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Custom Upload and Assay Updates (bug fixes) #16

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Custom Upload and Assay Updates (bug fixes) #16

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24 changes: 9 additions & 15 deletions inst/shiny/tests/testthat/test-edge-cases.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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.
Expand All @@ -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)
Expand Down Expand Up @@ -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.
Expand All @@ -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")
Expand Down
13 changes: 7 additions & 6 deletions inst/shiny/tests/testthat/test-upload.R
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Expand Up @@ -15,20 +15,21 @@ 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",
load_timeout = 120000,
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.
Expand Down
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