Feat/2 config

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: pacta.workflow.utils
 Title: Utility functions for PACTA workflows
-Version: 0.0.0.9004
+Version: 0.0.0.9005
 Authors@R: 
     c(person(given = "Alex",
              family = "Axthelm",
@@ -25,6 +25,7 @@ Imports:
 Suggests: 
     covr,
     devtools,
+    jsonvalidate,
     pak,
     testthat (>= 3.0.0),
     withr

R/parse_json_params.R

@@ -0,0 +1,124 @@
+parse_params <- function(
+  json,
+  inheritence_search_paths = NULL,
+  schema_file = NULL
+) {
+  log_trace("Parsing params.")
+  if (file.exists(json)) {
+    log_trace("Reading params from file: {json}.}")
+  } else {
+    log_trace("Reading params from string.")
+  }
+  raw_params <- jsonlite::fromJSON(json)
+  full_params <- inherit_params(
+    raw_params,
+    inheritence_search_paths
+  )
+
+  if (!is.null(schema_file)) {
+    if (requireNamespace("jsonvalidate", quietly = TRUE)) {
+      log_trace("Validating parameters.")
+      validation_results <- jsonvalidate::json_validate(
+        json = jsonlite::toJSON(full_params, auto_unbox = TRUE),
+        schema = schema_file,
+        verbose = TRUE
+      )
+      if (validation_results) {
+        log_trace("Validation successful.")
+      } else {
+        log_error("Validation against JSON Schema failed.")
+        log_error("Schema file: {schema_file}")
+        pretty_log_jsonvalidate_errors(validation_results)
+        stop("JSON Validation failed.")
+      }
+    } else {
+      log_error("jsonvalidate package not found.")
+      stop("jsonvalidate package not found.")
+    }
+  } else {
+    log_trace("No JSON Schema provided. Skipping validation.")
+  }
+
+  return(full_params)
+}
+
+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
+) {
+  errors <- attr(validation_object, "errors")
+  if (length(errors) == 0L) {
+    return(NULL)
+  }
+  for (row in seq(1L, nrow(errors))) {
+    logging_function("JSON Validation ({row} / {nrow(errors)}):")
+    logging_function("  Keyword: {errors[[row, 'keyword']]}")
+    logging_function("  instancePath: {errors[[row, 'instancePath']]}")
+    logging_function("  schemaPath: {errors[[row, 'schemaPath']]}")
+    logging_function("  Message: {errors[[row, 'message']]}")
+  }
+  return(errors)
+}