ie_file_server: Central file-management module

In isoexplorer: GUI Components to Explore Stable Isotope Data Files

Central file-management module

Description

The single source of truth for the isofiles in an isoexplorer app, and the hub every other module talks to. It maintains a running set of read isofiles (seeded from get_isofiles(), grown by uploads and watched folders), splits it into the three measurement types (scans / continuous flow / dual inlet) with isoreader2::ir_filter_for_scans() and friends, owns the shared intensity-units selection and the per-type file selection, and exposes the per-type metadata (for the ie_metadata_server() selector tables) and the selection-filtered aggregated data (for the ⁠*_plot_server()⁠ modules).

Usage

ie_file_server(
  id,
  get_isofiles,
  initial_selection = TRUE,
  upload_folder = NULL,
  monitoring_folders = NULL,
  examples_folder = NULL,
  temporary_storage = FALSE
)

ie_file_ui(id)

Arguments

id	the module id (namespace)
get_isofiles	a reactive returning an ir_isofiles to seed the app with (already read); reactive(NULL) is fine when files only arrive via upload / monitoring
initial_selection	what is selected, per type, before any selector pushes a selection. An expression evaluated as a dplyr::filter() on the type's aggregated metadata tibble: TRUE (default) selects everything, FALSE selects nothing, and any other expression selects the matching rows (e.g. grepl("std", file_name)). Captured via tidy evaluation, so it may reference variables from the calling environment. Passed pre-quoted (a quosure) by the ⁠ie_explore_*()⁠ / ie_run_app() wrappers.
upload_folder	directory where uploaded files are stored (created on demand); NULL (the default) means no upload button – set a directory path to enable uploads.
monitoring_folders	character vector of folders to watch; isofiles found there with isoreader2::ir_find_isofiles() are read and added automatically. NULL (default) disables monitoring.
examples_folder	directory the "Load examples" navbar button copies the isoreader2 bundled example files into (and then loads). NULL (the default) means no examples button.
temporary_storage	if TRUE, the upload dialog states that uploaded files are stored only for the duration of the session. Informational only – it does not change how or where files are stored (default FALSE).

Details

Selector tables read ⁠get_<type>_metadata()⁠ and push their selection via ⁠set_selected_<type>()⁠; plot modules read ⁠get_aggregated_<type>_data()⁠ and drive the shared units via get_units() / set_units().

Dynamic files. New files (uploaded, or appearing in monitoring_folders) are read with isoreader2::ir_read_isofiles() and appended; aggregation is incremental (only new files are read/aggregated, then combined with c()), so already-read files are never re-read.

Upload. When upload_folder is set the module owns a navbar upload button (the ie_file_ui() placeholder) that opens a modal to upload multiple files or whole folders bundled as .zip archives (the picker allows .zip, the file types isoreader2 reads, and .json – which covers their ⁠.<type>.json⁠ serializations such as foo.cf.json). Uploaded files are stored in upload_folder (archives unpacked), and only the just-uploaded files are read – files already present in upload_folder when the app started are left untouched. An "Auto-select the newly uploaded files" checkbox (off by default) exclusively selects the new files in the relevant type's table and, in the full multi-tab app, switches to that type's tab.

Monitoring. monitoring_folders are polled; any isofiles found there with isoreader2::ir_find_isofiles() (including files already present at startup) are read and added.

Getting started. When examples_folder and/or upload_folder is set but the app is launched without data (empty get_isofiles()), a prompt is shown once inviting the user to load the examples and/or upload their own files; an app launched with data never sees it.

Value

The "file handle": a list of reactive accessors / setters. For each ⁠<type>⁠ in scans / cf / di: get_units()/set_units(units) (shared intensity units, default "mV"); ⁠get_<type>_metadata()⁠; ⁠set_selected_<type>(rows)⁠; ⁠get_<type>_selection()⁠; ⁠get_aggregated_<type>_data()⁠; plus ⁠get_<type>_select_signal()⁠ (file paths a selector should select, fired by upload auto-select) and get_active_type() (the type whose tab to activate after an auto-select).

Functions

• ie_file_ui(): the navbar placeholders for the "Load examples" and "Upload" buttons (each rendered only when the server's examples_folder / upload_folder is set). Pair with ie_file_server() on the same id.

Examples

if (interactive()) {
  library(shiny)
  # read the bundled isoreader2 examples for some scans data
  iso <-
    isoreader2::ir_examples_folder() |>
    isoreader2::ir_find_isofiles() |>
    isoreader2::ir_read_isofiles()

  ui <- bslib::page_fillable(
    ie_type_explorer_ui("meta", ie_scans_plot_ui("scan"))
  )
  server <- function(input, output, session) {
    # the hub: every other module reads/writes through this handle
    file <- ie_file_server("files", get_isofiles = reactive(iso))
    ie_scans_metadata_server("meta", file) # selection -> file server
    ie_scans_plot_server("scan", file)     # file server -> plot
  }
  shinyApp(ui, server)
}

isoexplorer documentation built on Sept. 8, 2026, 1:07 a.m.