Merge pull request #705 from metrumresearchgroup/feat/run_nmtran

Function to run NMTRAN on a model

NAMESPACE

@@ -76,6 +76,7 @@ S3method(print,bbi_nmboot_summary)
 S3method(print,bbi_nonmem_summary)
 S3method(print,bbi_process)
 S3method(print,model_tree_static)
+S3method(print,nmtran_process)
 S3method(print_model_files,default)
 S3method(submit_model,bbi_base_model)
 S3method(submit_model,bbi_nmboot_model)
@@ -194,6 +195,7 @@ export(replace_model_field)
 export(replace_note)
 export(replace_tag)
 export(run_log)
+export(run_nmtran)
 export(setup_bootstrap_run)
 export(submit_model)
 export(submit_models)

R/aaa.R

@@ -53,7 +53,7 @@ BBI_ARGS = list(
   delay = list(
     type = "numeric",
     flag = "--delay",
-    description = "Selects a random number of seconds between 1 and this value to stagger / jitter job execution. Assists in dealing with large volumes of work dealing with the same data set. May avoid NMTRAN issues about not being able read / close files"
+    description = "Selects a random number of seconds between 1 and this value to stagger / jitter job execution. Assists in dealing with large volumes of work dealing with the same data set. May avoid NM-TRAN issues about not being able read / close files"
   ),
   ext_file = list(
     type = "character",
@@ -209,6 +209,7 @@ RUN_LOG_CLASS <- "bbi_run_log_df"
 CONF_LOG_CLASS <- "bbi_config_log_df"
 SUM_LOG_CLASS <- "bbi_summary_log_df"
 LOG_DF_CLASS <- "bbi_log_df"
+NMTRAN_PROCESS_CLASS <- "nmtran_process"
 
 # YAML keys that are hard-coded
 YAML_YAML_MD5 <- "yaml_md5"

R/get-path-from-object.R

@@ -367,7 +367,7 @@ get_data_path_nonmem <- function(
 
   if(isTRUE(.check_exists)){
     if(!fs::file_exists(data_path)){
-      # The first error message line is what NMTRAN would return in this situation
+      # The first error message line is what NM-TRAN would return in this situation
       rlang::abort(
         c(
           "x" = "Input data file does not exist or cannot be opened",

R/print.R

@@ -442,6 +442,58 @@ print.bbi_nmboot_summary <- function(x, .digits = 3, .nrow = 10, ...) {
   }
 }
 
+
+#' @describeIn print_bbi Prints the `NM-TRAN` evaluation of a `bbi_nonmem_model`
+#'  object
+#' @export
+print.nmtran_process <- function(x, ...){
+
+  is_valid_print <- function(.x) {
+    if (!is.null(.x)) {
+      length(.x) != 0
+    } else {
+      FALSE
+    }
+  }
+
+  heading <- cli_h1
+  subheading <- cli_h2
+  bullet_list <- cat_bullet
+
+  status <- x[["status"]]
+  if (x[["status_val"]] == 0) {
+    status <- col_green(status)
+  } else {
+    status <- col_red(status)
+  }
+
+  heading(cli::col_magenta("NM-TRAN Status"))
+  subheading(status)
+
+  heading("Absolute Model Path")
+  bullet_list(x[[ABS_MOD_PATH]])
+
+  heading("NM-TRAN Specifications")
+  cli::cli_bullets(
+    c(
+      "*" = "NONMEM Version: {.val {x[['nonmem_version']]}}",
+      "*" = "NM-TRAN Executable: {.path {x[['nmtran_exe']]}}",
+      "*" = "nmtran_presort: {cli::col_cyan(!is.null(x[['nmtran_presort_exe']]))}"
+    )
+  )
+
+  # Print run directory if it still exists (clean = FALSE)
+  if(fs::dir_exists(x[['run_dir']])){
+    cli::cli_bullets(c("*" = "Run Directory: {.path {x[['run_dir']]}}"))
+  }
+
+  if (is_valid_print(x[["output"]])) {
+    heading('Output')
+    cat_line(x[["output"]])
+  }
+}
+
+
 #' @describeIn print_bbi Draw model tree as a static plot
 #' @param x plot to display
 #' @param newpage Logical (T/F). If `TRUE`, draw new (empty) page first.
@@ -471,7 +523,6 @@ print.model_tree_static <- function(x, newpage = is.null(vp), vp = NULL, ...){
   return(invisible(x))
 }
 
-
 #####################
 # INTERNAL HELPERS
 #####################