Delays transform modules reactivity until tab is active

[averissimo]

Pull Request

Fixes #1303

Changes description

• Unifying function for delayed trigger of module and transformations
• Filter manager crash when clicked with an app that has module specific filters
• Fix bug detected when app is called with teal_data_module
  • One of my testing apps is failing (see below)
• Add tests

Topics to discuss

• Functionality change: this PR will delay the first module reactivity execution until data is pulled from teal_data_module

Sample app for bug

options(
  teal.log_level = "INFO",
  teal.show_js_log = TRUE,
  # teal.bs_theme = bslib::bs_theme(version = 5),
  shiny.bookmarkStore = "server"
)

# pkgload::load_all("../teal.data")
# pkgload::load_all("../teal.slice")
pkgload::load_all("../teal")

my_transformers <- list(
  teal_transform_module(
    label = "Keep first 6 from IRIS",
    ui = function(id) {
      ns <- NS(id)
      div(
        checkboxInput(ns("check"), label = "Toggle `head(iris)`"),
      )
    },
    server = function(id, data) {
      moduleServer(id, function(input, output, session) {
        eventReactive(input$check, {
          print("Check triggered")
          req(data())
          if (input$check) {
            within(data(), iris <- head(iris, 6))
          } else {
            data()
          }
        })
      })
    }
  )
)


data <- teal::teal_data_module(
  ui = function(id) {
    ns <- shiny::NS(id)
    shiny::tagList(
      shiny::tags$head(
        shiny::tags$style(shiny::HTML("
          .teal-data-module {
            border: 1px solid rgba(0, 0, 0, .5);
            border-radius: 4px;
            padding: 1em;
            margin: .2em;
          }
          .teal-data-module .shiny-options-group {
            display: flex;
            flex-wrap: wrap;
            column-gap: 1em;
          }
          .teal-data-module .shiny-options-group  .checkbox {
            margin-top: 1em;
            margin-bottom: 0;
          }
        "))
      ),
      shiny::tags$h2("Data Module"),
      shiny::div(
        class = "teal-data-module",
        shiny::checkboxGroupInput(
          ns("datasets"),
          "Datasets",
          choices = c("ADSL", "ADTTE", "iris", "CO2", "miniACC"),
          selected = c("ADSL", "ADTTE", "iris", "CO2")
        ),
        shiny::actionButton(ns("submit"), label = "Submit")
      )
    )
  },
  server = function(id, ...) {
    shiny::moduleServer(id, function(input, output, session) {
      code <- list(
        ADSL = expression(ADSL <- teal.data::rADSL),
        ADTTE = expression({
          ADTTE <- teal.data::rADTTE
          ADTTE$CNSRL <- as.logical(ADTTE$CNSR)
        }),
        iris = expression(iris <- iris),
        CO2 = expression({
          CO2 <- CO2
          factors <- names(Filter(isTRUE, vapply(CO2, is.factor, logical(1L))))
          CO2[factors] <- lapply(CO2[factors], as.character)
        }),
        miniACC = expression({
          data(
            "miniACC",
            package = "MultiAssayExperiment",
            envir = environment(),
            overwrite = TRUE
          )
          miniACC <- miniACC
        })
      )

      datasets <- reactive(input$datasets)

      shiny::eventReactive(input$submit, {
        code_to_eval <- do.call(c, code[datasets()])
        data <- teal.code::eval_code(teal.data::teal_data(), code_to_eval)

        join_keys(data) <- default_cdisc_join_keys[datasets()]
        teal.data::datanames(data) <- datasets()
        data
      })
    })
  }, once = FALSE
)

teal::init(
  data = data,
  modules = teal::modules(
    teal::example_module(label = "A", datanames = NULL, transformers = my_transformers),
    teal::example_module(label = "B", transformers = my_transformers)
  ),
  filter = teal::teal_slices(
    # # FilterRange
    teal.slice::teal_slice("ADSL", "AGE", selected = c(18L, 65L)),
    # # FilterExpr
    teal_slice(
      dataname = "ADSL",
      id = "Female adults",
      expr = "SEX == 'F' & AGE >= 18",
      title = "Female adults"
    ),
    # # FilterDatetime
    teal_slice(
      dataname = "ADTTE",
      varname = "ADTM",
      id = "Analysis DTM",
      selected = c("2019-03-25 07:06:18", "2020-01-22 15:03:58"),
      title = "Female adults"
    ),
    # # FilterDate with LSTALVDT
    teal_slice(
      dataname = "ADSL",
      varname = "LSTALVDT",
      id = "Last Alive Date",
      selected = c("2022-02-14", "2022-11-24"),
      title = "Last Alive Date"
    ),
    # FilterEmpty
    # FilterLogical with CNSRL
    teal_slice(
      dataname = "ADTTE",
      varname = "CNSRL",
      id = "Censored",
      selected = TRUE,
      title = "Censored"
    ),
    module_specific = FALSE,
    teal.slice::teal_slice("ADSL", "SEX")
  ),
  title = "yada"
) |>
  shiny::runApp()

[github-actions]

Unit Tests Summary

  1 files   25 suites   8m 15s ⏱️
255 tests 251 ✅ 4 💤 0 ❌
512 runs  508 ✅ 4 💤 0 ❌

Results for commit d885b10.

♻️ This comment has been updated with latest results.

[github-actions]

Unit Test Performance Difference

Test Suite	$Status$	Time on main	$±Time$	$±Tests$	$±Skipped$	$±Failures$	$±Errors$
module_teal	💚	$53.03$	$-3.95$	$+4$	$0$	$0$	$0$
shinytest2-module_bookmark_manager	💚	$35.98$	$-1.13$	$0$	$0$	$0$	$0$
shinytest2-reporter	💚	$68.43$	$-1.38$	$0$	$0$	$0$	$0$

Additional test case details

Test Suite	$Status$	Time on main	$±Time$	Test Case
module_teal	👶		$+0.45$	are_called_only_after_teal_data_module_is_resolved
module_teal	👶		$+0.38$	throws_warning_when_transformer_return_reactive.event

Results for commit ed38de6

♻️ This comment has been updated with latest results.

[github-actions]

Code Coverage Summary

Filename                          Stmts    Miss  Cover    Missing
------------------------------  -------  ------  -------  ----------------------------------------------------------------------------------------------------------------------------------------
R/checkmate.R                        24       0  100.00%
R/dummy_functions.R                  47      11  76.60%   27, 29, 41, 52-59
R/get_rcode_utils.R                  12       0  100.00%
R/include_css_js.R                   22      17  22.73%   12-38, 76-82
R/init.R                            108      50  53.70%   107-114, 160-169, 171, 183-204, 229-232, 239-245, 248-249, 251
R/landing_popup_module.R             25      25  0.00%    61-87
R/module_bookmark_manager.R         158     127  19.62%   47-68, 88-138, 143-144, 156, 203, 238-315
R/module_data_summary.R             189      68  64.02%   24-52, 93, 187, 227-267
R/module_filter_data.R               64       2  96.88%   22-23
R/module_filter_manager.R           230      57  75.22%   56-62, 73-82, 90-95, 108-112, 117-118, 291-314, 340, 367, 379, 386-387
R/module_init_data.R                 68       0  100.00%
R/module_nested_tabs.R              238      93  60.92%   40-144, 176, 201-203, 322, 362
R/module_snapshot_manager.R         216     146  32.41%   89-95, 104-113, 121-133, 152-153, 170-180, 184-199, 201-208, 215-230, 234-238, 240-246, 249-262, 265-273, 304-318, 321-332, 335-341, 355
R/module_teal_data.R                152      10  93.42%   41-48, 84, 135-136
R/module_teal_lockfile.R            131      44  66.41%   32-36, 44-56, 59-61, 75, 85-87, 99-101, 109-118, 121, 123, 125-126, 160-161
R/module_teal_with_splash.R          12      12  0.00%    22-38
R/module_teal.R                     190      87  54.21%   48-143, 158, 184-185, 216
R/module_transform_data.R            56      32  42.86%   17-51
R/modules.R                         181      32  82.32%   166-170, 225-228, 326-327, 359-373, 411, 423-431
R/reporter_previewer_module.R        19       2  89.47%   30, 34
R/show_rcode_modal.R                 24      24  0.00%    17-42
R/tdata.R                            14      14  0.00%    19-61
R/teal_data_module-eval_code.R       24       0  100.00%
R/teal_data_module-within.R           7       0  100.00%
R/teal_data_module.R                 52       0  100.00%
R/teal_data_utils.R                  32       0  100.00%
R/teal_reporter.R                    68       6  91.18%   69, 77, 125-126, 129, 146
R/teal_slices-store.R                29       0  100.00%
R/teal_slices.R                      63       0  100.00%
R/TealAppDriver.R                   353     353  0.00%    52-735
R/utils.R                           203       0  100.00%
R/validate_inputs.R                  32       0  100.00%
R/validations.R                      58      37  36.21%   110-377
R/zzz.R                              15      11  26.67%   4-18
TOTAL                              3116    1260  59.56%

Diff against main

Filename                  Stmts    Miss  Cover
----------------------  -------  ------  --------
R/module_nested_tabs.R      +18       0  +3.20%
R/module_teal_data.R          0      -1  +0.66%
R/teal_data_module.R         +9       0  +100.00%
TOTAL                       +27      -1  +0.39%

Results for commit: d885b10

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[gogonzo]

👍