diff --git a/R/generate_benchmark_script.R b/R/generate_benchmark_script.R
index a0880f5973ba1e6e6e07fbd07cd7f8521fb49129..f374434febb106a79541a4b3d1ee360f59672ff6 100644
--- a/R/generate_benchmark_script.R
+++ b/R/generate_benchmark_script.R
@@ -6,28 +6,45 @@
#'@description Wrapper function to generate benchmark scripts from all .prj
#' files in a directory
#'@param path string: Path to a benchmark directory to generate scripts from
-#'@param scripts_path string: Optional: Path where benchmark scripts will be
-#' saved. Change this to fit your system!
+#'@param sim_path string: Path where all simulation files will be saved
+#'@param scripts_path string: Path where benchmark scripts will be saved
#'@param starting_from_prj_path string: Optional:
#'@param skip_prj_paths character: Optional: .prj paths to skip
+#'@param read_in_vtus flag: Optional: Should .vtu files just be copied or read
+#' in too?
+#'@param read_in_gmls flag: Optional: Should .gml files just be copied or read
+#' in too?
#'@param test_mode flag: Optional: In test mode, if `path` is missing,
#' internal function `get_default_benchmark_path()` will be called
generate_all_benchmark_scripts <-
function(path,
- scripts_path = "D:/OGS_scripts/",
+ sim_path,
+ scripts_path,
starting_from_prj_path = "",
skip_prj_paths = character(),
+ read_in_vtus = FALSE,
+ read_in_gmls = TRUE,
test_mode = FALSE){
+ assertthat::assert_that(assertthat::is.flag(test_mode))
+
if(missing(path) && test_mode){
path <- get_default_benchmark_path()
}
+ if(missing(sim_path) && test_mode){
+ sim_path <- get_default_sim_path()
+ }
+
+ if(missing(scripts_path) && test_mode){
+ scripts_path <- get_default_script_path()
+ }
+
path <- validate_is_dir_path(path)
scripts_path <- validate_is_dir_path(scripts_path)
assertthat::assert_that(assertthat::is.string(starting_from_prj_path))
assertthat::assert_that(is.character(skip_prj_paths))
- assertthat::assert_that(assertthat::is.flag(test_mode))
+ assertthat::assert_that(assertthat::is.flag(read_in_vtus))
prj_paths <- list.files(path = path,
pattern = "\\.prj$",
@@ -68,7 +85,18 @@ generate_all_benchmark_scripts <-
cat("\nGenerating script from path", prj_paths[[i]])
- generate_benchmark_script(prj_paths[[i]], scripts_path)
+ # Put simulations in their own subfolders under sim_path
+ sim_subdir <-
+ paste0(sim_path,
+ basename(dirname(prj_paths[[i]])), "_",
+ tools::file_path_sans_ext(basename(prj_paths[[i]])))
+
+ generate_benchmark_script(prj_path = prj_paths[[i]],
+ sim_path = sim_subdir,
+ script_path = scripts_path,
+ read_in_vtu = read_in_vtus,
+ read_in_gml = read_in_gmls,
+ test_mode = test_mode)
}
cat("\nFailed parsing the following files:")
@@ -83,15 +111,41 @@ generate_all_benchmark_scripts <-
#'generate_benchmark_script
#'@description Generates a benchmark script from an existing .prj file.
-#'@param prj_path The path to the project file the script will be based on
-#'@param script_path string: Optional: Path where benchmark script will be
-#' saved. Change this to fit your system!
+#'@param prj_path string: .prj file the script will be based on
+#'@param sim_path string: Path where all simulation files will be saved
+#'@param ogs_bin_path string: OpenGeoSys bin folder path
+#'@param script_path string: Path where benchmark script will be saved
+#'@param read_in_vtu flag: Optional: Should .vtu file(s) just be copied or read
+#' in too?
+#'@param read_in_gml flag: Optional: Should .gml file just be copied or read
+#' in too?
+#'@param test_mode flag: Optional: In test mode, if `ogs_bin_path` is missing,
+#' internal function `get_default_ogs_bin_path()` will be called
#'@export
generate_benchmark_script <- function(prj_path,
- script_path = "D:/OGS_scripts/") {
+ sim_path,
+ ogs_bin_path,
+ script_path,
+ read_in_vtu = FALSE,
+ read_in_gml = TRUE,
+ test_mode = FALSE) {
+
+ assertthat::assert_that(assertthat::is.flag(test_mode))
+
+ if(missing(ogs_bin_path) && test_mode){
+ ogs_bin_path <- get_default_ogs_bin_path()
+ }
+
+ if(missing(script_path) && test_mode){
+ script_path <- get_default_script_path()
+ }
assertthat::assert_that(assertthat::is.string(prj_path))
+ assertthat::assert_that(assertthat::is.string(sim_path))
+ assertthat::assert_that(assertthat::is.string(ogs_bin_path))
assertthat::assert_that(assertthat::is.string(script_path))
+ assertthat::assert_that(assertthat::is.flag(read_in_vtu))
+ assertthat::assert_that(assertthat::is.flag(read_in_gml))
#Construct an object from a benchmark and then reverse engineer the call
ogs6_obj <- OGS6$new(sim_name = "",
@@ -100,7 +154,10 @@ generate_benchmark_script <- function(prj_path,
ogs_bin_path = "",
test_mode = TRUE)
- read_in_prj(ogs6_obj, prj_path)
+ read_in_prj(ogs6_obj,
+ prj_path,
+ read_in_vtu,
+ read_in_gml)
impl_classes = get_implemented_classes()
@@ -110,20 +167,47 @@ generate_benchmark_script <- function(prj_path,
"ogs6_obj <- OGS6$new(sim_name = \"",
sim_name, "\",\n",
"sim_id = 1,\n",
- "sim_path = \"your_sim_path\",\n",
- "ogs_bin_path = \"your_bin_path\")\n\n\n")
+ "sim_path = \"", sim_path, "\",\n",
+ "ogs_bin_path = \"", ogs_bin_path, "\")\n\n\n")
+
+ # If there is a .gml but it shouldn't be read in, add reference
+ if (!is.null(ogs6_obj$geometry) && !read_in_gml) {
+ script_str <- paste0(
+ script_str,
+ "ogs6_obj$add_gml(",
+ construct_add_call(ogs6_obj$geometry),
+ ")\n\n"
+ )
+ }
+ # Add .vtu references and optionally, OGS6_vtu objects
+ for(i in seq_len(length(ogs6_obj$meshes))){
+ script_str <- paste0(script_str,
+ "ogs6_obj$add_vtu(",
+ construct_add_call(ogs6_obj$meshes[[i]]), ",\n",
+ read_in_vtu,
+ ")\n\n")
+ }
+
+ # Add class objects (and such in wrapper lists)
for(i in seq_len(length(impl_classes))){
+
+ # We already handled the .vtus above
+ if(impl_classes[[i]] == "OGS6_vtu"){
+ next
+ }
+
get_component_call <- paste0("ogs6_obj$", names(impl_classes)[[i]])
ogs6_component <- eval(parse(text = get_component_call))
- #If benchmark doesn't have components of specified name, skip
+ # If benchmark doesn't have components of specified name, skip
if(is.null(ogs6_component) || length(ogs6_component) == 0){
next
}
#If objects are not in wrapper list, wrap them up for seq_along()
- if(any(grepl("r2ogs6_", class(ogs6_component), fixed = TRUE))){
+ if(any(grepl("r2ogs6_", class(ogs6_component), fixed = TRUE)) ||
+ any(grepl("OGS6_", class(ogs6_component), fixed = TRUE))){
ogs6_component <- list(ogs6_component)
}
@@ -242,7 +326,14 @@ construct_add_call <- function(object, nested_call = FALSE) {
#If call isn't nested, it has a OGS6$add_* function
if(!nested_call){
- ret_str <- paste0("ogs6_obj$add_", tag_name, "(", ret_str, ")\n")
+
+ # if(tag_name == "vtu"){
+ # filename_str <- paste0(",\npaste0(ogs6_obj$sim_path,\n",
+ # "basename(ogs6_obj$geometry))")
+ # }
+
+ ret_str <- paste0("ogs6_obj$add_", tag_name,
+ "(", ret_str, ")\n")
}
diff --git a/R/generate_class.R b/R/generate_class.R
index 6cfdc5c4f6f3dc07ab8265f2c30de4c7528805a4..2fdf25cbeb6751b79404823b7809a5235799c935 100644
--- a/R/generate_class.R
+++ b/R/generate_class.R
@@ -8,7 +8,6 @@
#'generate_constructor
#'@description Helper function to generate a constructor out of a tag name
#' and a flag vector
-#'@param tag_name The name of the XML element the class will be based on
#'@param params list: (Return value of analyse_xml())
#'@param prefix Optional: For subclasses whose represented elements have
#' the same tag name as an element for which a class was already specified,