360 [Bug]: unexpected reinitialization

R/experimentSpec.R

@@ -17,7 +17,7 @@ experimentSpecInput <- function(inputId, # nolint
   assert_string(inputId)
   assert_string(mae_name, min.chars = 1L)
   assert_string(label_experiments, min.chars = 1L)
-  mae <- data()[[mae_name]]
+  mae <- shiny::isolate(data()[[mae_name]])
   name_choices <- names(mae)
 
   ns <- NS(inputId)

tests/testthat/test-barplot.R

@@ -88,6 +88,7 @@ test_that("barplot module works as expected in the test app", {
     !!ns("facet-sample_var") := "AGE18"
   )
 
+  app$wait_for_idle()
   app$expect_select_screenshot(ns("plot-plot_out_main"))
 })
 

tests/testthat/test-experimentSpec.R

@@ -156,6 +156,10 @@ test_that("experimentSpec module works as expected in the test app", {
   app$set_inputs(!!ns2("active-MAE-subjects-MAE_SEX-inputs-selection") := character())
   app$wait_for_idle()
 
+  # Experiment selection is not affected by filtering
+  res <- app$get_value(input = ns("my_experiment-name"))
+  expect_identical(res, "hd2")
+
   res <- app$get_value(output = ns("summary"))
   expect_match(res$message, "No genes or samples included in this experiment, please adjust filters")
   app$click(ns2("active-MAE-remove_filters"))
@@ -174,8 +178,9 @@ test_that("experimentSpec module works as expected in the test app", {
   )
   app$wait_for_idle()
 
-  app$set_inputs(!!ns("my_experiment-name") := "hd2")
-  app$wait_for_idle()
+  # Experiment selection is not affected by filtering
+  res <- app$get_value(input = ns("my_experiment-name"))
+  expect_identical(res, "hd2")
 
   res <- app$get_value(output = ns("summary"))
   expect_match(res$message, "No genes or samples included in this experiment, please adjust filters")
@@ -184,8 +189,9 @@ test_that("experimentSpec module works as expected in the test app", {
   app$click(ns2("active-MAE-remove_filters"))
   app$wait_for_idle()
 
-  app$set_inputs(!!ns("my_experiment-name") := "hd2")
-  app$wait_for_idle()
+  # Experiment selection is not affected by removing filters
+  res <- app$get_value(input = ns("my_experiment-name"))
+  expect_identical(res, "hd2")
 
   res <- app$get_value(output = ns("summary"))
   expect_match(res, "HermesData object with 9 samples of 2500 genes")

tests/testthat/test-pca.R

@@ -56,7 +56,7 @@ test_that("pca module works as expected in the test app", {
   res <- app$get_value(input = ns("show_matrix"))
   expect_true(res)
 
-  app$expect_select_screenshot(ns("plot_pca-plot_main"))
+  app$expect_select_screenshot(ns("plot_pca-plot_main")) # 1
 
   # Add a gene filter and deselect everything and check that it does not crash.
   app$set_inputs(!!ns2("add-MAE-hd1-row_to_add") := "symbol")
@@ -88,31 +88,27 @@ test_that("pca module works as expected in the test app", {
   res <- app$get_value(input = ns("show_matrix"))
   expect_true(res)
 
-  app$expect_select_screenshot(ns("plot_cor-plot_main"))
-  app$expect_select_screenshot(ns("table_cor"))
+  app$expect_select_screenshot(ns("plot_cor-plot_main")) # 2
+  app$expect_select_screenshot(ns("table_cor")) # 3
 
   # Now update experiment name, assay name, cluster & matrix option on correlation tab.
-  app$set_inputs(
-    !!ns("experiment-name") := "hd2",
-    !!ns("assay-name") := "voom",
-    !!ns("cluster_columns") := TRUE,
-    !!ns("show_matrix") := FALSE
-  )
+  app$set_inputs(!!ns("experiment-name") := "hd2")
+  app$set_inputs(!!ns("assay-name") := "voom")
+  app$set_inputs(!!ns("cluster_columns") := TRUE)
+  app$set_inputs(!!ns("show_matrix") := FALSE)
 
   app$wait_for_idle()
-  app$expect_select_screenshot(ns("plot_cor-plot_main"))
+  app$expect_select_screenshot(ns("plot_cor-plot_main")) # 4
 
   # Now go back to pca tab and update experiment, assay name, variance % option,
   # label option and matrix option.
-  app$set_inputs(
-    !!ns("tab_selected") := "PCA",
-    !!ns("assay-name") := "rpkm",
-    !!ns("x_var") := "3",
-    !!ns("y_var") := "4",
-    !!ns("var_pct") := FALSE,
-    !!ns("label") := FALSE,
-    !!ns("show_matrix") := FALSE
-  )
+  app$set_inputs(!!ns("tab_selected") := "PCA")
+  app$set_inputs(!!ns("assay-name") := "rpkm")
+  app$set_inputs(!!ns("x_var") := "3")
+  app$set_inputs(!!ns("y_var") := "4")
+  app$set_inputs(!!ns("var_pct") := FALSE)
+  app$set_inputs(!!ns("label") := FALSE)
+  app$set_inputs(!!ns("show_matrix") := FALSE)
 
   app$wait_for_idle()
   app$expect_select_screenshot(ns("plot_pca-plot_main"))
@@ -153,16 +149,14 @@ test_that("pca module works as expected in the test app", {
   expect_identical(res$message, "please select two different principal components")
 
   # Update the inputs to PCA tab, hd1, counts, PC3, PC4, and add filters.
-  app$set_inputs(
-    !!ns("tab_selected") := "PCA",
-    !!ns("experiment-name") := "hd1",
-    !!ns("assay-name") := "counts",
-    !!ns("x_var") := "3",
-    !!ns("y_var") := "4",
-    !!ns("var_pct") := TRUE,
-    !!ns("label") := TRUE,
-    !!ns("show_matrix") := TRUE
-  )
+  app$set_inputs(!!ns("tab_selected") := "PCA")
+  app$set_inputs(!!ns("experiment-name") := "hd1")
+  app$set_inputs(!!ns("assay-name") := "counts")
+  app$set_inputs(!!ns("x_var") := "3")
+  app$set_inputs(!!ns("y_var") := "4")
+  app$set_inputs(!!ns("var_pct") := TRUE)
+  app$set_inputs(!!ns("label") := TRUE)
+  app$set_inputs(!!ns("show_matrix") := TRUE)
 
   app$set_inputs(!!ns2("add-MAE-subjects-var_to_add") := "SEX")
   app$wait_for_idle()

tests/testthat/test-scatterplot.R

@@ -59,13 +59,22 @@ test_that("scatterplot module works as expected in the test app", {
   expect_identical(res$message, "please select at least one gene")
 
   # Set one gene each.
-  app$set_inputs(
-    !!ns("x_spec-genes") := "GeneID:503538",
-    !!ns("y_spec-genes") := "GeneID:8086"
-  )
+  app$set_inputs(!!ns("x_spec-genes") := "GeneID:503538")
+  app$set_inputs(!!ns("y_spec-genes") := "GeneID:8086")
+
+  app$wait_for_idle()
 
   # Change the sample filter and confirm that genes are not updated.
-  app$set_inputs(!!ns2("add-MAE-subjects-add_filter") := "ARM")
+  app$set_inputs(!!ns2("add-MAE-subjects-var_to_add") := "SEX")
+  app$set_inputs(!!ns2("active-MAE-subjects-MAE_SEX-inputs-selection") := "F")
+
+  res <- app$get_value(input = ns("x_spec-genes"))
+  expect_identical(res, "GeneID:503538")
+  res <- app$wait_for_value(input = ns("y_spec-genes"))
+  expect_identical(res, "GeneID:8086")
+
+  # Remove sample filter
+  app$click(ns2("active-MAE-subjects-MAE_SEX-remove"))
   app$wait_for_idle()
 
   res <- app$get_value(input = ns("x_spec-genes"))
@@ -74,13 +83,11 @@ test_that("scatterplot module works as expected in the test app", {
   expect_identical(res, "GeneID:8086")
 
   # Now change the experiment_name, genes, method.
-  app$set_inputs(
-    !!ns("experiment-name") := "hd2",
-    !!ns("x_spec-genes") := "GeneID:441376",
-    !!ns("y_spec-genes") := "GeneID:79963",
-    !!ns("smooth_method") := "loess",
-    !!ns("facet_var-sample_var") := "AGE18"
-  )
+  app$set_inputs(!!ns("experiment-name") := "hd2")
+  app$set_inputs(!!ns("x_spec-genes") := "GeneID:441376")
+  app$set_inputs(!!ns("y_spec-genes") := "GeneID:79963")
+  app$set_inputs(!!ns("smooth_method") := "loess")
+  app$set_inputs(!!ns("facet_var-sample_var") := "AGE18")
 
   app$wait_for_idle()
   app$expect_select_screenshot(ns("plot-plot_out_main"))