SMD@UTK File Manager
A Robust User Interface to the Stanford Microarray Database (SDM)
M.S. Pilot Adviser: M. W. Berry
John Clayton England, III
04/10/2003
SMD@UTK File Manager
SMD@UTK File Manger
The Stanford Microarray Database (SMD)
● Problems with user file transfer to the SMD
● First file transfer solution at UTK
● How the SMD retrieves data from the client filesystem
● Designing a web based interface
● Using the web based interface
● Future work
●
SMD@UTK File Manager
The SMD is database that holds
genomic data. This data is accessed
through a web-based interface. From
this interface you can view, analyze,
and share data. You cannot upload
data from a local machine to the
database from this interface.
The graphic on the right shows an
example of a slide that has been
scanned and loaded into the database.
The grid on the graphic is over laid on
the spots by the user before the graphic
is uploaded. Though SMD can also
preform this action, it is not as the user
defined grid.
SMD@UTK File Manager
To get files into the database a user must transfer these files to a filesys
that the Oracle database, the back-end of the SMD, can access. Stanfo
suggests using a UNIX account to allow these transfers.
Problems with using a UNIX account for this transfer:
Users may not be familiar with UNIX file transfers
●Ftp, sftp, rcp, scp
●Creating and maintaining full UNIX accounts adds over head
for the system administrators
●User education
●Security concerns that arise from local accounts
●
SMD@UTK File Manager
The UNIX account solution has worked for Stanford but they have
found the large number of accounts they have to support has become
a problem. They have over 500 accounts and maintaining them is
beginning to stress the system administrators.
SMD@UTK File Manager
Here at UTK we have not given UNIX accounts to the users who use the
database. The solution implemented was Zip disk transfers. Meaning th
users copy their experiments to a Zip disk and physically hand the disk t
SMD system administrators.
1.User copies file to Zip disk
2.User gives disk to admins
3.Admins load data to client filesystem
4.Data is loaded into the database
1
2
3
4
SMD@UTK File Manager
This system works without requiring local UNIX accounts for the users. Th
was interesting and lead to the discovery that it does not matter what UNIX
user owns the files on the filesystem. The database is only concerned wit
the directory structure in which the files are stored.
/<basepath>/<username>/incoming
The username above is the only is the only key for the database to know
the files owner.
With this knowledge a system that did not require a UNIX account could
be implemented.
SMD@UTK File Manager
Designing a web based interface
A web based interface would require file transfers and filesystem access
●PHP does both of these well
●Authentication must be addressed
●PHP can handle authentication
●A simple user interface must be possible
●PHP again can fill this need
●
SMD@UTK File Manager
Parts of the web based file manager
Login Page / Authentication
●
Main Menu
●
File Uploads
●
File Lists
●
File Deletions
●
File Renaming
●
SMD@UTK File Manager
Authentication
A username and password are need to enter the file manager.
A perl script is provided to create a password file.
SMD@UTK File Manager
Main Menu
The main menu is base of the file manager. It leads the user to the othe
functions of the interface.
SMD@UTK File Manager
Uploads
From this page users can access local files on their machines and move
those files to the database client.
SMD@UTK File Manager
File Lists
A user can from this page see the files that have been uploaded to the
database client.
SMD@UTK File Manager
File Deletion
From this page uploaded files can be removed.
SMD@UTK File Manager
File Renaming
Uploaded files can be renamed from this page.
SMD@UTK File Manager
SMD@UTK File Manager adding a user demo
SMD@UTK File Manager demo
SMD@UTK File Manager
Future Work
Adding encryption via SSL
●Tying authentication to the SMD authentication
●Multiple file uploads
●
SMD@UTK File Manager
Acknowledgments
Comity
●
Dr. Berry
●
Dr. Moore
●
Dr. Becker
●
Web Services
●
Colton Smith
●
John Rose
●
Bob Hillhouse
●
Bhanu Prasad Rekapalli
●
SMD Developers
●