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#' Start the user interface
#'
#' @inheritParams app_server
#' @inheritParams app_ui
#' @param ... passed on to the \code{\link[shiny]{runApp}} call (only if \code{launch = TRUE}), can include server-specific parameters such as host or port
#' @param launch whether to launch the app (TRUE) or return a shiny app object (FALSE) that then can be launched via \code{\link[shiny]{runApp}}
#' @export
run <- function(data_dir = ".", allow_data_upload = FALSE, allow_folder_creation = FALSE, store_data = TRUE, ..., launch = TRUE) {
# safety checks
if (!file.exists(data_dir))
stop("Could not find data directory '", data_dir, " from the current working directory: ", getwd(), call. = FALSE)
# start-up message
message("\n***************************************************************",
"\nINFO: Launching isoviewer GUI (version ", packageVersion("isoviewer"), ")...",
if (setting("debug")) "\nINFO: Debug mode is turned ON" else "",
"\nINFO: App directory: ", getwd(),
"\nINFO: Data directory: ", data_dir
)
# make sure shinyBS on attach runs
shinyBS:::.onAttach()
# isoviewer information
cache_dir <- isoreader:::default("cache_dir")
isoviewer_info <- list(
isoreader_version = packageVersion("isoreader")
)
isoviewer_info_file <- file.path(cache_dir, "isoviewer.rds")
if (!file.exists(cache_dir)) dir.create(cache_dir)
# isoreader version
message("INFO: Isoreader version: ", packageVersion("isoreader"))
if (file.exists(isoviewer_info_file)) {
last_version <- readRDS(isoviewer_info_file)$isoreader_version
if (!isoreader:::same_as_isoreader_version(last_version)) {
# Note: this is not strictly necessary with the newest isoreader package (will not try to read old cache files)
# but it does help keeping the cache folder clean
message("WARNING: Isoreader version has changed majorly from previous run (",
as.character(last_version), ") - clearing out cache...")
iso_cleanup_reader_cache()
}
}
message("INFO: Storing isoviewer information: ", isoviewer_info_file)
saveRDS(isoviewer_info, file = isoviewer_info_file)
# generate app
app <- shinyApp(
ui = app_ui(allow_data_upload = allow_data_upload),
server = app_server(data_dir,
allow_data_upload = allow_data_upload,
allow_folder_creation = allow_folder_creation,
store_data = store_data)
)
# launch or return
if (launch)
runApp(app, display.mode = "normal", ...)
else
return(app)
}
# Install the user interface
#
# Installs the user interface in the target folder with the provided call parameters for launching it via \code{\link[shiny]{runApp}} or as a server application.
# @param install_dir the installation directory (has to exist)
# @param ... parameters for the \code{run} function
install <- function(install_dir, data_dir = ".", ...) {
if(!dir.exists(install_dir)) stop("directory does not exist: ", install_dir, call. = FALSE)
# generate function call
dots <- c(list(data_dir = data_dir), list(...))
parameters <-
lapply(dots, function(i)
if(is.numeric(i) || is.logical(i)) str_c("=", i)
else if (is.character(i)) str_c(" = \"", i, "\"")
else stop("don't know how to process ", class(i))
) %>%
{ str_c(names(.), unlist(.)) } %>%
str_c(collapse = ", ") %>%
{ if(length(.) > 0) str_c(., ", ") else "" } %>%
str_c("launch = FALSE")
# call
sprintf("library(isoviewer)\nrun(%s)", parameters) %>%
cat(file = file.path(install_dir, "app.R"))
message("Info: installed isoviewer app into directory '", install_dir, "'")
}
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