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Andreas Gammelgaard Damsbo 2025-10-07 13:59:36 +02:00
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28 changed files with 397 additions and 107 deletions
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123
app_docker/app.R
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@ -1,7 +1,7 @@
########
#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//RtmpWiu9wh/file1e9944acd364.R
#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//RtmprKaNhO/file2c9538b32097.R
########
i18n_path <- here::here("translations")
@ -62,7 +62,7 @@ i18n$set_translation_language("en")
#### Current file: /Users/au301842/FreesearchR/R//app_version.R
########
app_version <- function()'25.10.1'
app_version <- function()'25.10.2'
########
@ -4035,7 +4035,7 @@ data_types <- function() {
#### Current file: /Users/au301842/FreesearchR/R//hosted_version.R
########
hosted_version <- function()'v25.10.1-251002'
hosted_version <- function()'v25.10.2-251007'
########
@ -4567,7 +4567,7 @@ import_file_ui <- function(id,
shiny::tags$b(i18n$t("No file selected.")),
# shiny::textOutput(ns("trans_format_text")),
# This is the easiest solution, though not gramatically perfect
i18n$t("You can choose between these file types:"), paste(file_extensions,collapse=', '),
i18n$t("You can choose between these file types:"), paste(file_extensions, collapse = ", "),
# sprintf("You can import %s files", paste(file_extensions, collapse = ", ")),
dismissible = TRUE
)
@ -4600,7 +4600,8 @@ import_file_server <- function(id,
show_data_in = c("popup", "modal"),
trigger_return = c("button", "change"),
return_class = c("data.frame", "data.table", "tbl_df", "raw"),
reset = reactive(NULL)) {
reset = reactive(NULL),
limit=100000) {
read_fns <- list(
ods = "import_ods",
dta = "import_dta",
@ -4719,6 +4720,10 @@ import_file_server <- function(id,
extra = if (isTRUE(input$preview_data)) i18n$t("First five rows are shown below:")
)
)
## As a protective measure, the dataset size is capped at cell limit
imported <- limit_data_size(imported,limit = limit)
temporary_rv$status <- "success"
temporary_rv$data <- imported
temporary_rv$name <- input$file$name
@ -4927,9 +4932,20 @@ import_dta <- function(file) {
#' @export
#'
import_rds <- function(file) {
readr::read_rds(
out <- readr::read_rds(
file = file
)
if (is.data.frame(out)) {
out
} else if (is.vector(out) && !is.null(dim(out))) {
## If the data is a simple vector (simple test), it is coerced to a data.frame
as.data.frame(out)
} else {
## If not a data.frame and not a vector (probably a list of elements)
## Flattened to ensure no nested lists
as.data.frame(purrr::list_flatten(out)[[1]])
}
}
#' @title Create a select input control with icon(s)
@ -5035,6 +5051,42 @@ import_file_demo_app <- function() {
}
#' Limit the allowed data set size by number of cells
#'
#' @description
#' This function may act to guard a hosted app against very large data sets in
#' addition to the file size limitations.
#' The function will limit the data set by dropping rows.
#'
#'
#' @param data data.frame
#' @param limit cell number limit. Default is NULL.
#'
#' @returns data.frame
#' @export
#'
#' @examples
#' prod(dim(mtcars))
#' limit_data_size(mtcars)
#' limit_data_size(mtcars,100)
limit_data_size <- function(data, limit = NULL) {
## Add security to only allow dataset of 100.000 cells
## Ideally this should only go for the hosted version
if (is.null(limit)){
return(data)
}
data_dim <- dim(data)
if (prod(data_dim) > limit) {
head(data, floor(limit / data_dim[2]))
} else {
data
}
}
########
#### Current file: /Users/au301842/FreesearchR/R//launch_FreesearchR.R
########
@ -5520,7 +5572,8 @@ vertical_stacked_bars <- function(data,
t.size = 10,
l.color = "black",
l.size = .5,
draw.lines = TRUE) {
draw.lines = TRUE,
label.str="{n}\n{round(100 * p,0)}%") {
if (is.null(group)) {
df.table <- data[c(score, group, strata)] |>
dplyr::mutate("All" = 1) |>
@ -5565,7 +5618,8 @@ vertical_stacked_bars <- function(data,
y = p_prev + 0.49 * p,
color = as.numeric(score) > contrast_cut,
# label = paste0(sprintf("%2.0f", 100 * p),"%"),
label = sprintf("%2.0f", 100 * p)
# label = sprintf("%2.0f", 100 * p)
label = glue::glue(label.str)
)
) +
ggplot2::labs(fill = score_label) +
@ -9019,7 +9073,7 @@ ui_elements <- function(selection) {
"Yes" = "yes"
)
),
shiny::helpText("Option to perform statistical comparisons between strata in baseline table.")
shiny::helpText(i18n$t("Option to perform statistical comparisons between strata in baseline table."))
),
shiny::br(),
shiny::br(),
@ -9029,7 +9083,8 @@ ui_elements <- function(selection) {
width = "100%",
icon = shiny::icon("calculator"),
disabled = TRUE
)
),
shiny::helpText(i18n$t("Press 'Evaluate' to create the comparison table."))
)
)
),
@ -11427,9 +11482,9 @@ server <- function(input, output, session) {
files.to.keep <- list.files("www/")
## This works in a minimal working example, but not here. Will investigate.
# shinyjs::runjs("var language = window.navigator.userLanguage || window.navigator.language;
# var shortLang = language.split('-')[0];
# Shiny.onInputChange('browser_lang', shortLang);")
# shinyjs::runjs("var language = window.navigator.userLanguage || window.navigator.language;
# var shortLang = language.split('-')[0];
# Shiny.onInputChange('browser_lang', shortLang);")
load_data()
@ -11563,6 +11618,7 @@ server <- function(input, output, session) {
output$intro_text <- renderUI(includeHTML(i18n$t("www/intro.html")))
})
## This is not working but kept to try to solve if deemed necessary
shiny::observe(
output$footer_text_div <- renderUI({
shiny::tags$footer(
@ -11629,7 +11685,9 @@ server <- function(input, output, session) {
id = "file_import",
show_data_in = "popup",
trigger_return = "change",
return_class = "data.frame"
return_class = "data.frame",
## Added data.frame size limit (number of cells), rows are dropped to fit
limit = 100000
)
shiny::observeEvent(data_file$data(), {
@ -11677,7 +11735,7 @@ server <- function(input, output, session) {
modal_visual_summary(
id = "initial_summary",
footer = NULL,
size = "xl",title = i18n$t("Data classes and missing observations")
size = "xl", title = i18n$t("Data classes and missing observations")
)
},
error = function(err) {
@ -12275,6 +12333,19 @@ server <- function(input, output, session) {
data_description(rv$list$data, data_text = "The dataset without text variables")
})
## Only allow evaluation if the dataset has fewer then 50 variables
##
# shiny::observeEvent(
# list(
# rv$list$data
# ),
# {
# shiny::req(rv$list$data)
#
# })
shiny::observeEvent(
list(
input$act_eval
@ -12289,9 +12360,25 @@ server <- function(input, output, session) {
add.overall = TRUE
)
shiny::withProgress(message = "Creating the table. Hold on for a moment..", {
rv$list$table1 <- rlang::exec(create_baseline, !!!append_list(rv$list$data, parameters, "data"))
})
# Attempt to introduce error on analysing too large dataset
# tryCatch(
# {
# if (ncol(rv$list$data) > 10) {
# n_col <- ncol(rv$list$data)
# # stop(glue::glue(i18n$t("The data includes {n_col} variables. Please limit to 100.")))
# print("Please limit to 100.")
# } else {
shiny::withProgress(message = "Creating the table. Hold on for a moment..", {
rv$list$table1 <- rlang::exec(create_baseline, !!!append_list(rv$list$data, parameters, "data"))
})
# }
# },
# error = function(err) {
# showNotification(err, type = "err")
# }
# )
rv$code$table1 <- glue::glue("FreesearchR::create_baseline(df,{list2str(parameters)})")
}