WebDAV and BioCoRE

Introduction

It is possible to mount BioCoRE's BioFS filesystem from your own computer using a technology called WebDAV. This gives you many capabilities that are impossible via a standard webpage. For instance, you can copy more than one file at a time into and out of the BioFS. You can simply select the files that you want and drag them to another folder. In addition, you can often edit a file directly from the BioFS. If you and a collaborator are working on a Microsoft Word document you can edit the file directly from the BioFS, without needing to initially copy it to your local filesystem, edit it, and copy it back up.

Windows and Mac OS X have WebDAV clients built-in, so that the BioCoRE WebDAV server appears as a standard network drive on your desktop. Under Linux, the davfs program will also let you mount WebDAV partitions. In addition, there are a number of file browser programs that will let you access the BioCoRE WebDAV server from a variety of clients.


Windows Install

System Requirements: anything newer than or including Windows XP or 2000 with IE6

There are two ways to install WebDAV on Windows:

Opening files: double clicking will open the default application for the file, e.g. for txt/HTML files it would be IE. To edit such files they should be opened in MS word. In MS word click "open" and then "My Network Places" and then the BioCoRE WebDAV folder to navigate to the appropriate file.

For some installations of Windows you may have problems opening some types of files (txt etc.) as double clicking them may do nothing. Please update to the latest version of Windows and IE and it should solve the problem.


Mac

To connect to the the BioCoRE WebDAV server from Mac OS X, select Connect to Server... from the Go menu in the Finder. When the Connect to Server comes up, type the URL for the BioCoRE WebDAV server into the Address window. For the TCB BioCoRE server, the URL is https://biocore-s.ks.uiuc.edu/biocore/biofs/ if you are running on OS X 10.4 or later, and http://biocore.ks.uiuc.edu/biocore/biofs/ if you are running on an earlier version of OS X. For other BioCoRE servers, replace biocore.ks.uiuc.edu with the address of your BioCoRE server. Click Connect (you will probably receive a File System Security Notice on OS X 10.3 and lower. This is because HTTPS/SSL WebDAV connections were not supported, and your BioCoRE password is sent over the network as unencrypted text. If you are satisfied that your network is secure, click Continue and enter your BioCoRE username and password.) If you typed your password correctly, the WebDAV server will show up on your desktop named biofs. It is now ready for use.

OS X will store your password in the Keychain for you, so you don't have to type it every time you want to use the BioFS. You can also store references to the BioFS disk as aliases or in the Dock (on the right side) so you can easily mount it subsequently without having to retype the address.

To stop using the WebDAV server, simply eject the drive icon from the finder, or drag it to the trash.

A website that gives pictures for this on Mac OS X. Just replace the URLs in the pictures with the URL given above.

If SSL support is required, or if you're running Mac OS 8.X or 9.X, try Goliath at http://www.webdav.org/goliath.


UNIX

To use WebDAV and BioCoRE on a Unix platform, you can use one of the following mechanisms.

Using your window manager

If you are using one of the more modern window managers (such as a recent version of Gnome or KDE) there is a very high probability that you can access the BioFS directory from your window manager. This is also an excellent option if you don't have "root" on the machine that you are logged into.

Open a folder view from your window manager (usually an icon on the desktop that might be labeled something like 'Home') and type the following into the location bar at the top:

https://biocore-s.ks.uiuc.edu/biocore/biofs/
On some systems, such as KDE, you will probably need to type in:
webdavs://biocore-s.ks.uiuc.edu/biocore/biofs/
You should then be asked for your BioCoRE username and password, and then be presented with a view of the BioFS. Based on our testing, you can copy files into and out of the BioFS pretty reliably using the method, but might not have great amounts of luck opening the files directly from the BioFS within your favorite editors, etc due to lack of support within the Linux/Unix system you are using. To view or edit a file, we suggest that you first copy the file onto your own system, edit it, and then copy it back into the BioFS.

Davfs Linux Install

You probably already have a way to access WebDAV on your install. Below are some older docs that we had to help with this.

Davfs2 is a Linux file system driver that allows you to mount a WebDAV server as a local disk drive. The main davfs2 webpage is at:

http://savannah.nongnu.org/projects/davfs2

To install davfs with BioCoRE do the following:


Cadaver Install

Cadaver is a WebDAV client which looks a lot like an ftp client. Cadaver is available on most Unix platforms and might already be installed on your machine. The executable is normally named cadaver. Cadaver can be downloaded from
here.

To connect to a WebDAV server using cadaver do the following:

  1. The open command connects to a WebDAV server.
    >./cadaver
    dav:!>open http://biocore.ks.uiuc.edu/biocore/biofs
    Looking up hostname... Connecting to server... connected.
    Authentication required for BioCoRE on server `biocore.ks.uiuc.edu':
    Username: 
    Password:
    
    It will ask for a username and password which are your BioCoRE username and password.
  2. Use ls to list the files and directories.
    dav:/biocore/biofs/> ls
    Listing collection `/biocore/biofs/': (reconnecting...done) succeeded.
    Coll:  All User Test Project                   0  Aug 10  2001
    Coll:  MyDev                                   0  Oct  5  2001
    Coll:  Private                                 0  Dec 31  1969
    
    In the BioCoRE file system users have their own virtual roots which the projects the user has access to as sub directories.
  3. cd changes to a subdirectory. In cadaver, directories are called Collections, or 'Coll'.
    dav:/biocore/biofs/> cd MyDev
    dav:/biocore/biofs/MyDev/>ls
    Coll:  System                                  0  Oct  5  2001
    Coll:  new                                     0  Jan 15  2002
    Coll:  new1                                    0  Aug 15 08:13
           notes.txt                           17088  Aug 15 09:56
           notes2.txt                          17088  Nov  5 07:08
           test.txt                              222  Aug 15 09:56
           test.txt                              187  Oct 22 12:03
    
  4. 'move', 'copy' and 'rm' work the same and for other commands use 'help'.
Cadaver can be rather picky about files and directories that have nonstandard alphanumeric characters. It can be made more tolerant by using the '-t' tolerant flag, or you can put the command into your .cadaverrc file. One user suggested the following as a .cadaverrc:
set editor vim
set pager less
set tolerant
open https://biocore-s.ks.uiuc.edu/biocore/biofs/
This automatically sets the 'tolerant' flag and connects to the BioCoRE server at UIUC when you start cadaver.

Misc Notes

  • WebDAV has no concept of file permissions. BioCoRE's BioFS file permissions are still in effect, you just can't see them via WebDAV. If you want to change any permissions you will need to log into the web interface of the BioFS.
  • Most web browsers that we've seen don't want to upload files that are larger than 2 gigabytes. For that, you will probably need to use some sort of WebDAV client.