fix docs functions

packages/r/openproblems.docs/R/read_component_spec.R

@@ -18,7 +18,7 @@ read_component_spec <- function(path) {
 
   tryCatch(
     {
-      validate_object(spec_yaml, obj_source = file, what = "api_component_spec")
+      validate_object(spec_yaml, obj_source = path, what = "api_component_spec")
     },
     error = function(e) {
       cli::cli_warn(paste0("Component spec validation failed: ", e$message))

packages/r/openproblems.docs/R/read_file_format.R

@@ -3,7 +3,7 @@
 #' This function reads a file format spec from a yaml file.
 #'
 #' @param path Path to a file format yaml, usually in `src/api/file_*.yaml`
-#' @return A list with file format info and slots/columns
+#' @return A list with file format info and expected_format
 #'
 #' @export
 #' @examples
@@ -18,7 +18,7 @@ read_file_format <- function(path) {
 
   tryCatch(
     {
-      validate_object(spec, obj_source = file, what = "api_file_format")
+      validate_object(spec, obj_source = path, what = "api_file_format")
     },
     error = function(e) {
       cli::cli_warn(paste0("File format validation failed: ", e$message))

packages/r/openproblems.docs/R/read_task_config.R

@@ -1,25 +1,25 @@
 #' Read project config
 #'
-#' @param file Path to a project config file
+#' @param path Path to a project config file
 #'
 #' @importFrom cli cli_inform
 #' @importFrom openproblems.utils validate_object
 #'
 #' @export
 #'
 #' @examples
-#' file <- system.file(
+#' path <- system.file(
 #'   "extdata", "example_project", "_viash.yaml",
 #'   package = "openproblems.docs"
 #' )
 #'
-#' read_task_config(file)
-read_task_config <- function(file) {
-  proj_conf <- openproblems::read_nested_yaml(file)
+#' read_task_config(path)
+read_task_config <- function(path) {
+  proj_conf <- openproblems::read_nested_yaml(path)
 
   tryCatch(
     {
-      validate_object(proj_conf, obj_source = file, what = "task_config")
+      validate_object(proj_conf, obj_source = path, what = "task_config")
     },
     error = function(e) {
       cli::cli_warn(paste0("Project config validation failed: ", e$message))

packages/r/openproblems.docs/R/read_task_metadata.R

@@ -31,21 +31,17 @@ read_task_metadata <- function(path) {
   proj_conf <- read_task_config(proj_conf_file)
 
   cli::cli_inform("Reading component yamls")
-  comp_yamls <- list.files(path, pattern = "comp_.*\\.ya?ml", full.names = TRUE)
+  comp_yamls <- list.files(path, pattern = "comp_[a-zA-Z0-9_\\-]*\\.ya?ml", full.names = TRUE, recursive = TRUE)
   comps <- map(comp_yamls, read_component_spec)
   comp_info <- map_dfr(comps, "info")
   comp_args <- map_dfr(comps, "args")
   names(comps) <- comp_info$file_name
 
   cli::cli_inform("Reading file yamls")
-  file_yamls <- openproblems:::resolve_path(
-    path = na.omit(unique(comp_args$`__merge__`)),
-    project_path = project_path,
-    parent_path = path
-  )
+  file_yamls <- list.files(path, pattern = "file_[a-zA-Z0-9_\\-]*\\.ya?ml", full.names = TRUE, recursive = TRUE)
   files <- map(file_yamls, read_file_format)
   file_info <- map_dfr(files, "info")
-  file_slots <- map_dfr(files, "slots")
+  file_expected_format <- map_dfr(files, "expected_format")
   names(files) <- file_info$file_name
 
   cli::cli_inform("Generating task graph")
@@ -58,7 +54,7 @@ read_task_metadata <- function(path) {
     proj_conf = proj_conf,
     files = files,
     file_info = file_info,
-    file_slots = file_slots,
+    file_expected_format = file_expected_format,
     comps = comps,
     comp_info = comp_info,
     comp_args = comp_args,

packages/r/openproblems.utils/R/validate_object.R

@@ -40,7 +40,7 @@ validate_object <- function(
       "task_metric"
     ),
     obj_source = NULL,
-    engine = c("imjv", "ajv"),
+    engine = c("ajv", "imjv"),
     error = TRUE) {
   what <- match.arg(what)
   engine <- match.arg(engine)