Check dataset fix

NAMESPACE

@@ -3,11 +3,13 @@
 S3method(base::`$`, hyperion_nonmem_model)
 S3method(base::`[[`, hyperion_nonmem_model)
 S3method(base::names, hyperion_nonmem_model)
+S3method(base::print, hyperion_nonmem_dataset)
 S3method(base::print, hyperion_nonmem_model)
 S3method(base::print, hyperion_nonmem_summary)
 S3method(base::print, hyperion_nonmem_tree)
 S3method(base::print, parameter_audit)
 S3method(base::summary, hyperion_nonmem_model)
+S3method(knitr::knit_print,hyperion_nonmem_dataset)
 S3method(knitr::knit_print,hyperion_nonmem_model)
 S3method(knitr::knit_print,hyperion_nonmem_summary)
 S3method(knitr::knit_print,hyperion_nonmem_tree)
@@ -33,14 +35,17 @@ export(format_hyperion_sigfig_string)
 export(format_omega_display_name)
 export(get_comment)
 export(get_comment_type)
+export(get_data_path)
 export(get_eps_shrinkage)
 export(get_eta_labels)
 export(get_eta_shrinkage)
 export(get_final_estimates)
 export(get_gradients)
 export(get_model_ancestors)
 export(get_model_descendants)
+export(get_model_dir)
 export(get_model_lineage)
+export(get_model_name)
 export(get_model_parameter_info)
 export(get_model_summary)
 export(get_parameter_names)

NEWS.md

@@ -45,11 +45,22 @@
 - Expand NONMEM example data bundled with the package.
 - Refresh documentation, man pages, and vignettes to cover new APIs and examples.
 
+### Model Utilities
+
+- New model accessor functions:
+  - `get_model_name()` - Get the model name (filename without extension)
+  - `get_model_dir()` - Get the model directory path (relative to pharos.toml)
+  - `get_data_path()` - Get the dataset path from the model
+- `check_dataset()` now automatically derives the model directory from the
+  `model_source` attribute, removing the need for the `model_dir` argument.
+
 ## Breaking Changes
 
 - `get_model_summary()` is deprecated in favor of `summary(mod)`.
 - Parameter data frame column renamed: `value` is now `estimate`.
 - Test data relocated from `vignettes/test_data/` to `inst/extdata/`.
+- `check_dataset()` no longer accepts a `model_dir` argument; the directory is
+  now derived automatically from the model's `model_source` attribute.
 
 ## Dependencies
 

R/comments-parsing.R

@@ -69,7 +69,7 @@ read_model_from_lst_dir <- function(dir_path) {
 #' Derive output directory from model path and read from .lst file
 #' @noRd
 read_model_from_lst_path <- function(mod_path) {
-  mod_path <- resolve_model_source_path(mod_path)
+  mod_path <- from_config_relative(mod_path)
   # Derive output directory: run001.mod -> run001/
   base_name <- tools::file_path_sans_ext(basename(mod_path))
   parent_dir <- dirname(mod_path)
@@ -129,7 +129,7 @@ get_model_parameter_info <- function(mod, lookup_path = NULL) {
   } else if (inherits(mod, "hyperion_nonmem_model")) {
     mod_path <- attr(mod, "model_source") %||% "unknown"
     if (!identical(mod_path, "unknown")) {
-      mod_path <- resolve_model_source_path(mod_path)
+      mod_path <- from_config_relative(mod_path)
     }
     # If model was read from .mod/.ctl file, find and read from .lst instead
     if (!grepl("\\.lst$", mod_path, ignore.case = TRUE)) {
@@ -153,7 +153,7 @@ get_model_parameter_info <- function(mod, lookup_path = NULL) {
 
   mod_path <- attr(mod, "model_source") %||% "unknown"
   if (!identical(mod_path, "unknown")) {
-    mod_path <- resolve_model_source_path(mod_path)
+    mod_path <- from_config_relative(mod_path)
   }
 
   param_names <- get_model_parameter_names(mod)

R/dataset.R

@@ -0,0 +1,41 @@
+#' Print method for hyperion_nonmem_dataset objects
+#'
+#' @param x A hyperion_nonmem_dataset object
+#' @param ... Additional arguments (ignored)
+#' @return Invisible copy of x
+#' @rawNamespace S3method(base::print, hyperion_nonmem_dataset)
+print.hyperion_nonmem_dataset <- function(x, ...) {
+  rel_path <- to_config_relative(x$canonical_path)
+
+  cli::cli_h1("Dataset Check")
+  cli::cli_text("{.strong Path:} {rel_path}")
+  cli::cli_text("{.strong Hash:} {x$blake3_hash}")
+
+  invisible(x)
+}
+
+#' Knit print method for hyperion_nonmem_dataset objects
+#'
+#' @param x A hyperion_nonmem_dataset object
+#' @param ... Additional arguments (ignored)
+#' @return HTML output for rendered documents
+#' @exportS3Method knitr::knit_print
+knit_print.hyperion_nonmem_dataset <- function(x, ...) {
+  rel_path <- to_config_relative(x$canonical_path)
+
+  df <- data.frame(
+    Field = c("Path", "Hash"),
+    Value = c(rel_path, x$blake3_hash),
+    stringsAsFactors = FALSE
+  )
+
+  tbl <- knitr::kable(df, format = "html", col.names = NULL, escape = FALSE)
+
+  output <- c(
+    "<strong>Dataset Check</strong>",
+    "",
+    tbl
+  )
+
+  knitr::asis_output(paste(output, collapse = "\n"))
+}

R/extendr-wrappers.R

@@ -41,17 +41,16 @@ read_model <- function(path) .Call(wrap__read_model, path)
 
 #' Checks model dataset
 #'
-#' @param model list of model object from `read_model`
-#' @param model_dir directory of model output //TODO check this
+#' @param model hyperion_nonmem_model object from `read_model`
 #'
-#' @return nothing //todo maybe a true/false?
+#' @return Dataset check results
 #' @export
 #'
 #' @examples \dontrun{
 #' model <- read_model("model/nonmem/run001.mod")
-#' model |> check_dataset("model/nonmem/run001")
+#' model |> check_dataset()
 #' }
-check_dataset <- function(model, model_dir) .Call(wrap__check_dataset, model, model_dir)
+check_dataset <- function(model) .Call(wrap__check_dataset, model)
 
 #' Gets model object from lst file (internal)
 #'
@@ -421,15 +420,25 @@ get_pharos_config <- function() .Call(wrap__get_pharos_config)
 #' }
 get_comment_type <- function() .Call(wrap__get_comment_type_wrap)
 
+#' Validate and resolve a model path (.mod or .ctl).
+#'
+#' @keywords internal
+#' @noRd
+validate_model_path <- function(path) .Call(wrap__validate_model_path_wrap, path)
+
+#' Convert a config-relative path to absolute.
+#'
 #' @keywords internal
 #' @noRd
-resolve_input_model_path <- function(path) .Call(wrap__resolve_input_model_path_wrap, path)
+from_config_relative <- function(path) .Call(wrap__from_config_relative_wrap, path)
 
-#' Resolve a model_source string into an absolute or config-relative path.
+#' Convert an absolute path to be relative to the pharos config directory.
 #'
+#' @param path Absolute path to make relative.
+#' @return Path relative to pharos.toml directory, or original path if not under config dir.
 #' @keywords internal
 #' @noRd
-resolve_model_source_path <- function(path) .Call(wrap__resolve_model_source_path_wrap, path)
+to_config_relative <- function(path) .Call(wrap__to_config_relative_wrap, path)
 
 #' Submits a NONMEM model to SLURM for execution
 #'

R/hyperion-package.R

@@ -12,6 +12,9 @@
 #'   \item [copy_model()] - Copy a model to a new file with optional parameter updates
 #'   \item [check_model()] - Validate model syntax
 #'   \item [check_dataset()] - Validate model dataset
+#'   \item [get_model_name()] - Get the model name (filename without extension)
+#'   \item [get_model_dir()] - Get the model directory path
+#'   \item [get_data_path()] - Get the dataset path from the model
 #' }
 #'
 #' @section Model Summaries:

R/model-methods.R

@@ -684,3 +684,62 @@ knit_print.hyperion_nonmem_model <- function(x, ...) {
   # Return as HTML
   knitr::asis_output(paste(output, collapse = "\n"))
 }
+
+#' Get model name
+#'
+#' Extracts the model name from a hyperion_nonmem_model object.
+#'
+#' @param model A hyperion_nonmem_model object
+#' @return Character string with the model name (filename without extension)
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' mod <- read_model("models/run001.mod")
+#' get_model_name(mod) # "run001"
+#' }
+get_model_name <- function(model) {
+  model_source <- attr(model, "model_source")
+  if (is.null(model_source)) {
+    stop("Model object is missing model_source attribute")
+  }
+  tools::file_path_sans_ext(basename(model_source))
+}
+
+#' Get model directory
+#'
+#' Extracts the directory path from a hyperion_nonmem_model object.
+#'
+#' @param model A hyperion_nonmem_model object
+#' @return Character string with the model directory path (relative to pharos.toml)
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' mod <- read_model("models/run001.mod")
+#' get_model_dir(mod) # "models"
+#' }
+get_model_dir <- function(model) {
+  model_source <- attr(model, "model_source")
+  if (is.null(model_source)) {
+    stop("Model object is missing model_source attribute")
+  }
+  dirname(model_source)
+}
+
+#' Get data path
+#'
+#' Extracts the dataset path from a hyperion_nonmem_model object.
+#'
+#' @param model A hyperion_nonmem_model object
+#' @return Character string with the data path, or NULL if not found
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' mod <- read_model("models/run001.mod")
+#' get_data_path(mod) # "../data/derived/pk_data.csv"
+#' }
+get_data_path <- function(model) {
+  model$data$path
+}