handling initial teal_slice

[gogonzo]

teal.slice::teal_slices doesn't initialize filters as it doesn't have global_filters specified.

library(shiny)
library(scda)
library(scda.2022)
library(teal.data)
library(teal.transform)
pkgload::load_all("teal.slice")
pkgload::load_all("teal")
library(teal.modules.general)

funny_module <- function(label = "Filter states", datanames = "all") {
  checkmate::assert_string(label)
  module(
    label = label,
    datanames = datanames,
    ui = function(id, ...) {
      ns <- NS(id)
      div(
        h2("The following filter calls are generated:"),
        verbatimTextOutput(ns("filter_states")),
        verbatimTextOutput(ns("filter_calls")),
        actionButton(ns("reset"), "reset_to_default")
      )
    },
    server = function(input, output, session, data, filter_panel_api) {
      checkmate::assert_class(data, "tdata")
      observeEvent(input$reset, set_filter_state(filter_panel_api, default_filters))
      output$filter_states <- renderPrint({
        logger::log_trace("rendering text1")
        filter_panel_api %>% get_filter_state()
      })
      output$filter_calls <- renderText({
        logger::log_trace("rendering text2")
        attr(data, "code")()
      })
    }
  )
}
set.seed(1)

ADSL <- synthetic_cdisc_data("latest")$adsl
ADSL$empty <- NA
ADSL$logical1 <- FALSE
ADSL$logical <- sample(c(TRUE, FALSE), size = nrow(ADSL), replace = TRUE)
ADSL$numeric <- rnorm(nrow(ADSL))
ADSL$categorical2 <- sample(letters[1:10], size = nrow(ADSL), replace = TRUE)
ADSL$categorical <- sample(letters[1:3], size = nrow(ADSL), replace = TRUE, prob = c(.1, .3, .6))
ADSL$date <- Sys.Date() + seq_len(nrow(ADSL))
ADSL$date2 <- rep(Sys.Date() + 1:3, length.out = nrow(ADSL))
ADSL$datetime <- Sys.time() + seq_len(nrow(ADSL)) * 3600 * 12
ADSL$datetime2 <- rep(Sys.time() + 1:3 * 43200, length.out = nrow(ADSL))

ADSL$numeric[sample(1:nrow(ADSL), size = 10)] <- NA
ADSL$numeric[sample(1:nrow(ADSL), size = 10)] <- Inf
ADSL$logical[sample(1:nrow(ADSL), size = 10)] <- NA
ADSL$date[sample(1:nrow(ADSL), size = 10)] <- NA
ADSL$datetime[sample(1:nrow(ADSL), size = 10)] <- NA
ADSL$categorical2[sample(1:nrow(ADSL), size = 10)] <- NA
ADSL$categorical[sample(1:nrow(ADSL), size = 10)] <- NA

ADTTE <- synthetic_cdisc_data("latest")$adtte
ADRS <- synthetic_cdisc_data("latest")$adrs

ADTTE$numeric <- rnorm(nrow(ADTTE))
ADTTE$numeric[sample(1:nrow(ADTTE), size = 10, )] <- NA

default_filters <- teal.slice::teal_slices(
  teal_slice(dataname = "ADSL", varname = "categorical", selected = c("a"), id = "categorical", multiple = FALSE),
  teal_slice(dataname = "ADSL", varname = "categorical2", selected = c("a"), multiple = FALSE),
  teal_slice(dataname = "ADSL", varname = "numeric", selected = c(0, 140), keep_na = TRUE, keep_inf = TRUE),
  teal_slice(dataname = "ADSL", varname = "logical", selected = TRUE, keep_na = TRUE, keep_inf = TRUE),
  teal_slice(dataname = "ADSL", varname = "datetime"),
  teal_slice(dataname = "ADSL", varname = "date2"),
  teal_slice(dataname = "ADSL", varname = "COUNTRY", selected = c("USA", "CAN", "JPN"), fixed = TRUE),
  teal_slice(dataname = "ADSL", varname = "ARM"),
  teal_slice(dataname = "ADTTE", varname = "PARAMCD"),
  teal_slice(dataname = "ADRS", varname = "PARAMCD"),
  teal_slice(id = "AF", title = "ADULT FEMALE", dataname = "ADSL", expr = "SEX %in% 'F' & AGE >= 18L", anchored = TRUE),
  teal_slice(id = "SE", title = "Safety-Evaluable", dataname = "ADSL", expr = "SAFFL == 'Y'"),
  count_type = "none"
)

app <- init(
  data = cdisc_data(
    cdisc_dataset("ADSL", ADSL),
    cdisc_dataset("ADTTE", ADTTE),
    cdisc_dataset("ADRS", ADRS)
  ),
  modules = modules(
    tm_data_table(
      "table",
      variables_selected = list(ADSL = c("STUDYID", "USUBJID", "SUBJID", "SITEID", "AGE", "SEX")),
      dt_args = list(caption = "ADSL Table Caption")
    ),
    modules(
      label = "tab1",
      funny_module("funny"),
      funny_module("funny2", datanames = "ADTTE") # will limit datanames to ADTTE and ADSL (parent)
    )
  ),
  filter = default_filters
)

runApp(app)

[github-actions]

Code Coverage Summary

Filename                         Stmts    Miss  Cover    Missing
-----------------------------  -------  ------  -------  -----------------------------------------------------------------------------
R/dummy_functions.R                 88      63  28.41%   9-76, 101-104, 107-111
R/get_rcode_utils.R                 46       1  97.83%   49
R/include_css_js.R                  24       0  100.00%
R/init.R                            77      28  63.64%   171-178, 183-204, 216-218
R/module_filter_manager.R          103      29  71.84%   62-70, 79-84, 220, 225-238
R/module_nested_tabs.R             170      16  90.59%   72, 119, 123-124, 138-145, 163, 216, 238, 271
R/module_snapshot_manager.R        140     104  25.71%   71-82, 109-118, 122-134, 136-143, 149-164, 177-200, 203-214, 217-223, 250-273
R/module_tabs_with_filters.R        67       1  98.51%   95
R/module_teal_with_splash.R         33       2  93.94%   65, 77
R/module_teal.R                    164      12  92.68%   68, 71, 158-159, 209-210, 230-233, 235, 239
R/modules_debugging.R               18      18  0.00%    25-44
R/modules.R                        118      17  85.59%   206-211, 330-373
R/reporter_previewer_module.R       16       2  87.50%   23, 27
R/show_rcode_modal.R                20      20  0.00%    16-37
R/tdata.R                           41       2  95.12%   146, 172
R/teal_reporter.R                   60       5  91.67%   65, 116-117, 120, 137
R/teal_slices.R                     45       0  100.00%
R/utils.R                           21       0  100.00%
R/validate_inputs.R                 32       0  100.00%
R/validations.R                     60      37  38.33%   111-373
R/zzz.R                             11       7  36.36%   3-14
TOTAL                             1354     364  73.12%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  -------
R/init.R         +1       0  +0.48%
TOTAL            +1       0  +0.02%

Results for commit: 39e2c12

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

    1 files    16 suites   21s ⏱️
171 tests 171 ✔️ 0 💤 0 ❌
341 runs  341 ✔️ 0 💤 0 ❌

Results for commit 433176c.

[chlebowa]

Great catch 🏆

[chlebowa]

Suggested change

	# convert teal.slice::teal_slices to teal::teal_slices
	filter <- as.teal_slices(as.list(filter))
	# `filter` must be of class `modules_teal_slices` in order for global filters to be applied on app start.
	if (!inherits(filter, "modules_teal_slices")) {
	filter <- as.teal_slices(as.list(filter))
	}