inst/scripts/get_hmdb.R

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

start <- Sys.time()

library(tima)

paths <- get_default_paths()

log_debug(
  "This script",
  crayon::green("downloads HMDB structures. \n")
)
log_debug("Authors: ", crayon::green("AR"), "\n")
log_debug("Contributors: ...")

## TODO check md5 if possible
## (see https://twitter.com/Adafede/status/1592543895094788096)
log_debug("Downloading HMDB (might be long)")
get_file(
  url = paths$urls$hmdb$structures,
  export = paths$data$source$libraries$sop$hmdb
)

log_debug("Script finished in", crayon::green(format(end - start)))