tools/wasm/stage-shinylive-libraries.R

In OpenSpecy: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra

#!/usr/bin/env Rscript

args <- commandArgs(trailingOnly = TRUE)

value_after <- function(flag, default = NULL) {
  hit <- which(args == flag)
  if (!length(hit) || hit[[1]] == length(args)) return(default)
  args[[hit[[1]] + 1L]]
}

out_dir <- value_after("--out-dir", file.path("_wasm", "libraries"))
library_types_file <- value_after(
  "--library-types",
  file.path("inst", "shiny", "wasm", "library-types.txt")
)
manifest_out <- value_after("--manifest-out",
                            file.path(out_dir, "library-manifest.json"))

read_manifest_lines <- function(path) {
  x <- readLines(path, warn = FALSE)
  x <- sub("#.*$", "", x)
  x <- trimws(x)
  x[nzchar(x)]
}

library_types <- read_manifest_lines(library_types_file)
library_catalog <- getFromNamespace(
  ".openspecy_library_catalog", "OpenSpecy"
)()
missing_types <- setdiff(library_types, library_catalog$type)
if (length(missing_types)) {
  stop("Unknown library types: ", paste(missing_types, collapse = ", "),
       call. = FALSE)
}

dir.create(out_dir, recursive = TRUE, showWarnings = FALSE)

numeric_range <- function(x) {
  x <- suppressWarnings(as.numeric(x))
  x <- x[is.finite(x)]
  if (!length(x)) return(c(min = NA_real_, max = NA_real_))
  c(min = min(x), max = max(x))
}

library_summary <- function(lib) {
  if (is.list(lib) && !is.null(lib$spectra) && !is.null(lib$wavenumber)) {
    wn <- numeric_range(lib$wavenumber)
    return(list(
      spectra = ncol(lib$spectra),
      wavenumber_min = unname(wn[["min"]]),
      wavenumber_max = unname(wn[["max"]])
    ))
  }

  if (!is.list(lib)) {
    return(list(spectra = NA_real_, wavenumber_min = NA_real_,
                wavenumber_max = NA_real_))
  }

  spectra_counts <- vapply(lib, function(x) {
    if (is.list(x) && !is.null(x$spectra)) return(ncol(x$spectra))
    if (is.list(x) && !is.null(x$observation_count)) {
      count <- suppressWarnings(as.numeric(x$observation_count))
      count <- count[is.finite(count)]
      if (length(count)) return(sum(count))
    }
    NA_real_
  }, numeric(1))

  wavenumbers <- unlist(lapply(lib, function(x) {
    if (!is.list(x)) return(NULL)
    if (!is.null(x$wavenumber)) return(x$wavenumber)
    if (!is.null(x$all_variables)) return(x$all_variables)
    if (!is.null(x$variables_in)) return(x$variables_in)
    NULL
  }), use.names = FALSE)
  wn <- numeric_range(wavenumbers)

  list(
    components = length(lib),
    spectra = if (any(is.finite(spectra_counts))) {
      sum(spectra_counts, na.rm = TRUE)
    } else {
      NA_real_
    },
    wavenumber_min = unname(wn[["min"]]),
    wavenumber_max = unname(wn[["max"]])
  )
}

entries <- lapply(library_types, function(type) {
  message("Staging OpenSpecy library: ", type)
  OpenSpecy::get_lib(type, path = out_dir)

  lib <- OpenSpecy::load_lib(type, path = out_dir)
  file <- file.path(out_dir, paste0(type, ".rds"))
  md <- library_summary(lib)

  utils::modifyList(
    list(
      type = type,
      file = basename(file),
      source = "latest",
      sha256 = digest::digest(file, algo = "sha256", file = TRUE),
      bytes = file.info(file)$size
    ),
    md
  )
})

manifest <- list(
  library_types = library_types,
  libraries = entries,
  generated_at = format(Sys.time(), "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")
)

jsonlite::write_json(manifest, manifest_out, auto_unbox = TRUE, pretty = TRUE)
print(data.frame(
  type = vapply(entries, `[[`, character(1), "type"),
  bytes = vapply(entries, `[[`, numeric(1), "bytes")
))