Support Load Reporter #1120
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Support Load Reporter #1120
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CLA Assistant Lite bot ✅ All contributors have signed the CLA |
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I have read the CLA Document and I hereby sign the CLA |
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@Polkas could you please merge main to this branch. There are some changes in teal which are important in this context |
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@gogonzo done:) |
Signed-off-by: Maciej Nasinski <[email protected]>
gogonzo
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Apr 22, 2024
gogonzo
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Apr 23, 2024
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@Polkas we need to overcome some cicd issues. You will be able to merge soon 💪 |
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We need to merge the teal.reporter PR first. |
gogonzo
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Apr 24, 2024
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](#81). 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 insightsengineering/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): ```r 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): ```r 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) ``` --------- Signed-off-by: Maciej Nasinski <[email protected]> Co-authored-by: Dawid Kałędkowski <[email protected]> Co-authored-by: Dawid Kałędkowski <[email protected]>
gogonzo
reviewed
Apr 24, 2024
Signed-off-by: Dawid Kałędkowski <[email protected]>
auto-merge was automatically disabled
April 24, 2024 08:16
Head branch was pushed to by a user without write access
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connected with insightsengineering/teal.reporter#251
My work is done as a collaboration of UCB company with Roche.
insightengineering developers can edit this PR.
Objective: Support the Load Report functionality for
TealRerportCardandTealSliceBlockto_listandfrom_listTealSliceBlockmethods. They operate on a string output.TealSliceBlockwhich is needed for the teal.reporterReportCard.set_idfor theReporterso we protect that it can be reloaded only for the same teal app.