Implement shinytest2 for tmc

[donyunardi]

This is a continuation of #503

Using the shinytest2 helper class that we built for teal, let extend the feature for tmg.

We have 36 teal module functions in tmc

Note

• We stick to one app per test and open issue to optimize this by exploring one app for all tests in a module.
• Create function: app_driver_\<name of module\>
  • create this in tests/testthat/helper-TealAppDriver.R so we can call it as a function in the test case.
• Test if the example apps for the modules tm_* can be run without shiny errors
  • We won't be doing a snapshot test or confirm if the exact output based on the encoding. We will only check if the visualization is generated when the app initialized.
  • Run the app using different arguments other than what's provided in the example (when applicable)
• Test if visualization is updated when encoding is updated
• Prefix all the external function (i.e. within and specifying the module, everywhere!)

Pre-requirements

• Adds helper functions to initialize TealAppDriver - @averissimo Adds TealAppDriver and skip_if_too_deep for e2e testing #1124

Modules

Wave 1

• tm_a_gee @m7pr Wave 1 - tm_a_gee shinytests #1127
• tm_a_mmrm @kartikeyakirar Wave 1 - tm_a_mmrm shinytests #1131
• tm_g_barchart_simple @averissimo Wave 1 - tm_g_barchart_simple shinytest2 #1134
• tm_g_ci @gogonzo Wave 1 - tm_g_ci shinytests #1125
• tm_g_forest_rsp @vedhav Wave 1 - tm_g_forest_rsp shinytests #1129

Wave 2

• tm_g_forest_tte @averissimo Wave 2 - tm_g_forest_tte shinytest2 #1138
• tm_g_ipp @vedhav Wave 2 - tm_g_ipp shinytests #1141
• tm_g_km @m7pr Wave 2 - tm_g_km shinytests #1133
• tm_g_lineplot @kartikeyakirar Wave 2 - tm_g_lineplot shinytest2  #1137
• tm_g_pp_adverse_events @gogonzo Wave2 - tm_g_pp_adverse_events shinytests #1150

Wave 3

• tm_g_pp_patient_timeline @m7pr Wave 3 - tm_g_pp_patient_timeline shinytest2  #1146
• tm_g_pp_therapy @averissimo Wave 3 - tm_g_pp_therapy shinytest2 #1148
• tm_g_pp_vitals @vedhav Wave 3 - tm_g_pp_vitals shinytest2 #1143
• tm_t_abnormality @vedhav Wave 3 - tm_t_abnormality shinytest2 #1144
• tm_t_abnormality_by_worst_grade @vedhav Wave 3 - tm_t_abnormality_by_worst_grade shinytest2 #1145

Wave 4

• tm_t_ancova Wave 4 - tm_t_ancova shinytests #1154
• tm_t_binary_outcome Wave 4 - tm_t_binary_outcome shinytests #1155
• tm_t_coxreg Wave 4 - tm_t_coxreg shinytests #1156
• tm_t_events Wave 4 - tm_t_events shinytests #1157
• tm_t_events_by_grade Wave 4 - tm_t_events_by_grade shinytests #1158

Wave 5

• tm_t_events_patyear Wave 5 - tm_t_events_patyear shinytests #1159
• tm_t_events_summary Wave 5 - tm_t_events_summary shinytests #1160
• tm_t_exposure Wave 5 - tm_t_exposure shinytests #1161
• tm_t_logistic Wave 5 - tm_t_logistic shinytests #1162
• tm_t_mult_events Wave 5 - tm_t_mult_events shinytests #1163

Wave 6

• tm_t_pp_basic_info Wave 6 - tm_t_pp_basic_info shinytests #1164
• tm_t_pp_laboratory Wave 6 - tm_t_pp_laboratory shinytests #1165
• tm_t_pp_medical_history Wave 6 - tm_t_pp_medical_history shinytests #1166
• tm_t_pp_prior_medication Wave 6 - tm_t_pp_prior_medication shinytests #1167
• tm_t_shift_by_arm Wave 6 - tm_t_shift_by_arm shinytests #1168

Wave 7

• tm_t_shift_by_arm_by_worst Wave 7 - tm_t_shift_by_arm_by_worst shinytests #1169
• tm_t_shift_by_grade Wave 7 - tm_t_shift_by_grade shinytests #1170
• tm_t_smq Wave 7 - tm_t_smq shinytests #1171
• tm_t_summary Wave 7 - tm_t_summary shinytests #1172
• tm_t_summary_by Wave 7 - tm_t_summary_by shinytests #1173
• tm_t_tte Wave 7 - tm_t_tte shinytests #1174

Checklist of things to check on the feature branch

• Rename get_active_module_tws_output and get_active_module_pws_output with get_active_module_table_output and get_active_module_plot_output respectively after teal #1210 is merged. Also look for rvest::html_table() and use get_active_module_table_output for DT tables.
• Check if all the tests have skip_if_too_deep(5) and app_driver$stop()
• Make sure the test description is standard: Begin with a Capital letter and end with . uses variables like arm_var instead of arm_var-variable or ARM variable
• Verify that all the module params are covered in the test. Especially check for cases with fixed data transform. (leave parameter with deprecated status)
• prefix teal.data:: for teal_data(), datanames() and join_keys where ever its missing.

[vedhav]

There are two things that we are not going to focus during the scope of implementing the shinytest2 tests:

1. These 10 modules tm_a_gee, tm_a_mmm, tm_g_forest_rsp, forest_tte, tm_g_km, tm_t_ancova, tm_t_binary_outcome, tm_t_coxreg, tm_t_logistic, and tm_t_tte uses a draggable widget which was not easy to interact with using the app driver.

2. We have to circle back and check if we cover all the conditional widgets for the encoding that is being created.

[vedhav]

Template for the common test patterns we use.

Common first test for all the modules

For plot modules

testthat::test_that("e2e - tm_xxxxx: Module initializes in teal without errors and produces plot output.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_xxxxx()
  app_driver$expect_no_shiny_error()
  app_driver$expect_no_validation_error()

  testthat::expect_match(
    app_driver$get_active_module_pws_output("myplot"),
    "data:image/png;base64,"
  )

  app_driver$stop()
})

For table modules

testthat::test_that("e2e - tm_xxxxx: Module initializes in teal without errors and produces table output.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_xxxxx()
  app_driver$expect_no_shiny_error()
  app_driver$expect_no_validation_error()

  testthat::expect_true(
    app_driver$is_visible(app_driver$active_module_element("table-table-with-settings"))
  )
  app_driver$stop()
})

Check if the the module initializes with proper defaults

testthat::test_that("e2e - tm_xxxxx: Starts with specified label, XXXXX, ...", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_xxxxx()

  testthat::expect_equal(
    app_driver$get_text("#teal-main_ui-root-active_tab > li.active > a"),
    "Module tab label"
  )
  testthat::expect_equal(
    app_driver$get_active_module_input("XXXXX-dataset_ADXX_singleextract-select"),
    "XXXXX Value"
  )
  # ...

  app_driver$stop()
})

Check is a different selection works ✅

For a plot module

testthat::test_that("e2e - tm_xxxxx: Selecting XXXXX changes plot and doesn't throw validation errors.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_xxxxx()
  plot_before <- app_driver$get_active_module_pws_output("myplot")
  app_driver$set_active_module_input("XXXXX-dataset_ADXX_singleextract-select", "XXXXX New Value")
  testthat::expect_false(
    identical(
      plot_before,
      app_driver$get_active_module_pws_output("myplot")
    )
  )
  app_driver$expect_no_validation_error()
  app_driver$stop()
})

For a table module

testthat::test_that("e2e - tm_xxxxx: Selecting XXXXX changes the table and does not throw validation errors.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_xxxxx()
  table_before <- app_driver$get_active_module_tws_output("table")
  app_driver$set_active_module_input("XXXXX-dataset_ADXX_singleextract-select", "XXXXX New Value")
  testthat::expect_false(identical(table_before, app_driver$get_active_module_tws_output("table")))
  app_driver$expect_no_validation_error()
  app_driver$stop()
})

Check if no selection works ✅

For a plot module

testthat::test_that("e2e - tm_xxxxx: Deselecting XXXXX changes plot and doesn't throw validation error.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_xxxxx()
  plot_before <- app_driver$get_active_module_pws_output("myplot")
  app_driver$set_active_module_input("XXXXX-dataset_ADXX_singleextract-select", NULL)
  testthat::expect_false(identical(plot_before, app_driver$get_active_module_pws_output("myplot")))
  app_driver$expect_no_validation_error()
  app_driver$stop()
})

For a table module

testthat::test_that("e2e - tm_xxxxx: Deselecting XXXXX changes table and doesn't throw validation error.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_xxxxx()
  table_before <- app_driver$get_active_module_tws_output("table")
  app_driver$set_active_module_input("XXXXX-dataset_ADXX_singleextract-select", NULL)
  testthat::expect_false(identical(table_before, app_driver$get_active_module_tws_output("table")))
  app_driver$expect_no_validation_error()
  app_driver$stop()
})

Check if no selection shows validation error ❌

For a plot module

testthat::test_that("e2e - tm_xxxxx: Deselecting XXXXX column throws validation error.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_xxxxx()
  app_driver$set_active_module_input("XXXXX-dataset_ADXXX_singleextract-select", NULL)
  testthat::expect_identical(app_driver$get_active_module_pws_output("myplot"), character(0))
  testthat::expect_identical(
    app_driver$active_module_element_text("XXXXX-dataset_ADXXX_singleextract-select_input > div > span"),
    "Validation message"
  )
  app_driver$expect_validation_error()
  app_driver$stop()
})

For a table module

testthat::test_that("e2e - tm_xxxxx: Deselection of XXXXX throws validation error.", {
  skip_if_too_deep(5)
  app_driver <- app_driver_tm_xxxxx()
  app_driver$set_active_module_input("XXXXX-dataset_ADXX_singleextract-select", NULL)
  testthat::expect_identical(app_driver$get_active_module_tws_output("table"), data.frame())
  app_driver$expect_validation_error()
  testthat::expect_equal(
    app_driver$active_module_element_text("XXXXX-dataset_ADXX_singleextract-select_input .shiny-validation-message"),
    "Validation message"
  )
  app_driver$stop()
})