All datanames to transform@669 insert UI@main

[gogonzo]

Changed the way how datanames are passed between teal_data instances:

Previously:

1. loading data
2. filtering active* datasets + creating new teal_data with datanames(data) <- active_datanames + subsetting code and environment to the active datasets
3. transforming data
4. passing filtered and transformed data to the module. Adjusting datanames to the datasets added in teal_transform

• active means data for currently active module

Now:

1. loading data
2. filtering active datasets
3. transforming data
4. creating new teal_data with datanames(data) <- active_datanames + subsetting code and environment to the active datasets - passing to the module

Thanks to the new way it is possible now:

• create a new object in teal_transform_module for a module
• module$datanames doesn't need to include related datanames in order to execute teal_transform

See the app below on this branch and on the feature branch:

app

options(
  teal.log_level = "TRACE",
  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")

anl_transformer <- list(
  teal_transform_module(
    label = "ANL",
    ui = function(id) {
      ns <- NS(id)
      tagList(
        div("This transformer adds ANL (ADSL + ADTTE)")
      )
    },
    server = function(id, data) {
      moduleServer(id, function(input, output, session) {
        reactive({
          within(data(), {
            ANL <- dplyr::inner_join(
              ADSL,
              ADTTE[c("STUDYID", "USUBJID", setdiff(colnames(ADTTE), colnames(ADSL)))],
              by = c("USUBJID", "STUDYID")
            )
          })
        })
      })
    }
  )
)

data <- teal_data_module(
  once = FALSE,
  ui = function(id) {
    ns <- NS(id)
    tagList(
      numericInput(ns("obs"), "Number of observations to show", 1000),
      actionButton(ns("submit"), label = "Submit")
    )
  },
  server = function(id, ...) {
    moduleServer(id, function(input, output, session) {
      logger::log_trace("example_module_transform2 initializing.")
      eventReactive(input$submit, {
        data <- teal_data() |>
          within(
            {
              logger::log_trace("Loading data")
              ADSL <- head(teal.data::rADSL, n = n)
              ADTTE <- teal.data::rADTTE
              aaa <- iris
              CO2 <- CO2
              factors <- names(Filter(isTRUE, vapply(CO2, is.factor, logical(1L))))
              CO2[factors] <- lapply(CO2[factors], as.character)
            },
            n = as.numeric(input$obs)
          )
        join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADTTE")]
        teal.data::datanames(data) <- c("CO2", "ADTTE", "aaa", "ADSL")
        data
      })
    })
  }
)

app <- teal::init(
  data = data,
  modules = list(
    example_module("insufficient", datanames = c("ADSL", "insufficient")),
    example_module("anl from transform", dataname = "ANL", transformers = anl_transformer),
    example_module("anl (fails)", datanames = "ANL")
  ),
  filter = teal_slices(
    teal_slice("ADSL", "SEX"),
    teal_slice("ADSL", "AGE", selected = c(18L, 65L)),
    include_varnames = list(
      ADSL = c("SEX", "AGE")
    )
  )
)

runApp(app)

[m7pr]

Hey @gogonzo I left 2 comments. Would you be able to resolve conflicts?

[m7pr]

Hey, I can confirm I see the error on feature branch, but not on this branch

Main Feature Branch

This Branch

Devtools::test()

There are still 3 checks failining but I know you are aware

── Failed tests ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Failure (test-module_teal.R:537:9): receives all objects from @env except _raw when module$datanames = "all" and @datanames is empty
teal.data::datanames((modules_output$module_1())()) not identical to c("iris", "mtcars", "swiss").
Lengths differ: 8 is not 3
Backtrace:
     ▆
  1. ├─shiny::testServer(...) at test-module_teal.R:522:5
  2. │ ├─shiny:::withMockContext(...)
  3. │ │ ├─shiny::isolate(...)
  4. │ │ │ ├─shiny::..stacktraceoff..(...)
  5. │ │ │ └─ctx$run(...)
  6. │ │ │   ├─promises::with_promise_domain(...)
  7. │ │ │   │ └─domain$wrapSync(expr)
  8. │ │ │   ├─shiny::withReactiveDomain(...)
  9. │ │ │   │ └─promises::with_promise_domain(...)
 10. │ │ │   │   └─domain$wrapSync(expr)
 11. │ │ │   │     └─base::force(expr)
 12. │ │ │   └─env$runWith(self, func)
 13. │ │ │     └─shiny (local) contextFunc()
 14. │ │ │       └─shiny::..stacktraceon..(expr)
 15. │ │ ├─shiny::withReactiveDomain(...)
 16. │ │ │ └─promises::with_promise_domain(...)
 17. │ │ │   └─domain$wrapSync(expr)
 18. │ │ │     └─base::force(expr)
 19. │ │ └─withr::with_options(...)
 20. │ │   └─base::force(code)
 21. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env())
 22. └─testthat::expect_identical(...) at test-module_teal.R:537:9

Failure (test-module_teal.R:691:9): receives extra transform datasets if module$datanames == 'all' and @datanames empty
teal.data::datanames((modules_output$module_1())()) not identical to c("iris", "mtcars", "swiss").
Lengths differ: 5 is not 3
Backtrace:
     ▆
  1. ├─shiny::testServer(...) at test-module_teal.R:660:5
  2. │ ├─shiny:::withMockContext(...)
  3. │ │ ├─shiny::isolate(...)
  4. │ │ │ ├─shiny::..stacktraceoff..(...)
  5. │ │ │ └─ctx$run(...)
  6. │ │ │   ├─promises::with_promise_domain(...)
  7. │ │ │   │ └─domain$wrapSync(expr)
  8. │ │ │   ├─shiny::withReactiveDomain(...)
  9. │ │ │   │ └─promises::with_promise_domain(...)
 10. │ │ │   │   └─domain$wrapSync(expr)
 11. │ │ │   │     └─base::force(expr)
 12. │ │ │   └─env$runWith(self, func)
 13. │ │ │     └─shiny (local) contextFunc()
 14. │ │ │       └─shiny::..stacktraceon..(expr)
 15. │ │ ├─shiny::withReactiveDomain(...)
 16. │ │ │ └─promises::with_promise_domain(...)
 17. │ │ │   └─domain$wrapSync(expr)
 18. │ │ │     └─base::force(expr)
 19. │ │ └─withr::with_options(...)
 20. │ │   └─base::force(code)
 21. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env())
 22. └─testthat::expect_identical(...) at test-module_teal.R:691:9

Failure (test-module_teal.R:1709:9): displays Obs only column if all datasets have no join keys
module_output_table(output, "module_1") not identical to data.frame(...).
Attributes: < Component “row.names”: Numeric: lengths (4, 2) differ >
Component “Data Name”: Lengths (4, 2) differ (string compare on first 2)
Component “Data Name”: 1 string mismatch
Component “Obs”: Lengths (4, 2) differ (string compare on first 2)
Component “Obs”: 1 string mismatch
Backtrace:
     ▆
  1. ├─shiny::testServer(...) at test-module_teal.R:1696:5
  2. │ ├─shiny:::withMockContext(...)
  3. │ │ ├─shiny::isolate(...)
  4. │ │ │ ├─shiny::..stacktraceoff..(...)
  5. │ │ │ └─ctx$run(...)
  6. │ │ │   ├─promises::with_promise_domain(...)
  7. │ │ │   │ └─domain$wrapSync(expr)
  8. │ │ │   ├─shiny::withReactiveDomain(...)
  9. │ │ │   │ └─promises::with_promise_domain(...)
 10. │ │ │   │   └─domain$wrapSync(expr)
 11. │ │ │   │     └─base::force(expr)
 12. │ │ │   └─env$runWith(self, func)
 13. │ │ │     └─shiny (local) contextFunc()
 14. │ │ │       └─shiny::..stacktraceon..(expr)
 15. │ │ ├─shiny::withReactiveDomain(...)
 16. │ │ │ └─promises::with_promise_domain(...)
 17. │ │ │   └─domain$wrapSync(expr)
 18. │ │ │     └─base::force(expr)
 19. │ │ └─withr::with_options(...)
 20. │ │   └─base::force(code)
 21. │ └─rlang::eval_tidy(quosure, mask, rlang::caller_env())
 22. └─testthat::expect_identical(...) at test-module_teal.R:1709:9

[ FAIL 3 | WARN 0 | SKIP 49 | PASS 450 ]

[gogonzo]

There are still 3 checks failining [but I know you are aware]

fixed

[m7pr]

I started the Check Github Action manually for this branch https://github.com/insightsengineering/teal/actions/runs/10319726556

[m7pr]

Ok, the check is green - there was only one styling issue that I fixed
https://github.com/insightsengineering/teal/actions/runs/10319726556
Ready to be merged