Box
Command line access to box from UCSF.
WebDAV is no longer supported.
NOTES
The max file size limitation is stated to be 50GB but we've found it to be much less, at least when using curl to upload from the command line.
29949918869 - CS-4941-01A-01D-1465.bam - Succeeded
32556286377 - DU-5854-01A-11D-1703.bam - Succeeded
34011562949 - DB-5276-10A-01D-1465.bam - Succeeded
34553253061 - DH-5143-10A-01D-1465.bam - Failed
36992859467 - DU-5847-01A-11D-1703.bam - Failed
Credentials
Accessing box via the command line will require getting special credentials from Box.
Log in to box using your UCSF credentials.
Click on the icon in the upper right, mine is a "GW", then click on "Account Settings".
Scroll down to the "Authentication" section. It should say something like "Because you are using Single Sign On (SSO), you will need to create a unique password to use external applications that do not support SSO." Follow the directions to create a password.
Password in ~/.netrc
Add your username and new password to your ~/.netrc.
This file may or may not exist already.
#machine dav.box.com login XXXXXXXXX@ucsf.edu password XXXXXXXX
machine ftp.box.com login XXXXXXXX@ucsf.edu password XXXXXXXX
You may also want to change its permissions ...
chmod 600 ~/.netrc
Example upload
Because the box "path" includes a space it MUST by parenthesesed or perhaps escaped.
With FTP instead of DAV, the dirs can be created during the upload command.
#BOX="https://dav.box.com/dav/Francis _Lab_Share/CLI_TEST"
BOX="ftps://ftp.box.com/Francis _Lab_Share/CLI_TEST"
# Unnecessary
curl --ftp-create-dirs -netrc -X MKCOL "${BOX}/"
echo "Testing" > test_file.txt
curl --ftp-create-dirs -netrc -T test_file.txt "${BOX}/"
Note that the trailing "/" is essential.
Example download
If not told otherwise, curl writes the received data to stdout. It can be instructed to instead save that data into a local file, using the -o, --output or -O, --remote-name options. If curl is given multiple URLs to transfer on the command line, it similarly needs multiple options for where to save them.
#BOX="https://dav.box.com/dav/Francis _Lab_Share/CLI_TEST"
BOX="ftps://ftp.box.com/Francis _Lab_Share/CLI_TEST"
curl --ftp-create-dirs -netrc "${BOX}/test_file.txt" --output ./test_file.txt.download
cat test_file.txt.download
Testing
Also see ...
https://ucsf-cbi.github.io/c4/transfers/ucsf-box.html
Their tutorial is a bit different.
To download say a whole directory ...
Use wget / ftp
Add this slightly different line to your .netrc
machine ftp.box.com login XXXXXXXXXXXX@ucsf.edu password XXXXXXXX
Note that the path is a bit different here.
BOX="ftps://ftp.box.com/Francis _Lab_Share/Mayo-FrancisLab/Mayo/Observed"
wget --recursive "${BOX}"