From 62e189bf846143b6baefcc0cec8e316e824abd69 Mon Sep 17 00:00:00 2001
From: "Henrik Sparre Spiegelhauer (HSPU)" <hspu@novonordisk.com>
Date: Fri, 15 Mar 2024 09:05:14 +0100
Subject: [PATCH] Adds junit as reporter

---
 tests/testthat.R                    |  2 +-
 tests/testthat/binary_type_2.R      | 60 +++++++++++++++--------------
 tests/testthat/test-binary_type_2.R |  3 --
 vignettes/validation.Rmd            |  1 -
 4 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/tests/testthat.R b/tests/testthat.R
index 7ac6f20..4bf755d 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -9,4 +9,4 @@
 library(testthat)
 library(ramnog)
 
-test_check("ramnog")
+test_check("ramnog", reporter = JunitReporter$new(file = "junit_result.xml"))
diff --git a/tests/testthat/binary_type_2.R b/tests/testthat/binary_type_2.R
index 7ac42e7..ba3e643 100644
--- a/tests/testthat/binary_type_2.R
+++ b/tests/testthat/binary_type_2.R
@@ -2,19 +2,21 @@ test_that("Binary outcomes of type 2 work", {
   # SETUP -------------------------------------------------------------------
   testr::create_local_project()
 
-  mk_ep_def <- function(){
-  chef::mk_endpoint_str(
-    data_prepare = mk_adae,
-    pop_var = "SAFFL",
-    pop_value = "Y",
-    treatment_var = "TRT01A",
-    treatment_refval = "Xanomeline High Dose",
-    group_by = list(list(AESOC = c())),
-    stratify_by = list(c("AEDECOD")),
-    stat_by_strata_by_trt = list(chefStats::n_subj_event,
-                                 chefStats::n_event)
-  )
-}
+  mk_ep_def <- function() {
+    chef::mk_endpoint_str(
+      data_prepare = mk_adae,
+      pop_var = "SAFFL",
+      pop_value = "Y",
+      treatment_var = "TRT01A",
+      treatment_refval = "Xanomeline High Dose",
+      group_by = list(list(AESOC = c())),
+      stratify_by = list(c("AEDECOD")),
+      stat_by_strata_by_trt = list(
+        chefStats::n_subj_event,
+        chefStats::n_event
+      )
+    )
+  }
   chef::use_chef(
     pipeline_dir = "pipeline",
     r_functions_dir = "R/",
@@ -23,32 +25,34 @@ test_that("Binary outcomes of type 2 work", {
     mk_adam_fn = list(mk_adae),
   )
   # ACT ---------------------------------------------------------------------
-  browser()
   targets::tar_make()
   targets::tar_load(ep_stat)
 
   # EXPECT ------------------------------------------------------------------
   actual <-
-    tidyr::unnest(ep_stat[grepl("GASTRO", endpoint_group_filter) |
-                            grepl("CARDIAC", endpoint_group_filter),
-                          .(endpoint_group_filter,
-                            stat_filter,
-                            stat_empty,
-                            fn_name,
-                            stat_result)], cols = stat_result) |>
+    tidyr::unnest(ep_stat[
+      grepl("GASTRO", endpoint_group_filter) |
+        grepl("CARDIAC", endpoint_group_filter),
+      .(
+        endpoint_group_filter,
+        stat_filter,
+        stat_empty,
+        fn_name,
+        stat_result
+      )
+    ], cols = stat_result) |>
     setDT() |>
     setorder(-value)
 
   x <- mk_adae()
   n <- x[AESOC == "CARDIAC DISORDERS" &
-      AEDECOD == "SINUS BRADYCARDIA" & TRT01A == "Xanomeline High Dose"] |> uniqueN(by="USUBJID")
+    AEDECOD == "SINUS BRADYCARDIA" & TRT01A == "Xanomeline High Dose"] |> uniqueN(by = "USUBJID")
   E <- x[AESOC == "CARDIAC DISORDERS" &
-      AEDECOD == "SINUS BRADYCARDIA" & TRT01A == "Xanomeline High Dose"] |> nrow()
+    AEDECOD == "SINUS BRADYCARDIA" & TRT01A == "Xanomeline High Dose"] |> nrow()
 
   actual_values <- actual[grepl("CARDIAC", endpoint_group_filter) &
-           grepl("SINUS BRADYCARDIA", stat_filter) &
-           grepl("Xan", stat_filter)&(label == "n" |
-           label == "E")][order(label)][,value]
-expect_equal(actual_values, c(E, n))
-
+    grepl("SINUS BRADYCARDIA", stat_filter) &
+    grepl("Xan", stat_filter) & (label == "n" |
+    label == "E")][order(label)][, value]
+  expect_equal(actual_values, c(E, n))
 })
diff --git a/tests/testthat/test-binary_type_2.R b/tests/testthat/test-binary_type_2.R
index e340007..d1787d3 100644
--- a/tests/testthat/test-binary_type_2.R
+++ b/tests/testthat/test-binary_type_2.R
@@ -13,7 +13,6 @@ test_that("multiplication works", {
       stratify_by = list(c("AEDECOD")),
       stat_by_strata_by_trt = list(chefStats::p_subj_event)
     )
-
   }
 
 
@@ -27,6 +26,4 @@ test_that("multiplication works", {
   # ACT ---------------------------------------------------------------------
   targets::tar_make()
   targets::tar_load(ep_stat)
-  browser()
-
 })
diff --git a/vignettes/validation.Rmd b/vignettes/validation.Rmd
index dd84668..c0b4008 100644
--- a/vignettes/validation.Rmd
+++ b/vignettes/validation.Rmd
@@ -87,7 +87,6 @@ test_that("Valide stats when one strata level is not found",
             targets::tar_make()
             targets::tar_load(ep_stat)
             # EXPECT ------------------------------------------------------------------
-            browser()
             x <- mk_adae_demo()
             # Relative Risk
             actual <-