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https://github.com/agdamsbo/FreesearchR.git
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packaging
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parent
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commit
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7 changed files with 406 additions and 161 deletions
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@ -1,7 +1,7 @@
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########
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#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//RtmpxB1KWR/file173c978fea931.R
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#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//Rtmprp4Sq1/fileb60491b0ce8.R
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########
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i18n_path <- system.file("translations", package = "FreesearchR")
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@ -45,8 +45,7 @@ library(rlang)
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library(shiny.i18n)
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library(fontawesome)
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print(list.files("www/fonts/montserrat", full.names = TRUE))
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# print(list.files("www/fonts/montserrat", full.names = TRUE))
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## Translation init
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i18n <- shiny.i18n::Translator$new(translation_csvs_path = i18n_path)
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@ -54,16 +53,6 @@ i18n <- shiny.i18n::Translator$new(translation_csvs_path = i18n_path)
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# i18n <- shiny.i18n::Translator$new(translation_csvs_path = here::here("inst/translations/"))
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i18n$set_translation_language("en")
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## Global freesearchR vars
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if (!"global_freesearchR" %in% ls(name = globalenv())) {
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global_freesearchR <- list(
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include_globalenv = FALSE,
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data_limit_default = 1000,
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data_limit_upper = 10000,
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data_limit_lower = 1
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)
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}
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########
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#### Current file: /Users/au301842/FreesearchR/app/functions.R
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@ -75,7 +64,7 @@ if (!"global_freesearchR" %in% ls(name = globalenv())) {
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#### Current file: /Users/au301842/FreesearchR/R//app_version.R
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########
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app_version <- function()'26.3.2'
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app_version <- function()'26.3.3'
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########
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@ -4035,33 +4024,28 @@ missing_fraction <- function(data) {
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#' sample(c(1:8, NA), 20, TRUE)
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#' ) |> data_description()
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data_description <- function(data, data_text = "Data") {
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data <- if (shiny::is.reactive(data))
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data()
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else
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data
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# Resolve reactive once
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if (shiny::is.reactive(data)) data <- data()
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# Early return if null
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if (is.null(data)) return(i18n$t("No data present."))
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n <- nrow(data)
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# Early return if empty
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if (n == 0L) return(i18n$t("No data present."))
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n_var <- ncol(data)
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n_complete <- sum(complete.cases(data))
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# Faster complete.cases alternative using rowSums on NA matrix
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n_complete <- n - sum(rowSums(is.na(data)) > 0L)
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p_complete <- signif(100 * n_complete / n, 3)
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if (is.null(data)) {
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i18n$t("No data present.")
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} else {
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glue::glue(
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i18n$t(
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"{data_text} has {n} observations and {n_var} variables, with {n_complete} ({p_complete} %) complete cases."
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)
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glue::glue(
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i18n$t(
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"{data_text} has {n} observations and {n_var} variables, with {n_complete} ({p_complete} %) complete cases."
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)
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}
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# sprintf(
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# "%s has %s observations and %s variables, with %s (%s%%) complete cases.",
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# data_text,
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# n,
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# n_var,
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# n_complete,
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# p_complete
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# )
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)
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}
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@ -4527,7 +4511,7 @@ data_types <- function() {
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#### Current file: /Users/au301842/FreesearchR/R//hosted_version.R
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########
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hosted_version <- function()'v26.3.2-260311'
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hosted_version <- function()'v26.3.3-260312'
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########
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@ -5987,16 +5971,16 @@ landing_page_ui <- function(i18n) {
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#' data(mtcars)
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#' launch_FreesearchR(launch.browser = TRUE)
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#' }
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launch_FreesearchR <- function(inlcude_globalenv = TRUE,
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launch_FreesearchR <- function(include_globalenv = TRUE,
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data_limit_default = 1000,
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data_limit_upper = 100000,
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data_limit_lower = 1,
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...) {
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global_freesearchR <- list(
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include_globalenv = include_globalenv,
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data_limit_default = data_limit_default,
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data_limit_upper = data_limit_upper,
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data_limit_lower = data_limit_lower
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Sys.setenv(
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INCLUDE_GLOBALENV = include_globalenv,
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DATA_LIMIT_DEFAULT = data_limit_default,
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DATA_LIMIT_UPPER = data_limit_upper,
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DATA_LIMIT_LOWER = data_limit_lower
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)
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appDir <- system.file("apps", "FreesearchR", package = "FreesearchR")
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@ -6010,6 +5994,123 @@ launch_FreesearchR <- function(inlcude_globalenv = TRUE,
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}
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## Helper to set env variables
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get_config <- function(var_name, default = NULL) {
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val <- Sys.getenv(var_name, unset = NA_character_)
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# Only use env var if it is explicitly set and non-empty
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if (!is.na(val) && nzchar(trimws(val))) {
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if (is.logical(default)) return(to_logical(val))
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if (is.numeric(default)) return(as.numeric(val))
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return(val)
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}
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if (!is.null(default)) {
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return(default)
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}
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stop(paste("Required config variable not set:", var_name))
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}
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to_logical <- function(x) {
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result <- switch(tolower(trimws(as.character(x))),
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"true" = , "1" = , "yes" = TRUE,
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"false" = , "0" = , "no" = FALSE,
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NA
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)
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if (is.na(result)) stop(paste("Cannot coerce to logical:", x))
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result
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}
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## File loader - based on the module, uses hard coded default values
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load_file <- function(path) {
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read_fns <- list(
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ods = "import_ods",
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dta = "import_dta",
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csv = "import_delim",
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tsv = "import_delim",
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txt = "import_delim",
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xls = "import_xls",
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xlsx = "import_xls",
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rds = "import_rds"
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)
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ext <- tolower(tools::file_ext(path))
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if (!ext %in% names(read_fns)) {
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message("Unsupported file type, skipping: ", basename(path), " (.", ext, ")")
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return(NULL)
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}
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read_fn <- read_fns[[ext]]
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parameters <- list(
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file = path,
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sheet = 1,
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skip = 0,
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dec = ".",
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encoding = "unknown"
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)
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# Trim parameters to only those accepted by the target function
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parameters <- parameters[which(names(parameters) %in% rlang::fn_fmls_names(get(read_fn)))]
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result <- tryCatch(
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rlang::exec(read_fn, !!!parameters),
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error = function(e) {
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# Fall back to rio::import
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message("Primary loader failed for ", basename(path), ", trying rio::import")
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tryCatch(
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rio::import(path),
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error = function(e2) {
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message("Failed to load ", basename(path), ": ", e2$message)
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NULL
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}
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)
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}
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)
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if (!is.null(result) && NROW(result) < 1) {
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message("File loaded but contains no rows, skipping: ", basename(path))
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return(NULL)
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}
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result
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}
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load_folder <- function(folder = "/app/data", envir = .GlobalEnv) {
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if (is.null(folder) || !dir.exists(folder)) {
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message("No data folder found, skipping load")
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return(invisible(NULL))
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}
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files <- list.files(folder, full.names = TRUE)
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if (length(files) == 0) {
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message("Data folder is empty, skipping load")
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return(invisible(NULL))
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}
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loaded <- vapply(files, function(file) {
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result <- load_file(file)
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if (is.null(result))
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return(FALSE)
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name <- tools::file_path_sans_ext(basename(file))
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assign(name, default_parsing(result), envir = envir)
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TRUE
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}, logical(1))
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message(sprintf(
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"Loaded %d/%d files from %s",
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sum(loaded),
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length(files),
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folder
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))
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invisible(loaded)
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}
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########
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#### Current file: /Users/au301842/FreesearchR/R//missings-module.R
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########
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@ -10726,9 +10827,9 @@ ui_elements <- function(selection) {
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layout_params = "dropdown",
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# title = "Choose a datafile to upload",
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file_extensions = c(".csv", ".tsv", ".txt", ".xls", ".xlsx", ".rds", ".ods", ".dta"),
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limit_default = global_freesearchR$data_limit_default,
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limit_lower = global_freesearchR$data_limit_lower,
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limit_upper = global_freesearchR$data_limit_upper
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limit_default = DATA_LIMIT_DEFAULT,
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limit_lower = DATA_LIMIT_LOWER,
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limit_upper = DATA_LIMIT_UPPER
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)
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),
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id = "env",
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title = NULL,
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packages = c("NHANES", "stRoke", "datasets", "MASS"),
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globalenv = global_freesearchR$include_globalenv
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globalenv = isTruthy(INCLUDE_GLOBALENV)
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)
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),
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# shiny::conditionalPanel(
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}
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########
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#### Current file: /Users/au301842/FreesearchR/app/globals.R
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########
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## Setting global variables
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INCLUDE_GLOBALENV <- get_config("INCLUDE_GLOBALENV", default = FALSE)
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DATA_LIMIT_DEFAULT <- get_config("DATA_LIMIT_DEFAULT", default = 10000)
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DATA_LIMIT_UPPER <- get_config("DATA_LIMIT_UPPER", default = 100000)
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DATA_LIMIT_LOWER <- get_config("DATA_LIMIT_LOWER", default = 1)
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## Loads folder passed to the docker container and mounted as below:
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##
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## services:
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## shiny:
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## image: your-shiny-app
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## volumes:
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## - ./data:/app/data:ro
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##
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## All files in the ./data/ folder is attempted loaded
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load_folder()
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########
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#### Current file: /Users/au301842/FreesearchR/app/ui.R
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########
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@ -13798,9 +13921,9 @@ server <- function(input, output, session) {
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# selected = "file"
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# )
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if (isTRUE(global_freesearchR$include_globalenv)) {
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if (isTruthy(INCLUDE_GLOBALENV)) {
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env_label <- i18n$t("Local or sample data")
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output$data_sample_text <- shiny::renderText(shiny::helpText(
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output$data_sample_text <- shiny::renderUI(shiny::helpText(
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i18n$t(
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"Upload a file, get data directly from REDCap or use local or sample data."
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)
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trigger_return = "change",
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btn_show_data = FALSE,
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reset = reactive(input$hidden),
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limit_data = global_freesearchR$data_limit_upper
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limit_data = DATA_LIMIT_UPPER
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)
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shiny::observeEvent(from_env$data(), {
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