gridfs: GridFS API

Description

Connect to a GridFS database to search, read, write and delete files.

Usage

gridfs(
  db = "test",
  url = "mongodb://localhost",
  prefix = "fs",
  options = ssl_options()
)

Arguments

name of database

url

address of the mongodb server in mongo connection string URI format

prefix

string to prefix the collection name

options

additional connection options such as SSL keys/certs.

Methods

find(filter = "{}", options = "{}"): Search and list files in the GridFS
download(name, path = '.'): Download one or more files from GridFS to disk. Path may be an existing directory or vector of filenames equal to 'name'.
upload(path, name = basename(path), content_type = NULL, metadata = NULL): Upload one or more files from disk to GridFS. Metadata is an optional JSON string.
read(name, con = NULL, progress = TRUE): Reads a single file from GridFS into a writable R connection. If con is a string it is treated as a filepath; if it is NULL then the output is buffered in memory and returned as a raw vector.
write(con, name, content_type = NULL, metadata = NULL, progress = TRUE): Stream write a single file into GridFS from a readable R connection. If con is a string it is treated as a filepath; it may also be a raw vector containing the data to upload. Metadata is an optional JSON string.
remove(name): Remove a single file from the GridFS
drop(): Removes the entire GridFS collection, including all files

Details

We support two interfaces for sending/receiving data from/to GridFS. The fs$read() and fs$write() methods are the most flexible and can send data from/to an R connection, such as a file, socket or url. These methods support a progress counter and can be interrupted if needed. These methods are recommended for reading or writing single files.

The fs$upload() and fs$download() methods on the other hand copy directly between GridFS and your local disk. This API is vectorized so it can transfer many files at once. However individual transfers cannot be interrupted and will block R until completed. This API is only recommended to upload/download a large number of small files.

Modifying files in GridFS is currently unsupported: uploading a file with the same name will generate a new file.

Examples

Run this code

# NOT RUN {
# Upload a file to GridFS
fs <- gridfs(url = "mongodb+srv://readwrite:test@cluster0-84vdt.mongodb.net/test")
input <- file.path(R.home('doc'), "html/logo.jpg")
fs$upload(input, name = 'logo.jpg')

# Download the file back to disk
output <- file.path(tempdir(), 'logo1.jpg')
fs$download('logo.jpg', output)

# Or you can also stream it
con <- file(file.path(tempdir(), 'logo2.jpg'))
fs$read('logo.jpg', con)

# Delete the file on the server
fs$remove('logo.jpg')

files <- c(input, file.path(tempdir(), c('logo1.jpg', 'logo2.jpg')))
hashes <- tools::md5sum(files)
stopifnot(length(unique(hashes)) == 1)

# }
# NOT RUN {
# Insert Binary Data
fs <- gridfs()
buf <- serialize(nycflights13::flights, NULL)
fs$write(buf, 'flights')
out <- fs$read('flights')
flights <- unserialize(out$data)

tmp <- file.path(tempdir(), 'flights.rds')
fs$download('flights', tmp)
flights2 <- readRDS(tmp)
stopifnot(all.equal(flights, nycflights13::flights))
stopifnot(all.equal(flights2, nycflights13::flights))

# Show what we have
fs$find()
fs$drop()
# }

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