[Question]: What do display when missing datasets passed to teal

[gogonzo]

What is your question?

When missing data is passed to the application we need to show the warning somewhere. When data is loaded from teal_data_module, then the warnings about which-dataset-is-missing-for-which-module is displayed in "Data" tab. When one passes a data eagerly, then warning is displayed over tabs. For teal applications wrapped within other applications data can be passed as reactive. In this case "Data" tab is also ommited (as there is no teal_data_module), but otherwise warning is displayed over the tabs (as it needs to be displayed somewhere).

Static or wrapped	Dynamic

app with datanames (static)

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

library(bslib)
library(teal)

trans <- list(
  anl_w_datanames = teal_transform_module(
    label = "ANL with datanames",
    datanames = "ADTTE",
    ui = function(id) {
      ns <- NS(id)
      tagList(
        div("This transformer adds ANL based on specified ADSL, ADTTE"),
        numericInput(ns("obs"), "Number of subjects", value = 400, min = 0, max = 400)
      )
    },
    server = function(id, data) {
      moduleServer(id, function(input, output, session) {
        reactive({
          within(data(),
            {
              ANL <- dplyr::inner_join(
                head(ADSL, nobs),
                ADTTE[c("STUDYID", "USUBJID", setdiff(colnames(ADTTE), colnames(ADSL)))],
                by = c("USUBJID", "STUDYID")
              )
            },
            nobs = input$obs
          )
        })
      })
    }
  ),
  anl_wout_datanames = teal_transform_module(
    label = "ANL without datanames",
    ui = function(id) {
      ns <- NS(id)
      tagList(
        div("This transformer adds ANL based on unspecified ADSL, ADTTE"),
        numericInput(ns("obs"), "Number of subjects", value = 400, min = 0, max = 400)
      )
    },
    server = function(id, data) {
      moduleServer(id, function(input, output, session) {
        reactive({
          within(data(),
            {
              ANL <- dplyr::inner_join(
                head(ADSL, nobs),
                ADTTE[c("STUDYID", "USUBJID", setdiff(colnames(ADTTE), colnames(ADSL)))],
                by = c("USUBJID", "STUDYID")
              )
            },
            nobs = input$obs
          )
        })
      })
    }
  ),
  adsl_w_datanames = teal_transform_module(
    label = "modify ADSL",
    datanames = c("ADSL", "ADTTE"),
    ui = function(id) {
      ns <- NS(id)
      tagList(
        div("This transformer modifies ADSL based on specified ADTTE")
      )
    },
    server = function(id, data) {
      moduleServer(id, function(input, output, session) {
        reactive({
          within(data(),
            {
              ADTTE_summary <- ADTTE |>
                dplyr::group_by(STUDYID, USUBJID) |>
                dplyr::summarize(PARAMCD_AVAL = paste(paste(PARAMCD, "-", AVAL), collapse = "; "))
              ADSL <- dplyr::left_join(ADSL, ADTTE_summary)
            },
            nobs = input$obs
          )
        })
      })
    }
  ),
  adsl_wout_datanames = teal_transform_module(
    label = "modify ADSL",
    ui = function(id) {
      ns <- NS(id)
      tagList(
        div("This transformer modifies ADSL based on unspecified ADTTE")
      )
    },
    server = function(id, data) {
      moduleServer(id, function(input, output, session) {
        reactive({
          within(data(),
            {
              ADTTE_summary <- ADTTE |>
                dplyr::group_by(STUDYID, USUBJID) |>
                dplyr::summarize(PARAMCD_AVAL = paste(sprintf("%s - %.2f", PARAMCD, AVAL), collapse = "; "))
              ADSL <- dplyr::left_join(ADSL, ADTTE_summary)
            },
            nobs = input$obs
          )
        })
      })
    }
  )
)

data <- within(data = teal_data(), {
  library(MultiAssayExperiment)
  logger::log_trace("Loading data")
  z <- NULL
  ADSL <- teal.data::rADSL
  ADTTE <- teal.data::rADTTE
  iris <- iris
  `iris raw` <- iris
  `.iris_raw` <- iris
  data.with..dots <- data.frame(letters = letters)
  `1` <- iris
  data("miniACC", package = "MultiAssayExperiment", envir = environment())
  `mini ACC` <- miniACC
  iris <- iris
})
join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADTTE")]
data

mods <- modules(
  modules(
    label = "all",
    example_module("all", datanames = "all"),
    example_module("null", datanames = NULL)
  ),
  modules(
    label = "all+set_datanames",
    example_module("all", datanames = "all"),
    example_module("null", datanames = NULL)
  ),
  modules(
    label = "specified",
    example_module("exotic", datanames = c(".iris_raw", "iris raw")),
    example_module("adsl", datanames = "ADSL"),
    example_module("adsl+adtte", datanames = c("ADSL", "ADTTE")),
    example_module("adtte+parent", datanames = "ADTTE")
  ),
  modules(
    label = "transformers",
    example_module("anl - transform w/ datanames", dataname = "ANL", transformers = trans["anl_w_datanames"]),
    example_module("anl - transform w/o datanames", dataname = "ANL", transformers = trans["anl_wout_datanames"]),
    example_module("adsl - transform w/ datanames", dataname = "ADSL", transformers = trans["adsl_w_datanames"]),
    example_module("adsl - transform w/o datanames", dataname = "ADSL", transformers = trans["adsl_wout_datanames"]),
    example_module("all w/o datanames", dataname = "all", transformers = trans["anl_wout_datanames"]),
    example_module("all reset datanames", dataname = "all", transformers = trans["anl_wout_datanames"])
    #  |> set_datanames(c("ADSL", "ADTTE", "ANL"))
  ),
  modules(
    label = "missings",
    example_module("inexisting+existing", datanames = c("ADTTE", "inexisting")),
    example_module("inexisting", datanames = "inexisting")
  ),
  reporter_previewer_module()
)

slices <- teal_slices(
  teal_slice("ADSL", "SEX"),
  teal_slice("ADSL", "AGE", selected = c(18L, 65L)),
  teal_slice("ADTTE", "PARAMCD", selected = "CRSD"),
  include_varnames = list(
    ADSL = c("SEX", "AGE")
  )
)

app <- teal::init(
  data = data,
  modules = mods,
  filter = slices
)

runApp(app)

app with datanames (teal_data_module)

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

library(bslib)
pkgload::load_all("teal.code")
pkgload::load_all("teal.data")
pkgload::load_all("teal")
library(teal)

trans <- list(
  anl_w_datanames = teal_transform_module(
    label = "ANL with datanames",
    datanames = "ADTTE",
    ui = function(id) {
      ns <- NS(id)
      tagList(
        div("This transformer adds ANL based on specified ADSL, ADTTE"),
        numericInput(ns("obs"), "Number of subjects", value = 400, min = 0, max = 400)
      )
    },
    server = function(id, data) {
      moduleServer(id, function(input, output, session) {
        reactive({
          within(data(),
            {
              ANL <- dplyr::inner_join(
                head(ADSL, nobs),
                ADTTE[c("STUDYID", "USUBJID", setdiff(colnames(ADTTE), colnames(ADSL)))],
                by = c("USUBJID", "STUDYID")
              )
            },
            nobs = input$obs
          )
        })
      })
    }
  ),
  anl_wout_datanames = teal_transform_module(
    label = "ANL without datanames",
    ui = function(id) {
      ns <- NS(id)
      tagList(
        div("This transformer adds ANL based on unspecified ADSL, ADTTE"),
        numericInput(ns("obs"), "Number of subjects", value = 400, min = 0, max = 400)
      )
    },
    server = function(id, data) {
      moduleServer(id, function(input, output, session) {
        reactive({
          within(data(),
            {
              ANL <- dplyr::inner_join(
                head(ADSL, nobs),
                ADTTE[c("STUDYID", "USUBJID", setdiff(colnames(ADTTE), colnames(ADSL)))],
                by = c("USUBJID", "STUDYID")
              )
            },
            nobs = input$obs
          )
        })
      })
    }
  ),
  adsl_w_datanames = teal_transform_module(
    label = "modify ADSL",
    datanames = c("ADSL", "ADTTE"),
    ui = function(id) {
      ns <- NS(id)
      tagList(
        div("This transformer modifies ADSL based on specified ADTTE")
      )
    },
    server = function(id, data) {
      moduleServer(id, function(input, output, session) {
        reactive({
          within(data(),
            {
              ADTTE_summary <- ADTTE |>
                dplyr::group_by(STUDYID, USUBJID) |>
                dplyr::summarize(PARAMCD_AVAL = paste(paste(PARAMCD, "-", AVAL), collapse = "; "))
              ADSL <- dplyr::left_join(ADSL, ADTTE_summary)
            },
            nobs = input$obs
          )
        })
      })
    }
  ),
  adsl_wout_datanames = teal_transform_module(
    label = "modify ADSL",
    ui = function(id) {
      ns <- NS(id)
      tagList(
        div("This transformer modifies ADSL based on unspecified ADTTE")
      )
    },
    server = function(id, data) {
      moduleServer(id, function(input, output, session) {
        reactive({
          within(data(),
            {
              ADTTE_summary <- ADTTE |>
                dplyr::group_by(STUDYID, USUBJID) |>
                dplyr::summarize(PARAMCD_AVAL = paste(sprintf("%s - %.2f", PARAMCD, AVAL), collapse = "; "))
              ADSL <- dplyr::left_join(ADSL, ADTTE_summary)
            },
            nobs = input$obs
          )
        })
      })
    }
  )
)

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$submit, {
        data <- within(data = teal_data(), n = as.numeric(input$obs), {
          library(MultiAssayExperiment)
          logger::log_trace("Loading data")
          z <- NULL
          ADSL <- head(teal.data::rADSL, n = n)
          ADTTE <- teal.data::rADTTE
          iris <- iris
          `iris raw` <- iris
          `.iris_raw` <- iris
          data.with..dots <- data.frame(letters = letters)
          `1` <- iris
          data("miniACC", package = "MultiAssayExperiment", envir = environment())
          `mini ACC` <- miniACC
          iris <- iris
        })
        join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADTTE")]
        data
      })
    })
  }
)

mods <- modules(
  modules(
    label = "all",
    example_module("all", datanames = "all"),
    example_module("null", datanames = NULL)
  ),
  modules(
    label = "all+set_datanames",
    example_module("all", datanames = "all"),
    example_module("null", datanames = NULL)
  ),
  modules(
    label = "specified",
    example_module("exotic", datanames = c(".iris_raw", "iris raw")),
    example_module("adsl", datanames = "ADSL"),
    example_module("adsl+adtte", datanames = c("ADSL", "ADTTE")),
    example_module("adtte+parent", datanames = "ADTTE")
  ),
  modules(
    label = "transforms",
    example_module("anl - transform w/ datanames", dataname = "ANL", transforms = trans["anl_w_datanames"]),
    example_module("anl - transform w/o datanames", dataname = "ANL", transforms = trans["anl_wout_datanames"]),
    example_module("adsl - transform w/ datanames", dataname = "ADSL", transforms = trans["adsl_w_datanames"]),
    example_module("adsl - transform w/o datanames", dataname = "ADSL", transforms = trans["adsl_wout_datanames"]),
    example_module("all w/o datanames", dataname = "all", transforms = trans["anl_wout_datanames"]),
    example_module("all reset datanames", dataname = "all", transforms = trans["anl_wout_datanames"])
    #  |> set_datanames(c("ADSL", "ADTTE", "ANL"))
  ),
  modules(
    label = "missings",
    example_module("inexisting+existing", datanames = c("ADTTE", "inexisting")),
    example_module("inexisting", datanames = "inexisting")
  ),
  reporter_previewer_module()
)

slices <- teal_slices(
  teal_slice("ADSL", "SEX"),
  teal_slice("ADSL", "AGE", selected = c(18L, 65L)),
  teal_slice("ADTTE", "PARAMCD", selected = "CRSD"),
  include_varnames = list(
    ADSL = c("SEX", "AGE")
  )
)

app <- teal::init(
  data = data,
  modules = mods,
  filter = slices
)

runApp(app)