From ce99b599f8249e8740a059803ae6e08a9f6651bf Mon Sep 17 00:00:00 2001
From: aheinri5 <Anna@netzkritzler.de>
Date: Thu, 28 Jan 2021 18:35:32 +0100
Subject: [PATCH] [base] closes #11 , adding .prj components now via OGS()
---
R/export_prj.R | 2 +-
R/generate_benchmark_script.R | 13 +-
R/ogs6.R | 299 +++++-------------
R/read_in_prj.R | 2 +-
R/read_in_utils.R | 5 +-
R/utils.R | 24 +-
man/OGS6.Rd | 299 ++----------------
...j_tag_info.Rd => prj_top_level_classes.Rd} | 11 +-
man/prj_top_level_tags.Rd | 14 +
.../testthat/test-generate_benchmark_script.R | 4 +-
tests/testthat/test-ogs6.R | 6 +-
tests/testthat/test-ogs6_ensemble.R | 3 +-
tests/testthat/test-utils.R | 4 +-
vignettes/dev_workflow_vignette.Rmd | 3 +
vignettes/user_workflow_vignette.Rmd | 6 +-
15 files changed, 180 insertions(+), 515 deletions(-)
rename man/{get_prj_tag_info.Rd => prj_top_level_classes.Rd} (65%)
create mode 100644 man/prj_top_level_tags.Rd
diff --git a/R/export_prj.R b/R/export_prj.R
index a6d2609..078af44 100644
--- a/R/export_prj.R
+++ b/R/export_prj.R
@@ -29,7 +29,7 @@ export_prj <- function(ogs6_obj) {
xml2::as_xml_document(meshes_node))
#Get implemented classes
- prj_components <- get_prj_tag_info()
+ prj_components <- prj_top_level_classes()
# Include file reference
if(names(ogs6_obj$processes)[[1]] == "include"){
diff --git a/R/generate_benchmark_script.R b/R/generate_benchmark_script.R
index c3ba868..4dc8d06 100644
--- a/R/generate_benchmark_script.R
+++ b/R/generate_benchmark_script.R
@@ -177,7 +177,7 @@ generate_benchmark_script <- function(prj_path,
read_in_vtu,
read_in_gml = FALSE)
- prj_components = get_prj_tag_info()
+ prj_components = prj_top_level_classes()
sim_name <- tools::file_path_sans_ext(basename(prj_path))
@@ -355,13 +355,11 @@ construct_add_call <- function(object, nested_call = FALSE) {
ret_str <- paste0(class_name, init_prefix,
"(", content_str, ")")
- #If call isn't nested, it has a OGS6$add_* function
+ #If call isn't nested, it can be added
if(!nested_call){
- ret_str <- paste0("ogs6_obj$add_", tag_name,
- "(", ret_str, ")\n")
+ ret_str <- paste0("ogs6_obj$add(", ret_str, ")\n")
}
-
ret_str <- delete_nulls_from_str(ret_str)
ret_str <- delete_keywords_from_str(ret_str)
ret_str <- delete_empty_from_str(ret_str)
@@ -376,11 +374,8 @@ construct_add_call <- function(object, nested_call = FALSE) {
return(invisible(ret_str))
}
- #Positioning is important here - r2ogs6 objects are built on top of lists!
- #If is.list is checked before class, results will not be as intended!
-
#For lists we need to use recursion
- if(is.list(object)){
+ if(class(object) == "list"){
element_strs <- lapply(object, function(x){construct_add_call(x, TRUE)})
diff --git a/R/ogs6.R b/R/ogs6.R
index cf6bb70..73fc732 100644
--- a/R/ogs6.R
+++ b/R/ogs6.R
@@ -32,60 +32,20 @@ OGS6 <- R6::R6Class("OGS6",
},
- #===== ADDING COMPONENTS =====
+ #===== Adding components =====
#'@description
- #'Adds a simulation component (WIP)
- #'@param x An object of any class listed in addable_components(). If `x` is
- #' not of a proprietary `r2ogs6` class, it must be a string referencing a
- #' file. E.g. If you're adding a `python_script`, call
- #' `your_ogs6_obj$add("some_script.py")`. If you're adding a `geometry` or
- #' `mesh` reference, if `...` is not defined, they will be read in. To
- #' disable, define `read_in` as `FALSE`.
+ #'Adds a .prj simulation component
+ #'@param x An object of any .prj `r2ogs6` class
add = function(x){
- # Assert that class name is in implemented classes for OGS6
- ogs6_components <- get_prj_tag_info()
+ # Assert that class name is in implemented .prj classes for OGS6
+ ogs6_prj_classes <- prj_top_level_classes()
+ assertthat::assert_that(class(x) %in% ogs6_prj_classes)
- x_class_name <- ""
- x_of_r2ogs6_class <- FALSE
-
- if(any(grepl("r2ogs6", class(x), fixed = TRUE)) ||
- any(grepl("OGS6", class(x), fixed = TRUE))){
-
- x_class_name <- grep("r2ogs6", class(x), value = TRUE)
-
- if(length(x_class_name) == 0){
- x_class_name <- grep("OGS6", class(x), value = TRUE)
- }
-
- assertthat::assert_that(x_class_name %in% ogs6_components)
- x_of_r2ogs6_class <- TRUE
- }
-
- # Get name of corresponding OGS6 parameter
- if(x_of_r2ogs6_class){
- component_name <-
- names(ogs6_components)[ogs6_components == x_class_name]
- }else{
- assertthat::assert_that(assertthat::is.string(x))
-
- switch (tools::file_ext(x),
- gml = {
- },
-
- vtu = {
- },
-
- py = {
- component_name <- "python_script"
- },
-
- stop(paste("When adding a file reference to your OGS6 object, it",
- "must be a .gml, .vtu or .py file."), call. = FALSE)
- )
- }
+ # Get name of corresponding OGS6 component
+ component_name <- names(ogs6_prj_classes)[ogs6_prj_classes == class(x)]
component_class <-
eval(parse(text = paste0("class(self$", component_name, ")")))
@@ -100,7 +60,7 @@ OGS6 <- R6::R6Class("OGS6",
# If class has `name` variable, make it accessable by name
if(component_class == "list" &&
- "name" %in% names(as.list(formals(x_class_name)))){
+ "name" %in% names(as.list(formals(class(x))))){
name_call <- paste0("names(self$", component_name, ")[[length(self$",
component_name, ")]] <- x$name")
@@ -149,119 +109,8 @@ OGS6 <- R6::R6Class("OGS6",
}
},
- #'@description
- #'Adds a python script
- #'@param python_script string: File name of python script
- add_python_script = function(python_script){
- self$python_script <- python_script
- },
- #'@description
- #'Adds a r2ogs6_search_length_algorithm object
- #'@param search_length_algorithm r2ogs6_search_length_algorithm
- add_search_length_algorithm = function(search_length_algorithm){
- self$search_length_algorithm <- search_length_algorithm
- },
-
- #'@description
- #'Adds a r2ogs6_process object
- #'@param process r2ogs6_process
- add_process = function(process){
- self$processes <- c(self$processes,
- list(process))
-
- names(self$processes)[[length(self$processes)]] <- process$name
- },
-
- #'@description
- #'Adds a r2ogs6_time_loop object
- #'@param time_loop r2ogs6_time_loop
- add_time_loop = function(time_loop){
- self$time_loop <- time_loop
- },
-
- #'@description
- #'Adds a r2ogs6_local_coordinate_system object
- #'@param local_coordinate_system r2ogs6_local_coordinate_system
- add_local_coordinate_system = function(local_coordinate_system){
- self$local_coordinate_system <- local_coordinate_system
- },
-
- #'@description
- #'Adds a r2ogs6_medium object
- #'@param medium r2ogs6_medium
- add_medium = function(medium){
- self$media <- c(self$media,
- list(medium))
- },
-
- #'@description
- #'Adds a r2ogs6_parameter object
- #'@param parameter r2ogs6_parameter
- add_parameter = function(parameter){
- self$parameters <- c(self$parameters,
- list(parameter))
-
- names(self$parameters)[[length(self$parameters)]] <- parameter$name
- },
-
- #'@description
- #'Adds a r2ogs6_curve object
- #'@param curve r2ogs6_curve
- add_curve = function(curve){
- self$curves <- c(self$curves,
- list(curve))
- },
-
- #'@description
- #'Adds a r2ogs6_process_variable object
- #'@param process_variable r2ogs6_process_variable
- add_process_variable = function(process_variable){
- self$process_variables <- c(self$process_variables,
- list(process_variable))
-
- names(self$process_variables)[[length(self$process_variables)]] <-
- process_variable$name
- },
-
- #'@description
- #'Adds a r2ogs6_nonlinear_solver object
- #'@param nonlinear_solver r2ogs6_nonlinear_solver
- add_nonlinear_solver = function(nonlinear_solver){
- self$nonlinear_solvers <- c(self$nonlinear_solvers,
- list(nonlinear_solver))
-
- names(self$nonlinear_solvers)[[length(self$nonlinear_solvers)]] <-
- nonlinear_solver$name
- },
-
- #'@description
- #'Adds a r2ogs6_linear_solver object
- #'@param linear_solver r2ogs6_linear_solver
- add_linear_solver = function(linear_solver){
- self$linear_solvers <- c(self$linear_solvers,
- list(linear_solver))
-
- names(self$linear_solvers)[[length(self$linear_solvers)]] <-
- linear_solver$name
- },
-
- #'@description
- #'Adds a r2ogs6_vtkdiff object
- #'@param vtkdiff r2ogs6_vtkdiff
- add_vtkdiff = function(vtkdiff){
- self$test_definition <- c(self$test_definition, list(vtkdiff))
- },
-
- #'@description
- #'Adds a r2ogs6_insitu object
- #'@param insitu r2ogs6_insitu
- add_insitu = function(insitu){
- self$insitu <- insitu
- },
-
-
- #===== UTILITY FUNCTIONS =====
+ #===== Utility =====
#'@description
@@ -274,26 +123,18 @@ OGS6 <- R6::R6Class("OGS6",
flag <- TRUE
status_strs <- character()
-
- prj_reduxml <- system.file("extdata/xml_redux/", "prj_redu.xml",
- package = "r2ogs6")
-
- xml_doc <- xml2::read_xml(prj_reduxml)
- tag_names <- lapply(xml2::xml_children(xml_doc), xml2::xml_name)
+ tag_names <- lapply(prj_top_level_tags(), `[[`, 1)
+ required <- lapply(prj_top_level_tags(), `[[`, 2)
for(i in seq_len(length(tag_names))){
- prj_node <- xml2::xml_find_first(xml_doc,
- paste0("/OpenGeoSysProject/",
- tag_names[[i]]))
-
- is_optional <- (xml2::xml_attrs(prj_node)[["required"]] == "FALSE")
+ is_required <- required[[i]]
prj_obj_call <- paste0("private$.", tag_names[[i]])
prj_obj <- eval(parse(text = prj_obj_call))
if(length(prj_obj) == 0){
- if(!is_optional){
+ if(is_required){
status_str <- crayon::red("\u2717 ")
flag <- FALSE
}else{
@@ -304,11 +145,11 @@ OGS6 <- R6::R6Class("OGS6",
}
status_str <- paste0(status_str,
- "OGS6$",
+ "'",
tag_names[[i]],
ifelse(!class(prj_obj) == "list",
- " is defined",
- " has at least one element"))
+ "' is defined",
+ "' has at least one element"))
status_strs <- c(status_strs, status_str)
}
@@ -343,14 +184,14 @@ OGS6 <- R6::R6Class("OGS6",
#'Clears components from the OGS6 object
#'@param which character: The names of the components (all by default).
#' If you want to delete only some components, run
- #' names(get_prj_tag_info()) for the available options.
+ #' names(prj_top_level_classes()) for the available options.
clear = function(which){
if(missing(which)){
- which <- names(get_prj_tag_info())
+ which <- names(prj_top_level_classes())
}
- valid_input = names(get_prj_tag_info())
+ valid_input = names(prj_top_level_classes())
null_it <- c("geometry", "time_loop")
@@ -377,13 +218,13 @@ OGS6 <- R6::R6Class("OGS6",
),
- #===== ACTIVE FIELDS =====
+ #===== Active fields =====
active = list(
#'@field sim_name
- #'Access to private parameter '.sim_name'
+ #'Simulation name. `value` must be string
sim_name = function(value) {
if(missing(value)) {
private$.sim_name
@@ -394,13 +235,13 @@ OGS6 <- R6::R6Class("OGS6",
},
#'@field sim_id
- #'Getter for OGS6 private parameter '.sim_id'
+ #'Simulation ID. read-only
sim_id = function() {
private$.sim_id
},
#'@field sim_path
- #'Access to private parameter '.sim_path'
+ #'Simulation path. `value` must be string
sim_path = function(value) {
if(missing(value)) {
private$.sim_path
@@ -410,7 +251,7 @@ OGS6 <- R6::R6Class("OGS6",
},
#'@field logfile
- #'Access to private parameter '.logfile'
+ #'Logfile path. `value` must be string
logfile = function(value) {
if(missing(value)) {
private$.logfile
@@ -421,13 +262,13 @@ OGS6 <- R6::R6Class("OGS6",
},
#'@field gml
- #'Getter for OGS6 private parameter '.gml'
+ #'.gml. read-only
gml = function() {
private$.gml
},
#'@field geometry
- #'Access to private parameter '.geometry'
+ #'.prj `geometry` tag. `value` must be string
geometry = function(value) {
if(missing(value)) {
private$.geometry
@@ -438,7 +279,7 @@ OGS6 <- R6::R6Class("OGS6",
},
#'@field meshes
- #'Access to private parameter '.meshes'
+ #'.prj `meshes` tag. `value` must be list of strings
meshes = function(value) {
if(missing(value)) {
private$.meshes
@@ -452,19 +293,19 @@ OGS6 <- R6::R6Class("OGS6",
},
#'@field vtus
- #'Access to private parameter '.vtus'
+ #'.vtus. `value` must be list of `OGS_vtu` objects
vtus = function(value) {
if(missing(value)) {
private$.vtus
}else{
is_wrapper_list(value,
- get_prj_tag_info()[["vtus"]])
+ prj_top_level_classes()[["vtus"]])
private$.vtus <- value
}
},
#'@field python_script
- #'Access to private parameter '.python_script'
+ #'.prj `python_script` tag. `value` must be string
python_script = function(value) {
if(missing(value)) {
private$.python_script
@@ -475,30 +316,31 @@ OGS6 <- R6::R6Class("OGS6",
},
#'@field search_length_algorithm
- #'Access to private parameter '.search_length_algorithm'
+ #'.prj `search_length_algorithm` tag. `value` must be
+ #' `r2ogs6_search_length_algorithm` object
search_length_algorithm = function(value) {
if(missing(value)) {
private$.search_length_algorithm
}else{
assertthat::assert_that(
- get_prj_tag_info()[["search_length_algorithm"]] %in%
+ prj_top_level_classes()[["search_length_algorithm"]] %in%
class(value))
private$.search_length_algorithm <- value
}
},
#'@field processes
- #'Access to private parameter '.processes'
+ #'.prj `processes` tag. `value` must be list of `r2ogs6_process` objects
processes = function(value) {
if(missing(value)) {
private$.processes
}else{
# If there already is a process element
if(length(private$.processes) > 0){
- if(get_prj_tag_info()[["processes"]] %in%
+ if(prj_top_level_classes()[["processes"]] %in%
class(private$.processes[[1]])){
is_wrapper_list(value,
- get_prj_tag_info()[["processes"]])
+ prj_top_level_classes()[["processes"]])
}else{
assertthat::assert_that(assertthat::is.string(value))
value <- list(include = c(file = value))
@@ -509,7 +351,7 @@ OGS6 <- R6::R6Class("OGS6",
value <- list(include = c(file = value))
}else{
is_wrapper_list(value,
- get_prj_tag_info()[["processes"]])
+ prj_top_level_classes()[["processes"]])
}
}
@@ -518,132 +360,152 @@ OGS6 <- R6::R6Class("OGS6",
},
#'@field time_loop
- #'Access to private parameter '.time_loop'
+ #'.prj `time_loop` tag. `value` must be `r2ogs6_time_loop` object
time_loop = function(value) {
if(missing(value)) {
private$.time_loop
}else{
assertthat::assert_that(
- get_prj_tag_info()[["time_loop"]] %in%
+ prj_top_level_classes()[["time_loop"]] %in%
class(value))
private$.time_loop <- value
}
},
#'@field local_coordinate_system
- #'Access to private parameter '.local_coordinate_system'
+ #'.prj `local_coordinate_system` tag. `value` must be
+ #' `r2ogs6_local_coordinate_system` object
local_coordinate_system = function(value) {
if(missing(value)) {
private$.local_coordinate_system
}else{
assertthat::assert_that(
- get_prj_tag_info()[["local_coordinate_system"]] %in%
+ prj_top_level_classes()[["local_coordinate_system"]] %in%
class(value))
private$.local_coordinate_system <- value
}
},
#'@field media
- #'Access to private parameter '.media'
+ #'.prj `media` tag. `value` must be list of `r2ogs6_medium` objects
media = function(value) {
if(missing(value)) {
private$.media
}else{
is_wrapper_list(value,
- get_prj_tag_info()[["media"]])
+ prj_top_level_classes()[["media"]])
private$.media <- value
}
},
#'@field parameters
- #'Access to private parameter '.parameters'
+ #'.prj `parameters` tag. `value` must be list of `r2ogs6_parameter`
+ #' objects
parameters = function(value) {
if(missing(value)) {
private$.parameters
}else{
is_wrapper_list(value,
- get_prj_tag_info()[["parameters"]])
+ prj_top_level_classes()[["parameters"]])
private$.parameters <- value
}
},
+ #'@field chemical_system
+ #'.prj `chemical_system` tag. `value` must be `r2ogs6_chemical_system`
+ #' object
+ chemical_system = function(value) {
+ if(missing(value)) {
+ private$.chemical_system
+ }else{
+ assertthat::assert_that(
+ prj_top_level_classes()[["chemical_system"]] %in%
+ class(value))
+ private$.chemical_system <- value
+ }
+ },
+
#'@field curves
- #'Access to private parameter '.curves'
+ #'.prj `curves` tag. `value` must be list of `r2ogs6_curve` objects
curves = function(value) {
if(missing(value)) {
private$.curves
}else{
is_wrapper_list(value,
- get_prj_tag_info()[["curves"]])
+ prj_top_level_classes()[["curves"]])
private$.curves <- value
}
},
#'@field process_variables
- #'Access to private parameter '.process_variables'
+ #'.prj `process_variables` tag. `value` must be list of
+ #' `r2ogs6_process_variable` objects
process_variables = function(value) {
if(missing(value)) {
private$.process_variables
}else{
is_wrapper_list(
value,
- get_prj_tag_info()[["process_variables"]])
+ prj_top_level_classes()[["process_variables"]])
private$.process_variables <- value
}
},
#'@field nonlinear_solvers
- #'Access to private parameter '.nonlinear_solvers'
+ #'.prj `nonlinear_solvers` tag. `value` must be list of
+ #' `r2ogs6_nonlinear_solver` objects
nonlinear_solvers = function(value) {
if(missing(value)) {
private$.nonlinear_solvers
}else{
is_wrapper_list(
value,
- get_prj_tag_info()[["nonlinear_solvers"]])
+ prj_top_level_classes()[["nonlinear_solvers"]])
private$.nonlinear_solvers <- value
}
},
#'@field linear_solvers
- #'Access to private parameter '.linear_solvers'
+ #'.prj `linear_solvers` tag. `value` must be list of
+ #' `r2ogs6_linear_solver` objects
linear_solvers = function(value) {
if(missing(value)) {
private$.linear_solvers
}else{
is_wrapper_list(value,
- get_prj_tag_info()[["linear_solvers"]])
+ prj_top_level_classes()[["linear_solvers"]])
private$.linear_solvers <- value
}
},
#'@field test_definition
- #'Access to private parameter '.test_definition'
+ #'.prj `test_definition` tag. `value` must be list of `r2ogs6_vtkdiff`
+ #' objects
test_definition = function(value) {
if(missing(value)) {
private$.test_definition
}else{
is_wrapper_list(value,
- get_prj_tag_info()[["test_definition"]])
+ prj_top_level_classes()[["test_definition"]])
private$.test_definition <- value
}
},
#'@field insitu
- #'Access to private parameter '.insitu'
+ #'.prj `insitu` tag. `value` must be `r2ogs6_insitu` object
insitu = function(value) {
if(missing(value)) {
private$.insitu
}else{
assertthat::assert_that(
- get_prj_tag_info()[["insitu"]] %in%
+ prj_top_level_classes()[["insitu"]] %in%
class(value))
private$.insitu <- value
}
},
#'@field pvd
- #'Access to private parameter '.pvd'
+ #'.pvd. `value` must be `OGS6_pvd` object
pvd = function(value) {
if(missing(value)) {
private$.pvd
@@ -654,6 +516,8 @@ OGS6 <- R6::R6Class("OGS6",
}
),
+ #===== Private parameters =====
+
private = list(
# general parameters
.sim_name = NULL,
@@ -683,6 +547,7 @@ OGS6 <- R6::R6Class("OGS6",
.local_coordinate_system = NULL,
.media = list(),
.parameters = list(),
+ .chemical_system = NULL,
.curves = list(),
.process_variables = list(),
.nonlinear_solvers = list(),
diff --git a/R/read_in_prj.R b/R/read_in_prj.R
index 1920da4..d0dd5f8 100644
--- a/R/read_in_prj.R
+++ b/R/read_in_prj.R
@@ -61,7 +61,7 @@ read_in_prj <- function(ogs6_obj,
read_in_vtu = read_in_vtu)
}
- prj_components <- get_prj_tag_info()
+ prj_components <- prj_top_level_classes()
# Include file reference
processes_include_node <-
diff --git a/R/read_in_utils.R b/R/read_in_utils.R
index a251b07..9370fa4 100644
--- a/R/read_in_utils.R
+++ b/R/read_in_utils.R
@@ -56,9 +56,6 @@ read_in <- function(ogs6_obj,
r2ogs6_obj <- NULL
- #Code to be parsed when r2ogs6_obj has been defined
- add_call <- paste0("ogs6_obj$add_", child_name, "(r2ogs6_obj)")
-
#Parse all children
for (i in seq_len(length(nodes))) {
@@ -66,7 +63,7 @@ read_in <- function(ogs6_obj,
xpath)
#Add r2ogs6_obj with code snippet
- eval(parse(text = add_call))
+ eval(parse(text = "ogs6_obj$add(r2ogs6_obj)"))
}
return(invisible(r2ogs6_obj))
diff --git a/R/utils.R b/R/utils.R
index 44e0ee0..6403f8f 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -56,10 +56,30 @@ get_tag_from_xpath <- function(xpath){
}
-#'get_prj_tag_info
+#'prj_top_level_tags
+#'@description Gets top level .prj tags along with info if they are required.
+#'@return list: List of lists.
+prj_top_level_tags <- function(){
+
+ prj_reduxml <- system.file("extdata/xml_redux/", "prj_redu.xml",
+ package = "r2ogs6")
+
+ xml_doc <- xml2::read_xml(prj_reduxml)
+
+ prj_tag_info <- lapply(xml2::xml_children(xml_doc), function(x){
+ list(tag_name = xml2::xml_name(x),
+ is_required = as.logical(xml2::xml_attrs(x)[["required"]]))
+ })
+
+ return(prj_tag_info)
+}
+
+
+#'prj_top_level_classes
#'@description Returns named character vector of `OGS6` top level .prj tags
#' (names) represented by r2ogs6 classes along with their class names (values).
-get_prj_tag_info <- function(){
+#'@return character
+prj_top_level_classes <- function(){
xpaths_for_classes <- xpaths_for_classes
diff --git a/man/OGS6.Rd b/man/OGS6.Rd
index 3ccd5f7..971ebd0 100644
--- a/man/OGS6.Rd
+++ b/man/OGS6.Rd
@@ -9,49 +9,59 @@ Constructor for the OGS6 base class
\section{Active bindings}{
\if{html}{\out{<div class="r6-active-bindings">}}
\describe{
-\item{\code{sim_name}}{Access to private parameter '.sim_name'}
+\item{\code{sim_name}}{Simulation name. `value` must be string}
-\item{\code{sim_id}}{Getter for OGS6 private parameter '.sim_id'}
+\item{\code{sim_id}}{Simulation ID. read-only}
-\item{\code{sim_path}}{Access to private parameter '.sim_path'}
+\item{\code{sim_path}}{Simulation path. `value` must be string}
-\item{\code{logfile}}{Access to private parameter '.logfile'}
+\item{\code{logfile}}{Logfile path. `value` must be string}
-\item{\code{gml}}{Getter for OGS6 private parameter '.gml'}
+\item{\code{gml}}{.gml. read-only}
-\item{\code{geometry}}{Access to private parameter '.geometry'}
+\item{\code{geometry}}{.prj `geometry` tag. `value` must be string}
-\item{\code{meshes}}{Access to private parameter '.meshes'}
+\item{\code{meshes}}{.prj `meshes` tag. `value` must be list of strings}
-\item{\code{vtus}}{Access to private parameter '.vtus'}
+\item{\code{vtus}}{.vtus. `value` must be list of `OGS_vtu` objects}
-\item{\code{python_script}}{Access to private parameter '.python_script'}
+\item{\code{python_script}}{.prj `python_script` tag. `value` must be string}
-\item{\code{search_length_algorithm}}{Access to private parameter '.search_length_algorithm'}
+\item{\code{search_length_algorithm}}{.prj `search_length_algorithm` tag. `value` must be
+`r2ogs6_search_length_algorithm` object}
-\item{\code{processes}}{Access to private parameter '.processes'}
+\item{\code{processes}}{.prj `processes` tag. `value` must be list of `r2ogs6_process` objects}
-\item{\code{time_loop}}{Access to private parameter '.time_loop'}
+\item{\code{time_loop}}{.prj `time_loop` tag. `value` must be `r2ogs6_time_loop` object}
-\item{\code{local_coordinate_system}}{Access to private parameter '.local_coordinate_system'}
+\item{\code{local_coordinate_system}}{.prj `local_coordinate_system` tag. `value` must be
+`r2ogs6_local_coordinate_system` object}
-\item{\code{media}}{Access to private parameter '.media'}
+\item{\code{media}}{.prj `media` tag. `value` must be list of `r2ogs6_medium` objects}
-\item{\code{parameters}}{Access to private parameter '.parameters'}
+\item{\code{parameters}}{.prj `parameters` tag. `value` must be list of `r2ogs6_parameter`
+objects}
-\item{\code{curves}}{Access to private parameter '.curves'}
+\item{\code{chemical_system}}{.prj `chemical_system` tag. `value` must be `r2ogs6_chemical_system`
+object}
-\item{\code{process_variables}}{Access to private parameter '.process_variables'}
+\item{\code{curves}}{.prj `curves` tag. `value` must be list of `r2ogs6_curve` objects}
-\item{\code{nonlinear_solvers}}{Access to private parameter '.nonlinear_solvers'}
+\item{\code{process_variables}}{.prj `process_variables` tag. `value` must be list of
+`r2ogs6_process_variable` objects}
-\item{\code{linear_solvers}}{Access to private parameter '.linear_solvers'}
+\item{\code{nonlinear_solvers}}{.prj `nonlinear_solvers` tag. `value` must be list of
+`r2ogs6_nonlinear_solver` objects}
-\item{\code{test_definition}}{Access to private parameter '.test_definition'}
+\item{\code{linear_solvers}}{.prj `linear_solvers` tag. `value` must be list of
+`r2ogs6_linear_solver` objects}
-\item{\code{insitu}}{Access to private parameter '.insitu'}
+\item{\code{test_definition}}{.prj `test_definition` tag. `value` must be list of `r2ogs6_vtkdiff`
+objects}
-\item{\code{pvd}}{Access to private parameter '.pvd'}
+\item{\code{insitu}}{.prj `insitu` tag. `value` must be `r2ogs6_insitu` object}
+
+\item{\code{pvd}}{.pvd. `value` must be `OGS6_pvd` object}
}
\if{html}{\out{</div>}}
}
@@ -62,19 +72,6 @@ Constructor for the OGS6 base class
\item \href{#method-add}{\code{OGS6$add()}}
\item \href{#method-add_gml}{\code{OGS6$add_gml()}}
\item \href{#method-add_vtu}{\code{OGS6$add_vtu()}}
-\item \href{#method-add_python_script}{\code{OGS6$add_python_script()}}
-\item \href{#method-add_search_length_algorithm}{\code{OGS6$add_search_length_algorithm()}}
-\item \href{#method-add_process}{\code{OGS6$add_process()}}
-\item \href{#method-add_time_loop}{\code{OGS6$add_time_loop()}}
-\item \href{#method-add_local_coordinate_system}{\code{OGS6$add_local_coordinate_system()}}
-\item \href{#method-add_medium}{\code{OGS6$add_medium()}}
-\item \href{#method-add_parameter}{\code{OGS6$add_parameter()}}
-\item \href{#method-add_curve}{\code{OGS6$add_curve()}}
-\item \href{#method-add_process_variable}{\code{OGS6$add_process_variable()}}
-\item \href{#method-add_nonlinear_solver}{\code{OGS6$add_nonlinear_solver()}}
-\item \href{#method-add_linear_solver}{\code{OGS6$add_linear_solver()}}
-\item \href{#method-add_vtkdiff}{\code{OGS6$add_vtkdiff()}}
-\item \href{#method-add_insitu}{\code{OGS6$add_insitu()}}
\item \href{#method-get_status}{\code{OGS6$get_status()}}
\item \href{#method-print_log}{\code{OGS6$print_log()}}
\item \href{#method-clear}{\code{OGS6$clear()}}
@@ -107,7 +104,7 @@ saved}
\if{html}{\out{<a id="method-add"></a>}}
\if{latex}{\out{\hypertarget{method-add}{}}}
\subsection{Method \code{add()}}{
-Adds a simulation component (WIP)
+Adds a .prj simulation component
\subsection{Usage}{
\if{html}{\out{<div class="r">}}\preformatted{OGS6$add(x)}\if{html}{\out{</div>}}
}
@@ -115,12 +112,7 @@ Adds a simulation component (WIP)
\subsection{Arguments}{
\if{html}{\out{<div class="arguments">}}
\describe{
-\item{\code{x}}{An object of any class listed in addable_components(). If `x` is
-not of a proprietary `r2ogs6` class, it must be a string referencing a
-file. E.g. If you're adding a `python_script`, call
-`your_ogs6_obj$add("some_script.py")`. If you're adding a `geometry` or
-`mesh` reference, if `...` is not defined, they will be read in. To
-disable, define `read_in` as `FALSE`.}
+\item{\code{x}}{An object of any .prj `r2ogs6` class}
}
\if{html}{\out{</div>}}
}
@@ -164,227 +156,6 @@ read in too?}
}
}
\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_python_script"></a>}}
-\if{latex}{\out{\hypertarget{method-add_python_script}{}}}
-\subsection{Method \code{add_python_script()}}{
-Adds a python script
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_python_script(python_script)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{python_script}}{string: File name of python script}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_search_length_algorithm"></a>}}
-\if{latex}{\out{\hypertarget{method-add_search_length_algorithm}{}}}
-\subsection{Method \code{add_search_length_algorithm()}}{
-Adds a r2ogs6_search_length_algorithm object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_search_length_algorithm(search_length_algorithm)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{search_length_algorithm}}{r2ogs6_search_length_algorithm}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_process"></a>}}
-\if{latex}{\out{\hypertarget{method-add_process}{}}}
-\subsection{Method \code{add_process()}}{
-Adds a r2ogs6_process object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_process(process)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{process}}{r2ogs6_process}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_time_loop"></a>}}
-\if{latex}{\out{\hypertarget{method-add_time_loop}{}}}
-\subsection{Method \code{add_time_loop()}}{
-Adds a r2ogs6_time_loop object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_time_loop(time_loop)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{time_loop}}{r2ogs6_time_loop}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_local_coordinate_system"></a>}}
-\if{latex}{\out{\hypertarget{method-add_local_coordinate_system}{}}}
-\subsection{Method \code{add_local_coordinate_system()}}{
-Adds a r2ogs6_local_coordinate_system object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_local_coordinate_system(local_coordinate_system)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{local_coordinate_system}}{r2ogs6_local_coordinate_system}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_medium"></a>}}
-\if{latex}{\out{\hypertarget{method-add_medium}{}}}
-\subsection{Method \code{add_medium()}}{
-Adds a r2ogs6_medium object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_medium(medium)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{medium}}{r2ogs6_medium}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_parameter"></a>}}
-\if{latex}{\out{\hypertarget{method-add_parameter}{}}}
-\subsection{Method \code{add_parameter()}}{
-Adds a r2ogs6_parameter object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_parameter(parameter)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{parameter}}{r2ogs6_parameter}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_curve"></a>}}
-\if{latex}{\out{\hypertarget{method-add_curve}{}}}
-\subsection{Method \code{add_curve()}}{
-Adds a r2ogs6_curve object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_curve(curve)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{curve}}{r2ogs6_curve}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_process_variable"></a>}}
-\if{latex}{\out{\hypertarget{method-add_process_variable}{}}}
-\subsection{Method \code{add_process_variable()}}{
-Adds a r2ogs6_process_variable object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_process_variable(process_variable)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{process_variable}}{r2ogs6_process_variable}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_nonlinear_solver"></a>}}
-\if{latex}{\out{\hypertarget{method-add_nonlinear_solver}{}}}
-\subsection{Method \code{add_nonlinear_solver()}}{
-Adds a r2ogs6_nonlinear_solver object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_nonlinear_solver(nonlinear_solver)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{nonlinear_solver}}{r2ogs6_nonlinear_solver}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_linear_solver"></a>}}
-\if{latex}{\out{\hypertarget{method-add_linear_solver}{}}}
-\subsection{Method \code{add_linear_solver()}}{
-Adds a r2ogs6_linear_solver object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_linear_solver(linear_solver)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{linear_solver}}{r2ogs6_linear_solver}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_vtkdiff"></a>}}
-\if{latex}{\out{\hypertarget{method-add_vtkdiff}{}}}
-\subsection{Method \code{add_vtkdiff()}}{
-Adds a r2ogs6_vtkdiff object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_vtkdiff(vtkdiff)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{vtkdiff}}{r2ogs6_vtkdiff}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
-\if{html}{\out{<a id="method-add_insitu"></a>}}
-\if{latex}{\out{\hypertarget{method-add_insitu}{}}}
-\subsection{Method \code{add_insitu()}}{
-Adds a r2ogs6_insitu object
-\subsection{Usage}{
-\if{html}{\out{<div class="r">}}\preformatted{OGS6$add_insitu(insitu)}\if{html}{\out{</div>}}
-}
-
-\subsection{Arguments}{
-\if{html}{\out{<div class="arguments">}}
-\describe{
-\item{\code{insitu}}{r2ogs6_insitu}
-}
-\if{html}{\out{</div>}}
-}
-}
-\if{html}{\out{<hr>}}
\if{html}{\out{<a id="method-get_status"></a>}}
\if{latex}{\out{\hypertarget{method-get_status}{}}}
\subsection{Method \code{get_status()}}{
@@ -427,7 +198,7 @@ Clears components from the OGS6 object
\describe{
\item{\code{which}}{character: The names of the components (all by default).
If you want to delete only some components, run
-names(get_prj_tag_info()) for the available options.}
+names(prj_top_level_classes()) for the available options.}
}
\if{html}{\out{</div>}}
}
diff --git a/man/get_prj_tag_info.Rd b/man/prj_top_level_classes.Rd
similarity index 65%
rename from man/get_prj_tag_info.Rd
rename to man/prj_top_level_classes.Rd
index e7ac279..8906060 100644
--- a/man/get_prj_tag_info.Rd
+++ b/man/prj_top_level_classes.Rd
@@ -1,10 +1,13 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils.R
-\name{get_prj_tag_info}
-\alias{get_prj_tag_info}
-\title{get_prj_tag_info}
+\name{prj_top_level_classes}
+\alias{prj_top_level_classes}
+\title{prj_top_level_classes}
\usage{
-get_prj_tag_info()
+prj_top_level_classes()
+}
+\value{
+character
}
\description{
Returns named character vector of `OGS6` top level .prj tags
diff --git a/man/prj_top_level_tags.Rd b/man/prj_top_level_tags.Rd
new file mode 100644
index 0000000..dabe500
--- /dev/null
+++ b/man/prj_top_level_tags.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{prj_top_level_tags}
+\alias{prj_top_level_tags}
+\title{prj_top_level_tags}
+\usage{
+prj_top_level_tags()
+}
+\value{
+list: List of lists.
+}
+\description{
+Gets top level .prj tags along with info if they are required.
+}
diff --git a/tests/testthat/test-generate_benchmark_script.R b/tests/testthat/test-generate_benchmark_script.R
index 65f682d..359d5a7 100644
--- a/tests/testthat/test-generate_benchmark_script.R
+++ b/tests/testthat/test-generate_benchmark_script.R
@@ -26,7 +26,7 @@ test_that("construct_add_call works", {
ogs_param_call <- construct_add_call(ogs_param)
- expect_equal(ogs_param_call, paste0("ogs6_obj$add_parameter(",
+ expect_equal(ogs_param_call, paste0("ogs6_obj$add(",
"r2ogs6_parameter(name = \"a\",\n",
"type = \"t\",\n",
"values = c(0, 1)))\n"))
@@ -49,7 +49,7 @@ test_that("construct_add_call handles Ellipsis correctly", {
ogs_param_call <- construct_add_call(ogs_parameter)
expect_equal(ogs_param_call,
- paste0("ogs6_obj$add_parameter(r2ogs6_parameter(name = ",
+ paste0("ogs6_obj$add(r2ogs6_parameter(name = ",
"\"test\",\ntype = \"test\",\nindex_values = ",
"list(index_values = list(index = 1,\n",
"values = c(1, 2)))))\n"))
diff --git a/tests/testthat/test-ogs6.R b/tests/testthat/test-ogs6.R
index 8be33fe..9b1d820 100644
--- a/tests/testthat/test-ogs6.R
+++ b/tests/testthat/test-ogs6.R
@@ -8,7 +8,7 @@ test_that("OGS6$clear() works as expected", {
sim_id = 1,
sim_path = "sim_path")
- ogs6_obj$add_parameter(r2ogs6_parameter(
+ ogs6_obj$add(r2ogs6_parameter(
name = "pressure0",
type = "Constant",
values = 1e5
@@ -33,10 +33,8 @@ test_that("OGS6$add() works", {
values = 1e5
))
- ogs6_obj$add(x = "my_script.py")
-
+ expect_error(ogs6_obj$add("my_script.py"))
expect_equal(length(ogs6_obj$parameters), 1)
expect_equal(ogs6_obj$parameters[[1]]$values, 1e5)
- expect_equal(ogs6_obj$python_script, "my_script.py")
})
diff --git a/tests/testthat/test-ogs6_ensemble.R b/tests/testthat/test-ogs6_ensemble.R
index 5616a4b..f8fc44c 100644
--- a/tests/testthat/test-ogs6_ensemble.R
+++ b/tests/testthat/test-ogs6_ensemble.R
@@ -8,13 +8,12 @@ test_that("OGS6_Ensemble initialization works", {
sim_id = 1,
sim_path = "sim_path")
- ogs6_obj$add_parameter(r2ogs6_parameter(
+ ogs6_obj$add(r2ogs6_parameter(
name = "pressure0",
type = "Constant",
value = 1
))
-
ogs6_ens <- OGS6_Ensemble$new(
ogs6_obj = ogs6_obj,
parameters = list(list(ogs6_obj$parameters[[1]]$value, c(2, 3, 4)))
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index 9e50cbd..d9692b3 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -24,8 +24,8 @@ test_that("get_tag_from_xpath() works", {
})
-test_that("get_prj_tag_info() works", {
- expect_equal(get_prj_tag_info()[["processes"]], "r2ogs6_process")
+test_that("prj_top_level_classes() works", {
+ expect_equal(prj_top_level_classes()[["processes"]], "r2ogs6_process")
})
diff --git a/vignettes/dev_workflow_vignette.Rmd b/vignettes/dev_workflow_vignette.Rmd
index 6a125a9..45c2254 100644
--- a/vignettes/dev_workflow_vignette.Rmd
+++ b/vignettes/dev_workflow_vignette.Rmd
@@ -138,6 +138,9 @@ xpaths_for_classes[["r2ogs6_process"]]
xpaths_for_classes[["r2ogs6_convergence_criterion"]]
```
+If the class you've created is a `.prj` top level class or a child of a top level wrapper node like `processes`, add a corresponding `OGS6` private parameter and an active field. For example, the `processes` node is represented as a list, so I added the private parameter `.processes = list()` and the active field `processes`.
+
+
A lot of things in the `r2ogs6` package work in a way that is a bit "meta". Often times, functions are called via `eval(parse(text = call_string))` where `call_string` has for example been concatenated out of info about the parameter names of a certain class. This saves a lot of code regarding import, export and script generation but requires that you've made the respective info available as shown here.
So we've analysed some files, generated some code, created a new class and registered it with the package... what now? That's it actually, that's the workflow. Well, at least it's supposed to be.
diff --git a/vignettes/user_workflow_vignette.Rmd b/vignettes/user_workflow_vignette.Rmd
index 7322eb3..c1726db 100644
--- a/vignettes/user_workflow_vignette.Rmd
+++ b/vignettes/user_workflow_vignette.Rmd
@@ -99,12 +99,12 @@ As a rule of thumb, classes are named with the prefix `r2ogs6_` followed by thei
Let's try adding something now.
-### Adding input data via add_*
+### Adding input data via OGS6$add()
-To add data to our simulation object, we use one of ... .
+To add data to our simulation object, we use `OGS6$add()`.
```{r}
- ogs6_obj$add_parameter(r2ogs6_parameter(
+ ogs6_obj$add(r2ogs6_parameter(
name = "pressure0",
type = "Constant",
value = 1
--
GitLab