diff --git a/R/generate_benchmark_script.R b/R/generate_benchmark_script.R
index 3a3aef33e198356428095f06c86ccf6bc781ab7f..5f64e1b8772373d2ca376556e34b970a70f3020b 100644
--- a/R/generate_benchmark_script.R
+++ b/R/generate_benchmark_script.R
@@ -8,20 +8,20 @@
#'@param path string: Path to a benchmark directory to generate scripts from
#'@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 read_in_vtus flag: Optional: Should .vtu files just be copied or read
+#' in too?
+#'@param starting_from_prj_path string: Optional:
+#'@param skip_prj_paths character: Optional: .prj paths to skip
generate_all_benchmark_scripts <-
function(path,
sim_path,
scripts_path,
- starting_from_prj_path = "",
- skip_prj_paths = character(),
+ read_in_gmls,
read_in_vtus = FALSE,
- read_in_gmls = TRUE){
+ starting_from_prj_path = "",
+ skip_prj_paths = character()){
if(missing(path)){
path <- unlist(options("r2ogs6.default_benchmark_path"))
@@ -35,6 +35,8 @@ generate_all_benchmark_scripts <-
scripts_path <- unlist(options("r2ogs6.default_script_path"))
}
+ missing_read_in_gmls <- missing(read_in_gmls)
+
path <- validate_is_dir_path(path)
scripts_path <- validate_is_dir_path(scripts_path)
assertthat::assert_that(assertthat::is.string(starting_from_prj_path))
@@ -52,6 +54,7 @@ generate_all_benchmark_scripts <-
}
invalid_xml_paths <- character()
+ invalid_prj_paths <- character()
for(i in seq_len(length(prj_paths))){
@@ -59,8 +62,8 @@ generate_all_benchmark_scripts <-
next
}
- skip_to_next <- FALSE
- invalid_xml_path <- ""
+ skip_generate <- FALSE
+ generate_failed <- FALSE
out<- tryCatch(
{
@@ -68,17 +71,19 @@ generate_all_benchmark_scripts <-
encoding="ISO-8859-1")
},
error = function(cond){
- skip_to_next <<- TRUE
- invalid_xml_path <<- prj_paths[[i]]
+ message(paste("\nxml2::read_xml() failed for",
+ prj_paths[[i]], ". Original error message:"))
+ message(cond)
+ skip_generate <<- TRUE
}
)
- if(skip_to_next){
- invalid_xml_paths <- c(invalid_xml_paths, invalid_xml_path)
+ if(skip_generate){
+ invalid_xml_paths <- c(invalid_xml_paths, prj_paths[[i]])
next
}
- cat("\nGenerating script from path", prj_paths[[i]])
+ # cat("\nGenerating script from path", prj_paths[[i]])
# Put simulations in their own subfolders under sim_path
sim_subdir <-
@@ -86,17 +91,36 @@ generate_all_benchmark_scripts <-
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)
- }
+ out<- tryCatch(
+ {
+ if(missing_read_in_gmls){
+ generate_benchmark_script(prj_path = prj_paths[[i]],
+ sim_path = sim_subdir,
+ script_path = scripts_path,
+ read_in_vtu = read_in_vtus)
+ }else{
+ generate_benchmark_script(prj_path = prj_paths[[i]],
+ sim_path = sim_subdir,
+ script_path = scripts_path,
+ read_in_gml = read_in_gmls,
+ read_in_vtu = read_in_vtus)
+ }
+
+ },
+ error = function(cond){
+ message(paste("\ngenerate_benchmark_script() failed for",
+ prj_paths[[i]], ". Original error message:"))
+ message(cond)
+ generate_failed <<- TRUE
+ }
+ )
- cat("\nFailed parsing the following files:")
- print(invalid_xml_paths)
+ if(generate_failed){
+ invalid_prj_paths <- c(invalid_prj_paths, prj_paths[[i]])
+ }
+ }
- return(invisible())
+ return(invisible(list(invalid_xml_paths, invalid_prj_paths)))
}
@@ -109,17 +133,17 @@ generate_all_benchmark_scripts <-
#'@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 read_in_vtu flag: Optional: Should .vtu file(s) just be copied or read
+#' in too?
#'@export
generate_benchmark_script <- function(prj_path,
sim_path,
ogs_bin_path,
script_path,
- read_in_vtu = FALSE,
- read_in_gml = TRUE) {
+ read_in_gml,
+ read_in_vtu = FALSE) {
if(missing(ogs_bin_path)){
ogs_bin_path <- unlist(options("r2ogs6.default_ogs_bin_path"))
@@ -129,12 +153,12 @@ generate_benchmark_script <- function(prj_path,
script_path <- unlist(options("r2ogs6.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$new(sim_name = "",
@@ -146,9 +170,9 @@ generate_benchmark_script <- function(prj_path,
read_in_prj(ogs6_obj,
prj_path,
read_in_vtu,
- read_in_gml)
+ read_in_gml = FALSE)
- impl_classes = get_implemented_classes()
+ prj_components = addable_prj_components()
sim_name <- tools::file_path_sans_ext(basename(prj_path))
@@ -160,13 +184,29 @@ generate_benchmark_script <- function(prj_path,
"ogs_bin_path = \"", ogs_bin_path, "\")\n\n\n")
# If there is a .gml but it shouldn't be read in, add reference
- if (!is.null(ogs6_obj$geometry) && !read_in_gml) {
- script_str <- paste0(
- script_str,
- "ogs6_obj$add_gml(",
- construct_add_call(ogs6_obj$geometry),
- ")\n\n"
- )
+ if (!is.null(ogs6_obj$geometry)) {
+
+ # If read_in_gml isn't supplied, check number of lines in .gml file
+ # since string concatenation is slow
+ if(missing(read_in_gml)){
+ read_in_gml <- (length(readLines(ogs6_obj$geometry)) <=
+ unlist(options("r2ogs6.max_lines_gml")))
+ }
+
+ assertthat::assert_that(assertthat::is.flag(read_in_gml))
+
+ if(!read_in_gml){
+ script_str <- paste0(script_str,
+ "ogs6_obj$add_gml(",
+ construct_add_call(ogs6_obj$geometry),
+ ")\n\n"
+ )
+ }else{
+ ogs6_obj$add_gml(read_in_gml(ogs6_obj$geometry))
+ script_str <- paste0(script_str,
+ construct_add_call(ogs6_obj$gml),
+ "\n\n")
+ }
}
# Add .vtu references and optionally, OGS6_vtu objects
@@ -179,14 +219,9 @@ generate_benchmark_script <- function(prj_path,
}
# Add class objects (and such in wrapper lists)
- for(i in seq_len(length(impl_classes))){
-
- # We already handled the .vtus above
- if(impl_classes[[i]] == "OGS6_vtu"){
- next
- }
+ for(i in seq_len(length(prj_components))){
- get_component_call <- paste0("ogs6_obj$", names(impl_classes)[[i]])
+ get_component_call <- paste0("ogs6_obj$", names(prj_components)[[i]])
ogs6_component <- eval(parse(text = get_component_call))
# If benchmark doesn't have components of specified name, skip
@@ -201,9 +236,10 @@ generate_benchmark_script <- function(prj_path,
}
for(j in seq_along(ogs6_component)){
- add_call_str <- paste0(construct_add_call(ogs6_component[[j]]),
- "\n\n")
- script_str <- paste0(script_str, add_call_str)
+ script_str <-
+ paste0(script_str,
+ paste0(construct_add_call(ogs6_component[[j]]),
+ "\n\n"))
}
}