Find orphan files in a Zotero database.

find_orphan_files.R

# Install the packages below (in the `library` function) if you don't
# already have them.

# library(checkmate)
# library(magrittr)
# library(purrr)
# library(readr)
# library(stringr)

#' List all files linked to a reference in a Zotero library
#'
#' @description
#'
#' This function reads a CSV file exported from Zotero and extracts the
#' information about the files linked to the references in the library.
#'
#' @details
#'
#' To export your library from Zotero, go to the menu `File > Export Library...`
#' and choose the CSV format.
#'
#' @param lib_file A string with the path to the Zotero library exported as
#'    a CSV file (important!).
#' @param basename A [`logical`][base::logical()] flag indicating if the
#'   function should return the full path to the files or only the file names.
#'   (default: `TRUE`).
#'
#' @return A [`character`][base::as.character] vector with the names of the
#'  files linked to the references in the Zotero library.
#'
#' @noRd
list_linked_files <- function(lib_file = file.choose(),
                              basename = TRUE) {
  checkmate::assert_file_exists(lib_file, access = "r")
  checkmate::assert_flag(basename)

  out <-
    lib_file |>
    readr::read_csv(col_types = readr::cols(.default = "c")) |>
    magrittr::extract2("File Attachments") |>
    stringr::str_split("; (?=[A-Z]:)") |>
    unlist() |>
    stringr::str_squish() |>
    stringr::str_remove("[^A-Za-z0-9]$") |>
    purrr::discard(is.na)

  if (isTRUE(basename)) {
    basename(out)
  } else {
    out
  }
}

#' Find orphan files in a Zotero library
#'
#' @description
#'
#' This function compares the files in a folder with the files linked to the
#' references in a Zotero library and returns the names of the orphan files.
#'
#' @param lib_file A string with the path to the Zotero library exported as
#'   a CSV file (important!).
#' @param file_folder A string with the path to the folder containing the files
#'   linked to the references in the Zotero library.
#'
#' @return A [`character`][base::as.character] vector with the names of the
#'   orphan files.
#'
#' @noRd
find_orphan_files <- function(lib_file = file.choose(),
                              file_folder = utils::choose.dir()) {
  checkmate::assert_file_exists(lib_file, access = "r")
  checkmate::assert_directory_exists(file_folder, access = "rw")

  linked_files <- list_linked_files(lib_file, basename = TRUE)
  real_files <- list.files(file_folder) |> basename()

  real_files[!real_files %in% linked_files]
}

Hi was trying this code on a mac but am not sure what file to point this function to... I am on a max and it is stored as a zotero.sqlite - wonder if you could help at all - [email protected] - thanks

Hi @wlperry ,

I added some documentation to the functions. See if that helps.

Super cool - thanks - this is the best!!!

Wow - thank you so much bill

…

On Thu, Jun 13, 2024 at 2:02 AM Daniel Vartanian ***@***.***> wrote: ***@***.**** commented on this gist. ------------------------------ Hi @wlperry <https://github.com/wlperry> , I added some documentation to the functions. See if that helps. — Reply to this email directly, view it on GitHub <https://gist.github.com/danielvartan/924817b7e4b69212beb217f339c37a3f#gistcomment-5087413> or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEFHY4RW7WSKPSYSSIFAUKTZHEYY5BFKMF2HI4TJMJ2XIZLTSKBKK5TBNR2WLJDUOJ2WLJDOMFWWLO3UNBZGKYLEL5YGC4TUNFRWS4DBNZ2F6YLDORUXM2LUPGBKK5TBNR2WLJDHNFZXJJDOMFWWLK3UNBZGKYLEL52HS4DFVRZXKYTKMVRXIX3UPFYGLK2HNFZXIQ3PNVWWK3TUUZ2G64DJMNZZDAVEOR4XAZNEM5UXG5FFOZQWY5LFVEYTEOBQHEYTSNZXU52HE2LHM5SXFJTDOJSWC5DF> . You are receiving this email because you were mentioned. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub> .

-- ~~~~~ Bill Perry ***@***.*** ***@***.***