inherit` key is found. It is possible to specify multiple values in the
+#' `inherit` key; doing so will cause the parameters from each file to be
+#' overlaid onto the `params` list in the order specified. If inherit is
+#' `list("file01", "file02")`, then the `params` list will remain as-is, any
+#' _new_ values from `file01` will be added, and then any new values that
+#' aren't in `params` or `file01` will be added from `file02`.
+#'
+#' @param params list of parameters, which may include an inheritence key
+#' (`inherit`).
+#' @param inheritence_search_paths Paths to search for inherited parameters.
+#' @param inherited_files Paths of files that have already been inherited from
+#' (Used in recursive calls, not for user use).
+#' @return merged list of parameters, with inherited parameters overlaid onto
+#' `params`.
+#' @export
+inherit_params <- function(
+  params,
+  inheritence_search_paths,
+  inherited_files = NULL
+) {
+  inherit_key <- "inherit"
+
+  if (inherit_key %in% names(params)) {
+
+    # check for multiple inheritence keys
+    if (sum(names(params) == inherit_key) > 1L) {
+      log_error("Multiple inheritence keys found.")
+      stop("Multiple inheritence keys found.")
+    }
+
+    log_trace(
+      "Key \"{inherit_key}\" found in parameters. Inheriting parameters."
+    )
+
+    to_inherit_vec <- params[[inherit_key]]
+    if (anyDuplicated(to_inherit_vec) != 0L) {
+      log_error("Duplicate values found in inheritence key.")
+      stop("Duplicate values found in inheritence key.")
+    }
+    params[[inherit_key]] <- NULL # remove inherit key
+
+    for (to_inherit in to_inherit_vec) {
+
+      possible_paths <- file.path(
+        inheritence_search_paths,
+        paste0(to_inherit, ".json")
+      )
+      candidate_file <- possible_paths[file.exists(possible_paths)]
+      if (length(candidate_file) == 0L) {
+        log_error("Inheritence file not found: {possible_paths}.")
+        stop("Inheritence file not found.")
+      } else {
+        if (length(candidate_file) > 1L) {
+          log_warn("Multiple files matching inheritence pattern found:")
+          log_warn("{candidate_file}.")
+          warning("Multiple inheritence files found.")
+          candidate_file <- candidate_file[[1L]]
+          log_warn("Using first file: {candidate_file}.")
+        }
+      }
+      if (candidate_file %in% inherited_files) {
+        log_error(
+          "Inheritence loop detected while inheriting from {candidate_file}."
+        )
+        log_error("Inherited file: {inherited_files}.")
+        stop("Inheritence loop detected.")
+      }
+      inherited_files <- c(inherited_files, candidate_file)
+      log_trace("Inheriting parameters from file: {candidate_file}.")
+      params_to_inherit <- inherit_params(
+        params = jsonlite::fromJSON(candidate_file),
+        inheritence_search_paths = inheritence_search_paths,
+        inherited_files = inherited_files
+      )
+      params <- merge_lists(
+        base_list = params_to_inherit,
+        overlay_list = params
+      )
+    }
+  }
+
+  log_trace("No inheritence key (\"{inherit_key}\") found.")
+  return(params)
+}

R/parse_params.R

@@ -63,83 +63,6 @@ parse_params <- function(
   return(full_params)
 }
 
-#' inherit_params
-#'
-#' Inherit parameters from a JSON file. This function will search for a file
-#' (in `inheritence_search_paths`) with the name of the value of the `inherit`
-#' key in the `params` list. If found, the parameters in that file will be
-#' overlaid onto the `params` list. This process will continue until no
-#' `inherit` key is found.
-#'
-#' @param params list of parameters, which may include an inheritence key
-#' (`inherit`).
-#' @param inheritence_search_paths Paths to search for inherited parameters.
-#' @return merged list of parameters, with inherited parameters overlaid onto
-#' `params`.
-#' @export
-inherit_params <- function(
-  params,
-  inheritence_search_paths
-) {
-  inherit_key <- "inherit"
-
-  inherited_files <- NULL
-  while (inherit_key %in% names(params)) {
-
-    # check for multiple inheritence keys
-    if (sum(names(params) == inherit_key) > 1L) {
-      log_error("Multiple inheritence keys found.")
-      stop("Multiple inheritence keys found.")
-    }
-
-    log_trace(
-      "Key \"{inherit_key}\" found in parameters. Inheriting parameters."
-    )
-
-    to_inherit <- params[[inherit_key]]
-    if (length(to_inherit) > 1L) {
-      log_error("Multiple values in inherit key.")
-      stop("Multiple values in inherit key.")
-    }
-    params[[inherit_key]] <- NULL # remove inherit key
-
-    possible_paths <- file.path(
-      inheritence_search_paths,
-      paste0(to_inherit, ".json")
-    )
-    candidate_file <- possible_paths[file.exists(possible_paths)]
-    if (length(candidate_file) == 0L) {
-      log_error("Inheritence file not found: {possible_paths}.")
-      stop("Inheritence file not found.")
-    } else {
-      if (length(candidate_file) > 1L) {
-        log_warn("Multiple files matching inheritence pattern found:")
-        log_warn("{candidate_file}.")
-        warning("Multiple inheritence files found.")
-        candidate_file <- candidate_file[[1L]]
-        log_warn("Using first file: {candidate_file}.")
-      }
-    }
-    if (candidate_file %in% inherited_files) {
-      log_error(
-        "Inheritence loop detected while inheriting from {candidate_file}."
-      )
-      log_error("Inherited file: {inherited_files}.")
-      stop("Inheritence loop detected.")
-    }
-    inherited_files <- c(inherited_files, candidate_file)
-    log_trace("Inheriting parameters from file: {candidate_file}.")
-    inherit_params <- jsonlite::fromJSON(candidate_file)
-    params <- merge_lists(
-      base_list = inherit_params,
-      overlay_list = params
-    )
-  }
-
-  log_trace("No inheritence key (\"{inherit_key}\") found.")
-  return(params)
-}
-
 pretty_log_jsonvalidate_errors <- function(
   validation_object,
   logging_function = log_error