[bugfix] Fixed mesh read in error

R/export_prj.R

@@ -20,17 +20,16 @@ export_prj <- function(ogs6_obj) {
 
     #If there is a .gml defined, add "mesh" node, else add "meshes" node
     if(is.null(ogs6_obj$geometry)) {
-        basenames <- lapply(ogs6_obj$meshes, function(x){basename(x)})
-        meshes_node <- to_node(basenames, "meshes")
+        meshes_node <- meshes_to_xml(ogs6_obj$meshes)
     }else{
         xml2::xml_add_child(
             prj_xml,
             xml2::as_xml_document(to_node(ogs6_obj$geometry)))
-        meshes_node <- to_node(basename(ogs6_obj$meshes[[1]]), "mesh")
+        meshes_node <- meshes_to_xml(ogs6_obj$meshes)
     }
 
     xml2::xml_add_child(prj_xml,
-                        xml2::as_xml_document(meshes_node))
+                        meshes_node)
 
     #Get implemented classes
     prj_components <- ogs6_prj_top_level_classes()

R/ogs6.R

@@ -98,6 +98,7 @@ OGS6 <- R6::R6Class("OGS6",
     #' Adds a reference to a \code{.vtu} file and optionally, a \code{OGS6_vtu}
     #' object
     #' @param path string: A path
+    #' @param axisym flag: Is the mesh axially symmetrical?
     #' @param read_in_vtu flag: Optional: Should \code{.vtu} file just be
     #' copied or read in too?
     #' @examples
@@ -105,12 +106,16 @@ OGS6 <- R6::R6Class("OGS6",
     #' ogs6_obj$add_vtu("this_works.vtu")
     #' \dontrun{ogs6_obj$add_vtu("this_doesnt.oops")}
     add_vtu = function(path,
+                       axisym = FALSE,
                        read_in_vtu = FALSE){
       assertthat::assert_that(assertthat::is.string(path))
       assertthat::assert_that(grepl("\\.vtu$", path))
+      assertthat::assert_that(assertthat::is.flag(axisym))
       assertthat::assert_that(assertthat::is.flag(read_in_vtu))
 
-      self$meshes <- c(self$meshes, mesh = path)
+      self$meshes <- c(self$meshes,
+                       list(mesh = list(path = path,
+                                        axially_symmetric = axisym)))
 
       if(read_in_vtu){
         private$.vtus <- c(private$.vtus, list(OGS6_vtu$new(path)))
@@ -328,12 +333,15 @@ OGS6 <- R6::R6Class("OGS6",
         }else{
           assertthat::assert_that(is.list(value))
           lapply(value, function(x){
-            assertthat::assert_that(assertthat::is.string(x))
+            assertthat::assert_that(is.list(x), length(x) == 2)
+            assertthat::assert_that(assertthat::is.string(x[[1]]))
+            assertthat::assert_that(assertthat::is.flag(x[[2]]))
           })
           private$.meshes <- value
         }
       },
 
+
       #' @field vtus
       #' \code{.vtu}s. \code{value} must be list of \code{OGS6_vtu} objects
       vtus = function(value) {

R/ogs6_gml.R

@@ -146,12 +146,6 @@ OGS6_gml <- R6::R6Class(
             }
         },
 
-        #'@field is_subclass
-        #'Getter for private parameter '.is_subclass'
-        is_subclass = function(value) {
-            private$.is_subclass
-        },
-
         #'@field attr_names
         #'Getter for private parameter '.attr_names'
         attr_names = function(value) {
@@ -197,7 +191,6 @@ OGS6_gml <- R6::R6Class(
         .points = NULL,
         .polylines = NULL,
         .surfaces = NULL,
-        .is_subclass = TRUE,
         .attr_names = c("point", "name", "id", "element"),
         .flatten_on_exp = character()
     )

R/read_in_prj.R

@@ -58,8 +58,17 @@ read_in_prj <- function(ogs6_obj,
         vtu_ref <- xml2::xml_text(vtu_ref_nodes[[i]])
         vtu_path <- paste0(dirname(prj_path), "/", vtu_ref)
 
+        axisym_val <- xml2::xml_attr(vtu_ref_nodes[[i]], "axially_symmetric")
+
+        if(!is.na(axisym_val) && axisym_val == "true"){
+            axisym_val <- TRUE
+        }else{
+            axisym_val <- FALSE
+        }
+
         # Read in .vtu file(s) or just save their path
         ogs6_obj$add_vtu(path = vtu_path,
+                         axisym = axisym_val,
                          read_in_vtu = read_in_vtu)
     }
 

R/sim_utils.R

@@ -96,7 +96,7 @@ ogs6_export_sim_files <- function(ogs6_obj,
 
     # Copy all referenced .vtu files to ogs6_obj$sim_path
     lapply(ogs6_obj$meshes, function(x){
-        file.copy(x, ogs6_obj$sim_path)
+        file.copy(x[["path"]], ogs6_obj$sim_path)
     })
 
     if(!is.null(ogs6_obj$python_script)){