Wave 1 - tm_g_ci shinytests

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: teal.modules.clinical
 Title: 'teal' Modules for Standard Clinical Outputs
-Version: 0.9.0.9023
+Version: 0.9.0.9024
 Date: 2024-04-25
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre")),

NEWS.md

@@ -1,4 +1,4 @@
-# teal.modules.clinical 0.9.0.9023
+# teal.modules.clinical 0.9.0.9024
 
 ### Enhancements
 * Updated `tm_g_forest_rsp` and `tm_g_forest_tte` to use refactored version of `g_forest`. Plots are now displayed as `ggplot` objects instead of `grob` objects. Added parameters `font_size` and `rel_width_forest` to control font size and width of plot relative to table, respectively.

R/tm_a_gee.R

@@ -448,7 +448,7 @@ srv_gee <- function(id,
 
     iv_r <- reactive({
       iv <- shinyvalidate::InputValidator$new()
-      iv$add_rule("conf_level", shinyvalidate::sv_required("Please choose a confidence level."))
+      iv$add_rule("conf_level", shinyvalidate::sv_required("Please choose a confidence level"))
       iv$add_rule(
         "conf_level",
         shinyvalidate::sv_between(

tests/testthat/helper-TealAppDriver.R

@@ -23,3 +23,11 @@ init_teal_app_driver <- function(...) {
     .package = "teal"
   )
 }
+
+# returns base 64 encoded image
+active_module_pws_output <- function(app_driver) {
+  app_driver$get_attr(
+    app_driver$active_module_element("myplot-plot_main > img"),
+    "src"
+  )
+}

tests/testthat/test-shinytest2-tm_a_gee.R

@@ -0,0 +1,294 @@
+app_driver_tm_a_gee <- function() {
+  data <- teal.data::teal_data()
+  data <- within(data, {
+    library(dplyr)
+    ADSL <- tmc_ex_adsl
+    ADQS <- tmc_ex_adqs %>%
+      filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
+      mutate(
+        AVISIT = as.factor(AVISIT),
+        AVISITN = rank(AVISITN) %>%
+          as.factor() %>%
+          as.numeric() %>%
+          as.factor(),
+        AVALBIN = AVAL < 50 # Just as an example to get a binary endpoint.
+      ) %>%
+      droplevels()
+  })
+  datanames <- c("ADSL", "ADQS")
+  teal.data::datanames(data) <- datanames
+  teal.data::join_keys(data) <- teal.data::default_cdisc_join_keys[datanames]
+
+  init_teal_app_driver(
+    data = data,
+    modules = tm_a_gee(
+      label = "GEE",
+      dataname = "ADQS",
+      aval_var = teal.transform::choices_selected("AVALBIN", fixed = TRUE),
+      id_var = teal.transform::choices_selected(c("USUBJID", "SUBJID"), "USUBJID"),
+      arm_var = teal.transform::choices_selected(c("ARM", "ARMCD"), "ARM"),
+      visit_var = teal.transform::choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
+      paramcd = teal.transform::choices_selected(
+        choices = teal.transform::value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
+        selected = "FKSI-FWB"
+      ),
+      cov_var = teal.transform::choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL),
+      conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8, -1), 0.95, keep_order = TRUE)
+    )
+  )
+}
+
+testthat::test_that("e2e - tm_a_gee: Module initializes in teal without errors and produces table output.", {
+  skip_if_too_deep(5)
+
+  app_driver <- app_driver_tm_a_gee()
+  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$stop()
+})
+
+testthat::test_that(
+  "e2e - tm_a_gee: Starts with specified label, id_var, arm_var, visit_var, paramcd, cov_var,
+  conf_level and conf_struct.",
+  {
+    skip_if_too_deep(5)
+    app_driver <- app_driver_tm_a_gee()
+
+    testthat::expect_equal(
+      app_driver$get_text("#teal-main_ui-root-active_tab > li.active > a"),
+      "GEE"
+    )
+
+    testthat::expect_equal(
+      app_driver$get_active_module_input("aval_var-dataset_ADQS_singleextract-select"),
+      "AVALBIN"
+    )
+
+    testthat::expect_equal(
+      app_driver$get_active_module_input("id_var-dataset_ADQS_singleextract-select"),
+      "USUBJID"
+    )
+
+    testthat::expect_equal(
+      app_driver$get_active_module_input("arm_var-dataset_ADSL_singleextract-select"),
+      "ARM"
+    )
+
+    testthat::expect_equal(
+      app_driver$get_active_module_input("visit_var-dataset_ADQS_singleextract-select"),
+      "AVISIT"
+    )
+    testthat::expect_equal(
+      app_driver$get_active_module_input("paramcd-dataset_ADQS_singleextract-filter1-vals"),
+      "FKSI-FWB"
+    )
+
+    testthat::expect_equal(
+      app_driver$get_active_module_input("cov_var-dataset_ADQS_singleextract-select"),
+      NULL
+    )
+
+    testthat::expect_equal(app_driver$get_active_module_input("conf_level"), "0.95")
+
+    testthat::expect_equal(app_driver$get_active_module_input("cor_struct"), "unstructured")
+
+    radio_buttons <- app_driver$active_module_element_text("output_table")
+    testthat::expect_match(
+      radio_buttons,
+      "Output Type.*LS means.*Covariance.*Coefficients",
+      fixed = FALSE
+    )
+    app_driver$stop()
+  }
+)
+
+testthat::test_that("e2e - tm_a_gee: Selection of id_var changes the table and does not throw validation errors.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+  table_before <- app_driver$get_active_module_tws_output("table")
+  app_driver$set_active_module_input("id_var-dataset_ADQS_singleextract-select", "SUBJID")
+  testthat::expect_false(identical(table_before, app_driver$get_active_module_tws_output("table")))
+  app_driver$expect_no_validation_error()
+  app_driver$stop()
+})
+
+testthat::test_that("e2e - tm_a_gee: Deselection of id_var throws validation error.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+  app_driver$set_active_module_input("id_var-dataset_ADQS_singleextract-select", character(0))
+  testthat::expect_identical(app_driver$get_active_module_tws_output("table"), data.frame())
+  app_driver$expect_validation_error()
+  testthat::expect_equal(
+    app_driver$active_module_element_text("id_var-dataset_ADQS_singleextract-select_input > div > span"),
+    "A Subject identifier is required"
+  )
+  app_driver$stop()
+})
+
+testthat::test_that("e2e - tm_a_gee: Change in arm_var changes the table and does not throw validation errors.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+
+  table_before <- app_driver$get_active_module_tws_output("table")
+  app_driver$set_active_module_input("arm_var-dataset_ADSL_singleextract-select", "ARMCD")
+  testthat::expect_false(identical(table_before, app_driver$get_active_module_tws_output("table")))
+  app_driver$expect_no_validation_error()
+  app_driver$stop()
+})
+
+testthat::test_that("e2e - tm_a_gee: Deselection of arm_var throws validation error.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+  app_driver$set_active_module_input("arm_var-dataset_ADSL_singleextract-select", character(0))
+  testthat::expect_identical(app_driver$get_active_module_tws_output("table"), data.frame())
+  app_driver$expect_validation_error()
+  testthat::expect_equal(
+    app_driver$active_module_element_text("arm_var-dataset_ADSL_singleextract-select_input > div > span"),
+    "A treatment variable is required"
+  )
+  app_driver$stop()
+})
+
+
+testthat::test_that("e2e - tm_a_gee: Selection of visit_var changes the table and does not throw validation errors.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+  table_before <- app_driver$get_active_module_tws_output("table")
+  app_driver$set_active_module_input("visit_var-dataset_ADQS_singleextract-select", "AVISITN")
+  testthat::expect_false(identical(table_before, app_driver$get_active_module_tws_output("table")))
+  app_driver$expect_no_validation_error()
+  app_driver$stop()
+})
+
+testthat::test_that("e2e - tm_a_gee: Deselection of visit_var throws validation error.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+  app_driver$set_active_module_input("visit_var-dataset_ADQS_singleextract-select", character(0))
+  testthat::expect_identical(app_driver$get_active_module_tws_output("table"), data.frame())
+  app_driver$expect_validation_error()
+  testthat::expect_equal(
+    app_driver$active_module_element_text("visit_var-dataset_ADQS_singleextract-select_input > div > span"),
+    "A visit variable is required"
+  )
+  app_driver$stop()
+})
+
+testthat::test_that("e2e - tm_a_gee: Selection of paramcd changes the table and does not throw validation errors.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+  table_before <- app_driver$get_active_module_tws_output("table")
+  app_driver$set_active_module_input("paramcd-dataset_ADQS_singleextract-filter1-vals", "BFIALL")
+  testthat::expect_false(identical(table_before, app_driver$get_active_module_tws_output("table")))
+  app_driver$expect_no_validation_error()
+  app_driver$stop()
+})
+
+testthat::test_that("e2e - tm_a_gee: Deselection of paramcd throws validation error.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+  app_driver$set_active_module_input("paramcd-dataset_ADQS_singleextract-filter1-vals", character(0))
+  testthat::expect_identical(app_driver$get_active_module_tws_output("table"), data.frame())
+  app_driver$expect_validation_error()
+  testthat::expect_equal(
+    app_driver$active_module_element_text("paramcd-dataset_ADQS_singleextract-filter1-vals_input > div > span"),
+    "An endpoint is required"
+  )
+  app_driver$stop()
+})
+
+testthat::test_that("e2e - tm_a_gee: Selection of cov_var changes the table and does not throw validation errors.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+  table_before <- app_driver$get_active_module_tws_output("table")
+  app_driver$set_active_module_input("cov_var-dataset_ADQS_singleextract-select", "BASE")
+  testthat::expect_false(identical(table_before, app_driver$get_active_module_tws_output("table")))
+  app_driver$expect_no_validation_error()
+  app_driver$stop()
+})
+
+testthat::test_that("e2e - tm_a_gee: Deselection of cov_var throws validation error.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+  app_driver$set_active_module_input("cov_var-dataset_ADQS_singleextract-select", character(0))
+  testthat::expect_identical(app_driver$get_active_module_tws_output("table"), data.frame())
+  app_driver$expect_validation_error()
+  testthat::expect_equal(
+    app_driver$active_module_element_text("cov_var-dataset_ADQS_singleextract-select_input > div > span"),
+    "An endpoint is required"
+  )
+  app_driver$stop()
+})
+
+testthat::test_that("e2e - tm_a_gee: Selection of conf_level changes the table and does not throw validation errors.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+  table_before <- app_driver$get_active_module_tws_output("table")
+  app_driver$set_active_module_input("conf_level", 0.90)
+  testthat::expect_false(identical(table_before, app_driver$get_active_module_tws_output("table")))
+  app_driver$expect_no_validation_error()
+  app_driver$stop()
+})
+
+testthat::test_that("e2e - tm_a_gee: Selection of conf_level out of [0,1] range throws validation error.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+  table_before <- app_driver$get_active_module_tws_output("table")
+  app_driver$set_active_module_input("conf_level", -1)
+  testthat::expect_identical(app_driver$get_active_module_tws_output("table"), data.frame())
+  app_driver$expect_validation_error()
+  testthat::expect_equal(
+    app_driver$active_module_element_text("conf_level_input > div > span"),
+    "Confidence level must be between 0 and 1"
+  )
+  app_driver$stop()
+})
+
+testthat::test_that("e2e - tm_a_gee: Deselection of conf_level throws validation error.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+  app_driver$set_active_module_input("conf_level", character(0))
+  testthat::expect_identical(app_driver$get_active_module_tws_output("table"), data.frame())
+  app_driver$expect_validation_error()
+  testthat::expect_equal(
+    app_driver$active_module_element_text("conf_level_input > div > span"),
+    "Please choose a confidence level"
+  )
+  app_driver$stop()
+})
+
+
+testthat::test_that("e2e - tm_a_gee: Selection of cor_struct changes the table and does not throw validation errors.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+  table_before <- app_driver$get_active_module_tws_output("table")
+  app_driver$set_active_module_input("cor_struct", "auto-regressive")
+  testthat::expect_false(identical(table_before, app_driver$get_active_module_tws_output("table")))
+  app_driver$expect_no_validation_error()
+  app_driver$stop()
+})
+
+testthat::test_that("e2e - tm_a_gee: Deselection of cor_struct throws validation error.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+  app_driver$set_active_module_input("cor_struct", character(0))
+  testthat::expect_identical(app_driver$get_active_module_tws_output("table"), data.frame())
+  # TO BE FIXED - there is no error displayed
+  app_driver$expect_validation_error()
+  testthat::expect_equal(
+    app_driver$active_module_element_text("cov_struct_input > div > span"),
+    "Please choose a correlation structure"
+  )
+  app_driver$stop()
+})
+
+
+testthat::test_that("e2e - tm_a_gee: Selection of output_table changes the table and doesn't throw validation error.", {
+  skip_if_too_deep(5)
+  app_driver <- app_driver_tm_a_gee()
+  table_before <- app_driver$get_active_module_tws_output("table")
+  app_driver$set_active_module_input("output_table", "t_gee_cov")
+  testthat::expect_false(identical(table_before, app_driver$get_active_module_tws_output("table")))
+  app_driver$expect_no_validation_error()
+  app_driver$stop()
+})