From 73bbf90749a40c41a1f5b6038e44f1f4a16ef396 Mon Sep 17 00:00:00 2001
From: Sabila Bernard <sabila.bernard@gmail.com>
Date: Wed, 27 May 2026 15:47:40 -0400
Subject: [PATCH] Use normalizePath for fixture paths before AppDriver creation

test_path() can return a relative path if testthat state is not active
when the argument is evaluated (e.g. after AppDriver changes the working
directory). Resolve the fixture path to an absolute path at the top of
each test, before any AppDriver interaction.
---
 inst/shiny/tests/testthat/test-edge-cases.R | 24 ++++++++-------------
 inst/shiny/tests/testthat/test-upload.R     | 13 +++++------
 2 files changed, 16 insertions(+), 21 deletions(-)

diff --git a/inst/shiny/tests/testthat/test-edge-cases.R b/inst/shiny/tests/testthat/test-edge-cases.R
index e1d2cf3..39d47cd 100644
--- a/inst/shiny/tests/testthat/test-edge-cases.R
+++ b/inst/shiny/tests/testthat/test-edge-cases.R
@@ -55,16 +55,14 @@ test_that("app does not crash when accessed before uploading Seurat file", {
 # ── Bug 1: corrMat double transpose — compound dropdown must show drug names ──
 
 test_that("corrMat upload shows drug names in compound dropdown, not cell barcodes", {
-  skip_if_not(
-    file.exists(test_path("fixtures/downsampled_seuratObj.RDS")),
-    "Seurat fixture not available (requires Git LFS)"
-  )
+  fixture <- normalizePath(test_path("fixtures/downsampled_seuratObj.RDS"), mustWork = FALSE)
+  skip_if_not(file.exists(fixture), "Seurat fixture not available (requires Git LFS)")
   drug_names    <- c("DrugA", "DrugB", "DrugC")
   corr_mat_path <- make_corr_mat_csv(drug_names)
 
   app <- make_app("corr-mat-orientation")
 
-  app$upload_file(seurobjRDS = test_path("fixtures/downsampled_seuratObj.RDS"))
+  app$upload_file(seurobjRDS = fixture)
   app$wait_for_value(output = "seuratLoaded", timeout = 30000)
 
   app$set_inputs(uploadCorrelationMatrix = TRUE)
@@ -96,10 +94,8 @@ test_that("corrMat upload shows drug names in compound dropdown, not cell barcod
 # ── Bug 2: duplicate uiOutput — compound dropdown must not be empty ───────────
 
 test_that("reference compound dropdown is populated after corrMat upload", {
-  skip_if_not(
-    file.exists(test_path("fixtures/downsampled_seuratObj.RDS")),
-    "Seurat fixture not available (requires Git LFS)"
-  )
+  fixture <- normalizePath(test_path("fixtures/downsampled_seuratObj.RDS"), mustWork = FALSE)
+  skip_if_not(file.exists(fixture), "Seurat fixture not available (requires Git LFS)")
   # uiOutput('referenceCompound_ui') appears in two tabs in ui.R.
   # When the same output ID is bound twice, the second binding can
   # overwrite the first, leaving one tab's dropdown empty.
@@ -108,7 +104,7 @@ test_that("reference compound dropdown is populated after corrMat upload", {
 
   app <- make_app("duplicate-ui-output")
 
-  app$upload_file(seurobjRDS = test_path("fixtures/downsampled_seuratObj.RDS"))
+  app$upload_file(seurobjRDS = fixture)
   app$wait_for_value(output = "seuratLoaded", timeout = 30000)
 
   app$set_inputs(uploadCorrelationMatrix = TRUE)
@@ -136,10 +132,8 @@ test_that("reference compound dropdown is populated after corrMat upload", {
 # ── Bug 5: lowercase gene names in custom drug signature should not crash ─────
 
 test_that("custom drug signature with lowercase gene names does not crash app", {
-  skip_if_not(
-    file.exists(test_path("fixtures/downsampled_seuratObj.RDS")),
-    "Seurat fixture not available (requires Git LFS)"
-  )
+  fixture <- normalizePath(test_path("fixtures/downsampled_seuratObj.RDS"), mustWork = FALSE)
+  skip_if_not(file.exists(fixture), "Seurat fixture not available (requires Git LFS)")
   # If gene names in the uploaded CSV are lowercase (e.g. tp53) but the
   # Seurat object uses uppercase (TP53), overlap detection returns 0 and
   # the server calls stop(), crashing the reactive chain silently.
@@ -148,7 +142,7 @@ test_that("custom drug signature with lowercase gene names does not crash app",
 
   app <- make_app("gene-case-mismatch")
 
-  app$upload_file(seurobjRDS = test_path("fixtures/downsampled_seuratObj.RDS"))
+  app$upload_file(seurobjRDS = fixture)
   app$wait_for_value(output = "seuratLoaded", timeout = 30000)
 
   app$set_inputs(L1000_Release = "Custom Upload")
diff --git a/inst/shiny/tests/testthat/test-upload.R b/inst/shiny/tests/testthat/test-upload.R
index 68e2b48..8c56083 100644
--- a/inst/shiny/tests/testthat/test-upload.R
+++ b/inst/shiny/tests/testthat/test-upload.R
@@ -15,10 +15,13 @@ test_that("app loads without errors", {
 })
 
 test_that("uploading a valid Seurat RDS shows success message", {
-  skip_if_not(
-    file.exists(test_path("fixtures/downsampled_seuratObj.RDS")),
-    "Seurat fixture not available (requires Git LFS)"
+  # Resolve to absolute path NOW, before AppDriver can change the working dir
+  fixture <- normalizePath(
+    test_path("fixtures/downsampled_seuratObj.RDS"),
+    mustWork = FALSE
   )
+  skip_if_not(file.exists(fixture), "Seurat fixture not available (requires Git LFS)")
+
   app <- AppDriver$new(
     app_dir      = system.file("shiny", package = "scFOCAL"),
     name         = "seurat-upload",
@@ -26,9 +29,7 @@ test_that("uploading a valid Seurat RDS shows success message", {
     timeout      = 120000
   )
 
-  app$upload_file(
-    seurobjRDS = test_path("fixtures/downsampled_seuratObj.RDS")
-  )
+  app$upload_file(seurobjRDS = fixture)
 
   # Wait for seuratLoaded to be TRUE. Ignore NULL (pre-upload) and any
   # transient FALSE that may arrive while the 134 MB file is being read.