Fix integration test@main (#394)

fix namespace name after teal update. thank you for the review
insightsengineering · Oct 17, 2024 · af255ba · af255ba
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diff --git a/tests/testthat/_snaps/boxplot.md b/tests/testthat/_snaps/boxplot.md
@@ -7,14 +7,14 @@
        $ fill       : chr  "#F8766D" "#F8766D" "#F8766D" "#F8766D" ...
        $ x          : 'mapped_discrete' num  1 1 1 1 1 1 1 1 1 1 ...
        $ density    : num  0.000161 0.000161 0.000161 0.00016 0.00016 ...
-       $ scaled     : num  0.492 0.492 0.492 0.492 0.492 ...
-       $ ndensity   : num  0.492 0.492 0.492 0.492 0.492 ...
+       $ scaled     : num  0.493 0.492 0.492 0.492 0.492 ...
+       $ ndensity   : num  0.493 0.492 0.492 0.492 0.492 ...
        $ count      : num  0.000642 0.000642 0.000642 0.000642 0.000641 ...
        $ n          : int  4 4 4 4 4 4 4 4 4 4 ...
        $ y          : num  650 659 667 676 684 ...
        $ PANEL      : Factor w/ 1 level "1": 1 1 1 1 1 1 1 1 1 1 ...
        $ group      : int  1 1 1 1 1 1 1 1 1 1 ...
-       $ violinwidth: num  0.492 0.492 0.492 0.492 0.492 ...
+       $ violinwidth: num  0.493 0.492 0.492 0.492 0.492 ...
        $ flipped_aes: logi  FALSE FALSE FALSE FALSE FALSE FALSE ...
        $ width      : num  0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 ...
        $ xmin       : 'mapped_discrete' num  0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 ...

diff --git a/tests/testthat/_snaps/pca.md b/tests/testthat/_snaps/pca.md
@@ -54,16 +54,6 @@
       8 -0.30521740 -0.58893592     1    -1    19  black  1.5   NA    NA    0.5
       9 -0.44180789  0.50479025     1    -1    19  black  1.5   NA    NA    0.5
 
----
-
-    Code
-      cat(res)
-    Output
-         colour           x          y PANEL group shape size fill alpha stroke
-      1 #F8766D -0.08263642  0.6615253     1     1    19  1.5   NA    NA    0.5
-      2 #F8766D -0.53157947 -0.4023279     1     1    19  1.5   NA    NA    0.5
-      3 #F8766D  0.61421589 -0.2591974     1     1    19  1.5   NA    NA    0.5
-
 ---
 
     Code

diff --git a/tests/testthat/adtteSpec/app.R b/tests/testthat/adtteSpec/app.R
@@ -1,3 +1,4 @@
+library(dplyr)
 library(teal.modules.hermes)
 
 ui <- function(id) {

diff --git a/tests/testthat/helper-shinytest2.R b/tests/testthat/helper-shinytest2.R
@@ -9,7 +9,6 @@ module_ns_shiny2 <- function(app) {
   NS(paste0(module_id, "-module"))
 }
 
-ns2 <- NS("teal-main_ui-filter_panel")
 default_app_seed <- 123
 
 # expect_select_screenshot ----

diff --git a/tests/testthat/test-adtteSpec.R b/tests/testthat/test-adtteSpec.R
@@ -223,23 +223,23 @@ test_that("adtteSpecServer module works as expected in the test app", {
   res <- app$get_value(input = ns("adtte-paramcd"))
 
   # Test what happens if selected endpoint (here PFS) is no longer in filtered data.
-  app$set_inputs(!!ns2("add-ADTTE-filter-var_to_add") := "PARAMCD")
-  app$set_inputs(!!ns2("active-ADTTE-filter-ADTTE_PARAMCD-inputs-selection") := "OS")
-
+  app$set_inputs(`teal-teal_modules-adttespec_example-filter_panel-filters-ADTTE-ADTTE-filter-var_to_add` = "PARAMCD", allow_no_input_binding_ = TRUE)
+  app$set_inputs(`teal-teal_modules-adttespec_example-filter_panel-filters-ADTTE-filter-ADTTE_PARAMCD-inputs-selection` = "OS")
   app$wait_for_idle(timeout = 20000)
-  # We expect to get a validation message (also a notification box but we cannot test that)
+  # We expect to get a validation message
+  res <- app$get_value(input = ns("adtte-paramcd"))
+  expect_identical(res, "")
   res <- app$get_value(output = ns("summary"))
   expect_equal(res$message, "please select an endpoint")
-  res <- app$get_value(input = ns("adtte-paramcd"))
-  expect_equal(res, "")
 
   # Now we update the filter by adding PFS back. However the user would have to
   # actively select it.
-  app$set_inputs(!!ns2("active-ADTTE-filter-ADTTE_PARAMCD-inputs-selection") := c("PFS", "OS"))
+  app$set_inputs(`teal-teal_modules-adttespec_example-filter_panel-filters-ADTTE-filter-ADTTE_PARAMCD-inputs-selection` := c("PFS", "OS"))
   app$wait_for_idle()
   res <- app$get_value(output = ns("summary"))
   expect_equal(res$message, "please select an endpoint")
 
+  app$click("teal-teal_modules-adttespec_example-filter_panel-filters-ADTTE-filter-ADTTE_PARAMCD-remove")
   app$stop()
 })
 

diff --git a/tests/testthat/test-experimentSpec.R b/tests/testthat/test-experimentSpec.R
@@ -149,45 +149,16 @@ test_that("experimentSpec module works as expected in the test app", {
   res <- app$get_value(output = ns("summary"))
   expect_match(res, "HermesData object with 9 samples of 2500 genes")
 
-  # Filtering out all samples does give a validation message, so we are safe
-  # downstream.
-  app$set_inputs(!!ns2("add-MAE-subjects-var_to_add") := "SEX")
+  # Filtering out all samples using right side panel
+  app$set_inputs(`teal-teal_modules-experimentspec_example-filter_panel-filters-MAE-MAE-subjects-var_to_add` = "AGE18", allow_no_input_binding_ = TRUE)
+  app$set_inputs(`teal-teal_modules-experimentspec_example-filter_panel-filters-MAE-subjects-MAE_AGE18-inputs-selection` = character(0))
   app$wait_for_idle()
-  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"))
-
-  # Same for filtering out all genes.
-  app$set_inputs(!!ns2("add-MAE-hd2-row_to_add") := "chromosome")
-  app$wait_for_idle()
-  app$set_inputs(
-    !!ns2("active-MAE-hd2-MAE_chromosome_hd2_subset-inputs-selection_open") := TRUE,
-    allow_no_input_binding_ = TRUE
-  )
-  app$set_inputs(!!ns2("active-MAE-hd2-MAE_chromosome_hd2_subset-inputs-selection") := character(0))
-  app$set_inputs(
-    !!ns2("active-MAE-hd2-MAE_chromosome_hd2_subset-inputs-selection_open") := FALSE,
-    allow_no_input_binding_ = TRUE
-  )
-  app$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$message, "No genes or samples included in this experiment, please adjust filters")
-
-  # return to initial situation
-  app$click(ns2("active-MAE-remove_filters"))
-  app$wait_for_idle()
+  app$click("teal-teal_modules-experimentspec_example-filter_panel-filters-MAE-subjects-MAE_AGE18-remove")
 
   # Experiment selection is not affected by removing filters
   res <- app$get_value(input = ns("my_experiment-name"))

diff --git a/tests/testthat/test-geneSpec.R b/tests/testthat/test-geneSpec.R
@@ -72,21 +72,14 @@ test_that("geneSpec module works as expected in the test app", {
   res <- app$get_value(output = ns("result"))
   expect_identical(res, "mean(ABCF2, ABO, ..., ADAMTS5)")
 
-  # Add chromosome filters for the first experiment.
-  app$set_inputs(!!ns2("add-MAE-hd1-row_to_add") := "chromosome")
 
-  # Lock the gene selection.
+  # lock the gene selection
   app$set_inputs(!!ns("my_genes-lock_button") := TRUE)
-  app$wait_for_idle()
-  app$set_inputs(
-    !!ns2("active-MAE-hd2-MAE_chromosome_hd1_subset-inputs-selection_open") := TRUE,
-    allow_no_input_binding_ = TRUE
-  )
-  app$set_inputs(!!ns2("active-MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection") := c("1", "2"))
-  app$set_inputs(
-    !!ns2("active-MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection_open") := FALSE,
-    allow_no_input_binding_ = TRUE
-  )
+
+  # Filter data using the right side panel
+  app$set_inputs(`teal-teal_modules-genespec_example-filter_panel-filters-MAE-MAE-hd1-row_to_add` = "chromosome", allow_no_input_binding_ = TRUE)
+  app$set_inputs(`teal-teal_modules-genespec_example-filter_panel-filters-MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection` = c("1", "2"))
+  app$set_inputs(`teal-teal_modules-genespec_example-filter_panel-filters-MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection_open` = FALSE, allow_no_input_binding_ = TRUE)
   app$wait_for_idle()
 
   # Confirm that gene selection was not changed.
@@ -115,7 +108,7 @@ test_that("geneSpec module works as expected in the test app", {
   expect_identical(res, "mean(ACP1, ACTN2)")
 
   # Remove the filter.
-  app$click(ns2("active-MAE-hd1-MAE_chromosome_hd1_subset-remove"))
+  app$click("teal-teal_modules-genespec_example-filter_panel-filters-MAE-hd1-MAE_chromosome_hd1_subset-remove")
 
   # Select a gene via text input.
   app$click(ns("my_genes-text_button"))

diff --git a/tests/testthat/test-pca.R b/tests/testthat/test-pca.R
@@ -62,19 +62,17 @@ test_that("pca module works as expected in the test app", {
   )
 
   # Add a gene filter and deselect everything and check that it does not crash.
-  app$set_inputs(!!ns2("add-MAE-hd1-row_to_add") := "chromosome_name")
+  app$set_inputs(`teal-teal_modules-pca-filter_panel-filters-MAE-MAE-hd1-row_to_add` = "chromosome", allow_no_input_binding_ = TRUE)
+  app$set_inputs(`teal-teal_modules-pca-filter_panel-filters-MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection` = character())
+  app$set_inputs(`teal-teal_modules-pca-filter_panel-filters-MAE-hd1-MAE_chromosome_hd1_subset-inputs-selection_open` = FALSE, allow_no_input_binding_ = TRUE)
   app$wait_for_idle()
-  app$set_inputs(!!ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-inputs-selection_open") := TRUE, allow_no_input_binding_ = TRUE)
-  app$set_inputs(!!ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-inputs-keep_na-value") := FALSE)
-  app$set_inputs(!!ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-inputs-selection") := character())
-  app$set_inputs(!!ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-inputs-selection_open") := FALSE, allow_no_input_binding_ = TRUE)
 
-  app$wait_for_idle()
   res <- app$get_value(output = ns("test_pca"))
   expect_match(res$message, "No genes or samples included in this experiment, please adjust filters")
 
   # Remove filters
-  app$click(ns2("active-MAE-hd1-MAE_chromosome_name_hd1_subset-remove"))
+  app$click("teal-teal_modules-pca-filter_panel-filters-MAE-hd1-MAE_chromosome_hd1_subset-remove")
+  app$wait_for_idle()
 
   # Update the tab selection.
   app$set_inputs(!!ns("tab_selected") := "PC and Sample Correlation")
@@ -171,33 +169,24 @@ test_that("pca module works as expected in the test app", {
   app$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(timeout = 40000)
-  app$set_inputs(!!ns2("active-MAE-subjects-MAE_SEX-inputs-selection") := "M")
+  app$set_inputs(`teal-teal_modules-pca-filter_panel-filters-MAE-MAE-subjects-var_to_add` = "SEX", allow_no_input_binding_ = TRUE)
+  app$set_inputs(`teal-teal_modules-pca-filter_panel-filters-MAE-subjects-MAE_SEX-inputs-selection` = "F")
+  app$set_inputs(`teal-teal_modules-pca-filter_panel-filters-MAE-subjects-MAE_SEX-inputs-selection_open` = FALSE, allow_no_input_binding_ = TRUE)
 
-  # Ensure xvar and yvar get resetted to pc1 and pc2.
+  # Ensure xvar and yvar DONT get reset.
   app$wait_for_idle(timeout = 20000)
   res <- app$get_value(input = ns("x_var"))
-  expect_identical(res, "1")
+  expect_identical(res, "3")
   res <- app$get_value(input = ns("y_var"))
-  expect_identical(res, "2")
-
-  res <- app$get_value(output = ns("test_pca"))
-  expect_snapshot(
-    cat(res)
-  )
-
-  # Update to cor tab.
-  app$set_inputs(!!ns2("active-MAE-subjects-MAE_SEX-inputs-selection_open") := TRUE, allow_no_input_binding_ = TRUE)
-  app$set_inputs(!!ns2("active-MAE-subjects-MAE_SEX-inputs-selection") := "F")
-  app$set_inputs(!!ns2("active-MAE-subjects-MAE_SEX-inputs-selection_open") := FALSE, allow_no_input_binding_ = TRUE)
+  expect_identical(res, "4")
 
   app$wait_for_idle()
   res <- app$get_value(output = ns("test_pca"))
   expect_identical(res$message, "Sample size is too small. PCA needs more than 2 samples.")
 
   # Remove filter.
-  app$click(ns2("active-MAE-subjects-MAE_SEX-remove"))
+  app$click("teal-teal_modules-pca-filter_panel-filters-MAE-subjects-MAE_SEX-remove")
 
   # Initiate the use of Top Variance Genes filtering functionality.
   app$set_inputs(!!ns("filter_top") := TRUE)

diff --git a/tests/testthat/test-scatterplot.R b/tests/testthat/test-scatterplot.R
@@ -65,8 +65,11 @@ test_that("scatterplot module works as expected in the test app", {
   app$wait_for_idle()
 
   # Change the sample filter and confirm that genes are not updated.
-  app$set_inputs(!!ns2("add-MAE-subjects-var_to_add") := "SEX")
-  app$set_inputs(!!ns2("active-MAE-subjects-MAE_SEX-inputs-selection") := "F")
+
+  # Filtering out all samples using right side panel
+  app$set_inputs(`teal-teal_modules-scatterplot-filter_panel-filters-MAE-MAE-subjects-var_to_add` = "SEX", allow_no_input_binding_ = TRUE)
+  app$set_inputs(`teal-teal_modules-scatterplot-filter_panel-filters-MAE-subjects-MAE_SEX-inputs-selection` = "F")
+  app$wait_for_idle()
 
   app$wait_for_idle()
   res <- app$get_value(input = ns("x_spec-genes"))
@@ -75,7 +78,7 @@ test_that("scatterplot module works as expected in the test app", {
   expect_identical(res, "GeneID:8086")
 
   # Remove sample filter
-  app$click(ns2("active-MAE-subjects-MAE_SEX-remove"))
+  app$click("teal-teal_modules-scatterplot-filter_panel-filters-MAE-subjects-MAE_SEX-remove")
   app$wait_for_idle()
 
   res <- app$get_value(input = ns("x_spec-genes"))