more test adjustments and bug fix

- move data path fix to above parsing the control stream. This previously wasnt necessary since we parsed the parent model
metrumresearchgroup · Sep 19, 2024 · df3566e · df3566e
1 parent 47c8301
commit df3566e
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Showing 2 changed files with 15 additions and 18 deletions.
diff --git a/R/bootstrap-model.R b/R/bootstrap-model.R
@@ -174,6 +174,16 @@ setup_bootstrap_run <- function(
     writeLines(ignore_lines, file.path(boot_dir, ".gitignore"))
 
     if(is.null(data)){
+      # Overwrite data path in control stream
+      #  - This is not necessary in most cases, but is if overwriting a previous
+      #    run where a starting dataset was provided. The data path must then
+      #    be updated to reflect the original control stream
+      data_path <- get_data_path(.boot_run, .check_exists = FALSE)
+      if(!fs::file_exists(data_path)){
+        data_path_rel <- get_data_path_from_ctl(orig_mod, normalize = FALSE)
+        modify_data_path_ctl(.boot_run, data_path_rel)
+      }
+
       # Only include subjects that entered the original problem by default
       starting_data <- tryCatch({
         nm_data(.boot_run, filter = TRUE) %>% suppressMessages()
@@ -222,16 +232,6 @@ setup_bootstrap_run <- function(
           )
         )
       }
-
-      # Overwrite data path in control stream
-      #  - This is not necessary in most cases, but is if overwriting a previous
-      #    run where a starting dataset was provided. The data path must then
-      #    be updated to reflect the original control stream
-      data_path <- get_data_path(.boot_run, .check_exists = FALSE)
-      if(!fs::file_exists(data_path)){
-        data_path_rel <- get_data_path_from_ctl(orig_mod, normalize = FALSE)
-        modify_data_path_ctl(.boot_run, data_path_rel)
-      }
     }else{
       checkmate::assert_data_frame(data)
       # Get input columns from dataset referenced in based_on model

diff --git a/tests/testthat/test-workflow-bootstrap.R b/tests/testthat/test-workflow-bootstrap.R
@@ -151,7 +151,7 @@ withr::with_options(
 
       # Set filter that should error
       data_rec$values[[7]]$value <- "(ID.EQ.2, SEX.EQ.1)"
-      nmrec::write_ctl(ctl, get_model_path(mod2))
+      nmrec::write_ctl(ctl, get_model_path(boot_run2))
 
       expect_error(
         setup_bootstrap_run(boot_run2, n = 3),
@@ -172,10 +172,7 @@ withr::with_options(
     })
 
     test_that("setup_bootstrap_run works as expected", {
-      expect_message(
-        setup_bootstrap_run(.boot_run, n = 3, .overwrite = TRUE, seed = NULL),
-        "Dropped 20 records from starting data"
-      )
+      setup_bootstrap_run(.boot_run, n = 3, .overwrite = TRUE, seed = NULL)
 
       # Check print method - strat_cols are made to be NA if none provided
       bullets <- capture.output({
@@ -422,9 +419,9 @@ withr::with_options(
       # Copy model files and output directory of simulation
       new_dir <- tempdir()
       new_dir_path <- file.path(new_dir, basename(.boot_run[[ABS_MOD_PATH]]))
-      fs::file_copy(ctl_ext(.boot_run[[ABS_MOD_PATH]]), ctl_ext(new_dir_path))
-      fs::file_copy(yaml_ext(.boot_run[[ABS_MOD_PATH]]), yaml_ext(new_dir_path))
-      fs::dir_copy(.boot_run[[ABS_MOD_PATH]], new_dir_path)
+      fs::file_copy(ctl_ext(.boot_run[[ABS_MOD_PATH]]), ctl_ext(new_dir_path), overwrite = TRUE)
+      fs::file_copy(yaml_ext(.boot_run[[ABS_MOD_PATH]]), yaml_ext(new_dir_path), overwrite = TRUE)
+      fs::dir_copy(.boot_run[[ABS_MOD_PATH]], new_dir_path, overwrite = TRUE)
       fake_boot <- read_model(new_dir_path)
       on.exit(delete_models(fake_boot, .tags = NULL, .force = TRUE))