Appendix A — Download and Upload Files From and To OSF

doi:10.17605/OSF.IO/S4TBZ

Appendix A — Download and Upload Files From and To OSF

A.1 Overview

This notebook aim to help download or upload files to OSF.

A.2 Set the Environment

A.2.1 Load Packages

Code

library(askpass)
library(cli)
library(clipr)
library(dplyr)
library(fs)
library(here)
library(lubritime)
library(magrittr)
library(osfr)
library(readr)
library(stringr)
library(utils)

A.2.2 Set Data Directories

Code

data_dir <- here("data")

Code

if (!dir_exists(data_dir)) {
  dir_create(data_dir, recurse = TRUE)
}

A.2.3 Set Keys

Code

osf_auth(Sys.getenv("OSF_PAT")) # askpass()

Code

gs4_auth(cache = ".secrets")

Code

private_key <- here::here("_ssh", "id_rsa")

Code

public_key <- here::here("_ssh", "id_rsa.pub")

Code

password <- Sys.getenv("PREGNANCY_PASSWORD") # askpass()

Code

salt <- Sys.getenv("PREGNANCY_SALT") # askpass()

A.2.4 Set OSF IDs

Code

osf_pilot_data_id <- "tj5u2"
osf_raw_data_id <- "7kg34"
osf_processed_data_id <- "a2dsw"
osf_bundles_id <- "fvh4u"
osf_tidy_data_id <- "npkjw"
osf_feedbacks_id <- "8hs7v"

Code

for (i in ls(pattern = "^osf_.*_id$")) {
  assign(
    x = i,
    value = paste0("https://osf.io/", get(i)),
    envir = .GlobalEnv
  )
}

A.3 Download Metadata for Pilot Data Files

A.4 Download Metadata for Raw Actigraphy Files

A.5 Download Metadata for Processed Actigraphy Files

A.5.1 Set Data Subdirectory

Code

data_dir <- here("data", "processed", "actigraphy")

Code

if (!dir_exists(data_dir)) {
  dir_create(data_dir, recurse = TRUE)
}

A.5.2 Retrieve Files Metadata

Code

osf_files <-
  osf_processed_data_id |>
  osf_retrieve_node() |>
  osf_ls_files(n_max = Inf) |>
  filter(name == "actigraphy") |>
  pull(id) |>
  osf_retrieve_file() |>
  osf_ls_files(n_max = Inf) |>
  filter(str_detect(name, "actigraphy-processed-data"))

osf_files

A.6 Download Metadata for Bundle Files

A.7 Download Metadata for Tidy Actigraphy Files

A.8 Download Metadata for Feedback Files

A.9 Download Files

Code

files <-
  osf_files |>
  osf_download(
    path = data_dir,
    conflicts = "overwrite",
    progress = TRUE
  ) |>
  extract2("local_path") |>
  here()

A.10 Unlock Files

Code

unlocked_files <- character()

for (i in files) {
  # if (!file_exists(i)) next

  i_path <-
    i |>
    unlock_file(
      private_key = private_key,
      suffix = ".lockr",
      remove_file = TRUE,
      password = password
    )

  cat_line()

  unlocked_files <- c(unlocked_files, i_path)
}

A.11 Upload Files

Code

osf_id <- osf_bundles_id

Code

# Create the README.md file

readme_file <- tempdir() |> file.path("README.md")

c(
  "# {pregnancy}",
  "",
  "* All files were locked with the project's public key. Ask the project administrators for the key if you need access.",
  "",
  paste0("* Last update: ", lubritime::round_time(Sys.time()), ".")
) |>
  readr::write_lines(readme_file)

readr::read_lines(readme_file)

Code

osf_id |>
  osf_retrieve_node() |>
  osf_upload(
    path = readme_file,
    conflicts = "overwrite",
    progress = TRUE
  )

Code

path <- NULL # Use `NULL` to refer to the root.

Code

osf_data <-
  osf_id |>
  osf_retrieve_node() |>
  osf_ls_files(
    path = path,
    n_max = Inf
  ) |>
  dplyr::arrange(name)

osf_data

Code

dir_path <- read_clip() |> normalizePath("/", mustWork = FALSE)

Code

files <-
  list.files(dir_path) |>
  paste0(".lockr") |>
  setdiff(osf_data$name) |>
  stringr::str_subset("^README", negate = TRUE) |>
  stringr::str_remove("\\.lockr$")

# files <- list.files(dir_path)

files

Code

file.path(dir_path, files)|>
  vapply( prettycheck:::test_file_exists, logical(1)) |>
  unname()

Code

files |> write_clip()

Code

new_files <- character()

for (i in seq_along(files)) {
  i_from <- file.path(dir_path, files[i])
  i_to <- file.path(tempdir(), files[i])

  test <- file.copy(from = i_from, to = i_to, overwrite = TRUE)

  if (isTRUE(test)) new_files <- c(new_files, i_to)
}

locked_files <- character()

for (i in new_files) {
  i_path <- lock_file(
    i,
    public_key = public_key,
    remove_file = TRUE
  )

  cat_line()

  locked_files <- c(locked_files, i_path)
}

Code

osf_id |>
  osf_retrieve_node() |>
  osf_upload(
    path = locked_files,
    conflicts = "overwrite",
    progress = TRUE
  )

A.12 Lock Files

Code

for (i in unlocked_files) {
  # if (!file_exists(i)) next

  i |>
    lock_file(
      public_key = public_key,
      suffix = ".lockr",
      remove_file = TRUE
  )

  cat_line()
}