Box.com bulk transfer

UAB has an Enterprise contract with Box.com, which is currently in BETA.

This page describes what we have learned about doing bulk-transfers of data.

Warning: size limitations

Box.com claims to have a 5G max filesize limit

• Now 15G max filesize (2/18/016; private email), but "that file size limit is still considered to be in a beta phase"

There was a rumor this would be increased in early 2016. Offically, this is all we know: https://community.box.com/t5/Managing-Your-Content/What-s-the-maximum-file-size-I-can-upload/ta-p/307

If you need to work around this, you can use the Linux "split" utility

# chop file into 4G pieces split \ --bytes=4000m \ big_file.fastq.gz \ big_file.fastq.gz.split4g.

# record checksums of original and chunks md5sum \ big_file.fastq.gz \ big_file.fastq.gz.split4g.* \ > big_file.fastq.gz.md5

Warning: time stamps

When using an FTP client to transfer data up, it is easy to lose both modification and creation timestamps. In particular, many clients will (optionally) preserve modification time, but few will (optionally) preserve creation date.

FTP client	cost	platform	preserve mod_date	preserve create_date
lftp	free	linux/cmd_line	yes	no
SmartFTP	$$	Win Only/GUI	yes	can be enabled
fileZilla	free	linux & win/GUI_only	can be enabled	no
ftp_ssl	free	linux/cmd_line	yes	no

Filezilla on create times

• request closed, no plans to fix: https://trac.filezilla-project.org/ticket/2347

Warning: Shared-to-you folders can't be moved

If someone creates a folder and shares it to you (as an reader, editor, co-owner, etc), it will live in your top level directory, and you will NOT be able to move it into any subfolder.

"Currently, users can't rearrange their own view of folders they are invited to collaborate within. As you note, when someone invites you to collaborate in a folder that you have never had access to before, you will see that folder on your root level." [box.com]

Workaround: if your collaborator makes you the full owner of the folder, then you will be able to move it.

Fix timeframe: "We've heard requests that people be able to rearrange their views before, and this is being considered as part of a larger product experience change next year" [box.com]

Rclone

Check out our YouTube video: Setting up rclone for Box.com file transfer to/from Cheaha

rclone config

Data Transfer Cheaha to BOX. In the terminal (inside the VNC session), load the module rclone

module load rclone/1.48.0

The initial setup for Box involves getting a token from Box rclone config walks you through it. Here is an example of how to make a remote called remote. First run:

 rclone config

This will guide you through an interactive setup process:

No remotes found - make a new one
n) New remote
s) Set configuration password
q) Quit config
n/s/q> n
name> remote
Type of storage to configure.
Choose a number from below, or type in your own value
[snip]
XX / Box
   \ "box"
[snip]
Storage> box
Box App Client Id - leave blank normally.
client_id> 
Box App Client Secret - leave blank normally.
client_secret> 
Edit advanced config? (y/n)
y) Yes
n) No
y/n> n
Remote config
Use auto config?
 * Say Y if not sure
 * Say N if you are working on a remote or headless machine
y) Yes
n) No
y/n> y
If your browser doesn't open automatically go to the following link: http://127.0.0.1:53682/auth
Log in and authorize rclone for access
Waiting for code...
Got code
--------------------
[remote]
client_id = 
client_secret = 
token = {"access_token":"XXX","token_type":"bearer","refresh_token":"XXX","expiry":"XXX"}
--------------------
y) Yes this is OK
e) Edit this remote
d) Delete this remote
y/e/d> y

rclone ls

List the objects in the path with size and path.

rclone ls remote:path [flags]
 -h, --help   help for ls

Note that ls and lsl recurse by default - use “--max-depth 1” to stop the recursion. There are several options related list commands

• ls to list size and path of objects only
• lsl to list modification time, size and path of objects only
• lsd to list directories only

The commands do not recurse by default - use “-R” to make them recurse. Listing a nonexistent directory will produce an error.

rclone mkdir

Make the path if it doesn’t already exist.

rclone mkdir remote:path [flags]
  -h, --help   help for mkdir

rclone copy

Copy files from source to dest, skipping already copied. Note: Use the -P/--progress flag to view real-time transfer statistics

rclone copy source:sourcepath dest:destpath

rclone copy directory

Pending issue : https://github.com/rclone/rclone/issues/1228 Work around solution

rclone copy source:sourcepath "dest:DIR" 
 DIR when passed as a variable creates a remote directory

rclone delete

Remove the contents of path. rclone delete only deletes objects but leaves the directory structure alone. If you want to delete a directory and all of its contents use rclone purge

rclone delete remote:path [flags]
  -h, --help   help for delete

rclone purge

Remove the path and all of its contents.

rclone purge remote:path [flags]
  -h, --help   help for purge

lftp mirror -R examples (UPload)

lftp mirror

• "mirror" copies directory hierarchies DOWN from box.com to local
• "mirror -R" copies directory hierarchies UP from local to box.com

error handling

• the box server frequently looses connection (fails) on particular files
• just re-run the "mirror -R" and it will upload only new/failed files..

Interactive lftp

lftp ftp.box.com > user BLAZERID@uab.edu users_BOX_external_password > mirror --parallel=10 -R local_src_dir box_dest_dir

Single-line lftp (non-shared box)

Warning: This one makes the password visible to "ps" so should only be used on personal machines

lftp -u BLAZERID@uab.edu,users_BOX_external_password ftp.box.com << EOF mirror --parallel=10 -R local_src_dir box_dest_dir EOF

scripted lftp

cat > box_upload.lftp << EOF open ftp.box.com user BLAZERID@uab.edu users_BOX_external_password mirror --parallel=10 -R local_src_dir /box_dest_dir EOF chmod 700 box_upload.lftp lftp -f box_upload.lftp ; echo lftp_RC=$?

scripted lftp - externalize password

file ~/.netrc contains your box external password once (works for wget, lftp, etc)

cat >> ~/.netrc << EOF machine ftp.box.com login BLAZERID@uab.edu password user_Box_External_PW EOF chmod 700 ~/.netrc

then for each transfer, you create a local .lftp file w/o a password. Much more secure and easy to keep up to date.

cat > box_upload.lftp << EOF open ftp.box.com mirror -R local_src_dir /box_dest_dir EOF lftp -f box_upload.lftp ; echo lftp_RC=$?

lftp mirror examples (DOWNload)

scripted lftp

Arguments

• --loop keep restarting until there are no new files left to download - helps if someone else is uploading to that directory while you're downloading it!
• -v verbose level 1: includes bytes transferred and transfer speed.
• --parallel=10 use 10 concurrent TCP/IP connections (much faster)

cat > box_download.lftp << EOF open ftp.box.com user BLAZERID@uab.edu users_BOX_external_password mirror --loop -v --parallel=10 /box_remote_src_dir local_dest_dir EOF chmod 700 box_download.lftp lftp -f box_download.lftp ; echo lftp_RC=$?

Issues to resolve

• Routing over Iternet2

 * we see our traffic randomly going over the commodity internet

Linux Support

Unfortunately, Box doesn't provide a Linux client (is it on the road map?).