Simple - Load Reporter - Inbuild

[Polkas]

closes #81
continuation of #177
linked to insightsengineering/teal#1120 Please install this teal branch when testing the code

I created a new PR from the fork as I am no longer part of the insightengineering group.
My work is done as a collaboration of UCB company with Roche.
insightengineering developers can edit this PR.

I followed a simple design, which was evaluated positively in the discussion.

DONE:

• New modules report_load_srv and report_load_ui; similar direct update for Previewer.
• REMOVE the Archiver Class as we not need it for this simplified scenario.
• Improve to_list and from_list Reporter methods
• Add set_id and get_id Reporter methods. Optionally add id to a Report which will be compared when it is rebuilt from a list. To test it in the teal example app please download a report and then add a new module or dataset to the app and try to load it back. The report can be loaded back to teal app only with the same datasets and modules. The id is added to the downloaded file name if exists.
• Improve to_list and from_list ReportCard methods (linked with Support Load Reporter teal#1120)
• Both already existing vignette apps are updated automatically.
• warning(cond) everywhere to be consistent. We should send the error/warning to the R console when STH fails.
• Add testServer tests for report_load_srv/report_load_ui modules.
• UI tested with all 3 bootstrap versions.

Points to consider:

• The JSON format Report representation seems to be enough, so an Archiver is unnecessary. The DB solution to save/load seems overcomplex for the project.
• No update will be required to introduce it into teal modules. Simple reporter is updated automatically and can be customized with a new teal.reporter option.
• When reloading, the Report is validated by the "report_" file name prefix later by the slot name "teal Report" and optionally by ID if it is non-empty.

Example Teal App (play with bootstrap versions, simple reporter modules, and add new data/module to confirm the report can not be then reloaded):

library(teal.modules.general)
# one of c("3", "4", "5")
options("teal.bs_theme" = bslib::bs_theme(version = "4"))

data <- teal_data()
data <- within(data, {
  library(nestcolor)
  ADSL <- teal.modules.general::rADSL
})
datanames <- c("ADSL")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]

app <- teal::init(
  data = data,
  modules = teal::modules(
    teal.modules.general::tm_a_regression(
      label = "Regression",
      response = teal.transform::data_extract_spec(
        dataname = "ADSL",
        select = teal.transform::select_spec(
          label = "Select variable:",
          choices = "BMRKR1",
          selected = "BMRKR1",
          multiple = FALSE,
          fixed = TRUE
        )
      ),
      regressor = teal.transform::data_extract_spec(
        dataname = "ADSL",
        select = teal.transform::select_spec(
          label = "Select variables:",
          choices = teal.transform::variable_choices(data[["ADSL"]], c("AGE", "SEX", "RACE")),
          selected = "AGE",
          multiple = TRUE,
          fixed = FALSE
        )
      ),
      ggplot2_args = teal.widgets::ggplot2_args(
        labs = list(subtitle = "Plot generated by Regression Module")
      )
    )
  )
)
runApp(app, launch.browser = TRUE)

Example general shiny app (play with bootstrap versions, simple reporter modules):

library(shiny)
library(teal.reporter)
library(ggplot2)
library(rtables)
library(DT)
library(bslib)

ui <- fluidPage(
    # please, specify specific bootstrap version and theme
    theme = bs_theme(version = "4"),
    titlePanel(""),
    tabsetPanel(
        tabPanel(
            "main App",
            tags$br(),
            sidebarLayout(
                sidebarPanel(
                    uiOutput("encoding")
                ),
                mainPanel(
                    tabsetPanel(
                        id = "tabs",
                        tabPanel("Plot", plotOutput("dist_plot")),
                        tabPanel("Table", verbatimTextOutput("table")),
                        tabPanel("Table DataFrame", verbatimTextOutput("table2")),
                        tabPanel("Table DataTable", dataTableOutput("table3"))
                    )
                )
            )
        ),
        ### REPORTER
        tabPanel(
            "Previewer",
            reporter_previewer_ui("prev")
        )
        ###
    )
)
server <- function(input, output, session) {
    output$encoding <- renderUI({
        tagList(
            ### REPORTER
            teal.reporter::simple_reporter_ui("simple_reporter"),
            ###
            if (input$tabs == "Plot") {
                sliderInput(
                    "binwidth",
                    "binwidth",
                    min = 2,
                    max = 10,
                    value = 8
                )
            } else if (input$tabs %in% c("Table", "Table DataFrame", "Table DataTable")) {
                selectInput(
                    "stat",
                    label = "Statistic",
                    choices = c("mean", "median", "sd"),
                    "mean"
                )
            } else {
                NULL
            }
        )
    })
    plot <- reactive({
        req(input$binwidth)
        x <- mtcars$mpg
        ggplot(data = mtcars, aes(x = mpg)) +
            geom_histogram(binwidth = input$binwidth)
    })
    output$dist_plot <- renderPlot(plot())
    
    table <- reactive({
        req(input$stat)
        lyt <- basic_table() %>%
            split_rows_by("Month", label_pos = "visible") %>%
            analyze("Ozone", afun = eval(str2expression(input$stat)))
        build_table(lyt, airquality)
    })
    output$table <- renderPrint(table())
    
    table2 <- reactive({
        req(input$stat)
        data <- aggregate(
            airquality[, c("Ozone"), drop = FALSE], list(Month = airquality$Month), get(input$stat),
            na.rm = TRUE
        )
        colnames(data) <- c("Month", input$stat)
        data
    })
    output$table2 <- renderPrint(print.data.frame(table2()))
    output$table3 <- renderDataTable(table2())
    
    ### REPORTER
    reporter <- Reporter$new()
    card_fun <- function(card = ReportCard$new(), comment) {
        if (input$tabs == "Plot") {
            card$set_name("Plot Module")
            card$append_text("My plot", "header2")
            card$append_plot(plot())
            card$append_rcode(
                paste(
                    c(
                        "x <- mtcars$mpg",
                        "ggplot2::ggplot(data = mtcars, ggplot2::aes(x = mpg)) +",
                        paste0("ggplot2::geom_histogram(binwidth = ", input$binwidth, ")")
                    ),
                    collapse = "\n"
                ),
                echo = TRUE,
                eval = FALSE
            )
        } else if (input$tabs == "Table") {
            card$set_name("Table Module rtables")
            card$append_text("My rtables", "header2")
            card$append_table(table())
            card$append_rcode(
                paste(
                    c(
                        "lyt <- rtables::basic_table() %>%",
                        'rtables::split_rows_by("Month", label_pos = "visible") %>%',
                        paste0('rtables::analyze("Ozone", afun = ', input$stat, ")"),
                        "rtables::build_table(lyt, airquality)"
                    ),
                    collapse = "\n"
                ),
                echo = TRUE,
                eval = FALSE
            )
        } else if (input$tabs %in% c("Table DataFrame", "Table DataTable")) {
            card$set_name("Table Module DF")
            card$append_text("My Table DF", "header2")
            card$append_table(table2())
            # Here r code added as a regular verbatim text
            card$append_text(
                paste0(
                    c(
                        'data <- aggregate(airquality[, c("Ozone"), drop = FALSE], list(Month = airquality$Month), ',
                        input$stat,
                        ", na.rm = TRUE)\n",
                        'colnames(data) <- c("Month", ', paste0('"', input$stat, '"'), ")\n",
                        "data"
                    ),
                    collapse = ""
                ), "verbatim"
            )
        }
        if (!comment == "") {
            card$append_text("Comment", "header3")
            card$append_text(comment)
        }
        card
    }
    teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)
    teal.reporter::reporter_previewer_srv("prev", reporter)
    ###
}

if (interactive()) shinyApp(ui = ui, server = server)

[Polkas]

@gogonzo done:)

[gogonzo]

Nice solution, we will need to make some changes on our side but in general it is fine. Please check out bookmark-restore of an app which had a Report loaded

Image shows an app which has been restored from a bookmarking

[Polkas]

I have to leave all print(cond) as the warning(cond) passes the error and the Shiny app crashes.

[gogonzo]

I have to leave all print(cond) as the warning(cond) passes the error and the Shiny app crashes.

What about message()?

[Polkas]

I have to leave all print(cond) as the warning(cond) passes the error and the Shiny app crashes.

What about message()?

Unfortunately, a message() materializes the error and causes an app crash.

[gogonzo]

Please don't render load button for now - proposed solution in the comment. Please update NEWS file and we will be very close to merge

[Polkas]

Load is not included in the teal previewer now. Please consider additional teal.option for that, as my team will be happy to have the ability to add a load feature to teal.

I fixed bookmarking with the code below; please write if you do not want to merge it here

    session$onBookmark(function(state) {
      reporterdir <- file.path(state$dir, "reporter")
      dir.create(reporterdir)
      reporter$to_jsondir(reporterdir)
    })
    session$onRestored(function(state) {
      reporterdir <- file.path(state$dir, "reporter")
      reporter$from_jsondir(reporterdir)
    })

[gogonzo]

Load is not included in the teal previewer now. Please consider additional teal.option for that, as my team will be happy to have the ability to add a load feature to teal.

We don't yet decided about the recommended way in teal to load reporter this is why we don't want to have another "restore" functionality (after snapshot manager and bookmarking). teal::previewer_module will have load disabled but you will be able to create own previewer module and include it into teal::init(modules = list(..., <your previewer module>).

I fixed bookmarking with the code below; please write if you do not want to merge it here

    session$onBookmark(function(state) {
      reporterdir <- file.path(state$dir, "reporter")
      dir.create(reporterdir)
      reporter$to_jsondir(reporterdir)
    })
    session$onRestored(function(state) {
      reporterdir <- file.path(state$dir, "reporter")
      reporter$from_jsondir(reporterdir)
    })

Thanks, this is good 👍

---

I will make a final review next week as I have few days off. PR looks good both here and teal 👍 Thanks!

[gogonzo]

Just these two and we are fine here

[Polkas]

Danke, great collabo:)

[gogonzo]

@Polkas do the honors ;)

[Polkas]

@Polkas do the honors ;)

Thanks:D but you have to be the one as “Only those with write access to this repository can merge pull requests.”
Once more thanks for the collab:)