[base] make file refs absolute when creating ogs6_obj from prj file

    When an ogs6_obj is created from a prj file, the prj file may contain
    references to external files. This makes shure file references (gml,
    meshes, dat, py) have absolute paths. Then it is more easy to handle
    file references when sim_path and prj_path differ.

R/read_in_prj.R

@@ -19,9 +19,11 @@ read_in_prj <- function(ogs6_obj,
                         read_in_vtu = FALSE){
 
     assertthat::assert_that("OGS6" %in% class(ogs6_obj))
+    assertthat::assert_that(assertthat::is.string(prj_path))
+    assertthat::assert_that(assertthat::is.flag(read_in_vtu))
     xml_doc <- validate_read_in_xml(prj_path)
 
-    assertthat::assert_that(assertthat::is.flag(read_in_vtu))
+    prj_base_path <- dirname(prj_path)
 
     # Geometry reference
     gml_ref_node <- xml2::xml_find_first(xml_doc, "/OpenGeoSysProject/geometry")
@@ -30,8 +32,9 @@ read_in_prj <- function(ogs6_obj,
     vtu_ref_nodes <- NULL
 
     if(!any(grepl("xml_missing", class(gml_ref_node), fixed = TRUE))){
-        gml_path <- paste0(dirname(prj_path), "/",
-                           xml2::xml_text(gml_ref_node))
+
+        gml_path <- xml2::xml_text(gml_ref_node)
+        gml_path <- make_abs_path(gml_path, prj_base_path)
 
         # If read_in_gml isn't supplied, check number of lines in .gml file
         # since string concatenation is slow
@@ -56,7 +59,8 @@ read_in_prj <- function(ogs6_obj,
 
     for(i in seq_along(vtu_ref_nodes)){
         vtu_ref <- xml2::xml_text(vtu_ref_nodes[[i]])
-        vtu_path <- paste0(dirname(prj_path), "/", vtu_ref)
+        vtu_path <- make_abs_path(vtu_ref, prj_base_path)
+        # vtu_path <- paste0(dirname(prj_path), "/", vtu_ref)
 
         axisym_val <- xml2::xml_attr(vtu_ref_nodes[[i]], "axially_symmetric")
 
@@ -74,38 +78,35 @@ read_in_prj <- function(ogs6_obj,
 
     prj_components <- ogs6_prj_top_level_classes()
 
-    # Include file reference
+    # Read include file reference
     processes_include_node <-
         xml2::xml_find_first(xml_doc,
                              "/OpenGeoSysProject/processes/include")
 
     if(!any(grepl("xml_missing", class(processes_include_node), fixed = TRUE))){
         file_reference <- xml2::xml_attrs(processes_include_node)[["file"]]
-
-        if(grepl("^\\.\\.", file_reference)){
-            file_reference <- gsub("^\\.\\.", "", file_reference)
-            file_reference <- paste0(dirname(dirname(prj_path)), file_reference)
-        }else{
-            file_reference <- paste0(dirname(prj_path), "/", file_reference)
-        }
+        file_reference <- make_abs_path(file_reference, prj_base_path)
 
         ogs6_obj$processes <- file_reference
         prj_components <- prj_components[names(prj_components) != "processes"]
     }
 
-    # Check for python script
+    # Read python script references
     python_script_node <-
         xml2::xml_find_first(xml_doc,
                              "/OpenGeoSysProject/python_script")
 
     if(!any(grepl("xml_missing", class(python_script_node), fixed = TRUE))){
-        ogs6_obj$python_script <- xml2::xml_text(python_script_node)
+        python_script_path <- xml2::xml_text(python_script_node)
+        python_script_path <- make_abs_path(python_script_path, prj_base_path)
+        ogs6_obj$python_script <- python_script_path
     }
 
     prj_components <-
         prj_components[names(prj_components) != "python_script"]
 
 
+    # read additional prj file tags
     for(i in seq_len(length(prj_components))){
 
         class_tag_name <- get_tag_from_class(prj_components[[i]])
@@ -121,4 +122,12 @@ read_in_prj <- function(ogs6_obj,
                                                class_tag_name))
         }
     }
+
+    # update file references in wrapper lists of created ogs6_obj
+    if(!is.null(ogs6_obj$chemical_system)){
+        dbase_path <- ogs6_obj$chemical_system$database
+        ogs6_obj$chemical_system$database <- make_abs_path(dbase_path,
+                                                           prj_base_path)
+    }
+
 }