biocore-l: Recent Changes to the BioCoRE Server at TCB

From: Kirby Vandivort (
Date: Tue Oct 11 2005 - 10:28:00 CDT

Changes since August 25...

Summary of major changes:

* Job Management can now stage files from the BioFS to the remote
* The TCL API now has Control Panel functionality. This could be used,
   for instance, to add chatting capabilities to any program that can
   work with TCL.
* The web interface now has clickable module summaries. In the menu
   on the left side of each page you can now click on the heading text
   for the modules (Documents, Workbench, Notebook) and get summary
   text for what each component provides.

More details of the changes:

* Job Management:File staging updates so that files are now transmitted
   to and from the BioFS and the computational machines.
* Job Management:Fixed some bugs that were preventing accurate account

* API: Added a proof-of-concept TCL control panel to the distribution.
   This code assumes that you have a valid .biocoreSession file
   (typically obtained from having an open control panel) with user
   authentication information. It then creates a socket connection with
   the BioCoRE server and listens for new messages. It also has the
   functionality of allowing a user to add chats from TCL.
   Discussed at the TCL API page
           ( ).

* Added in summary pages for the Documents, Workbench, and Notebook
   modules that new users can click on to get more information about what
   the various components provide.

* BioFS:Fixed a bug that was causing file deletion notices to not get
   sent to the control panel.
* BioFS:Had a case where a user aborted a file upload and the file
   remained locked. Configured partial file uploads so that they will
   release the lock on the file. If anyone notices problems with this
   behavior, please let us know.
* BioFS: Tweaked http://.../biocore/biofs so that it doesn't include
   links to projects that don't have an index.html file.

* Control Panel:Added text to the About box to tell users if they are
   not running the current version of the Control Panel.
* Control Panel:Fixed a bug where system messages weren't getting sent
   to private chat windows.
* Control Panel:Fixed a bug in the XML parsing that occurred when the
   XML document contained comments.
* Control Panel: Scripting - Menu and menu items can now be removed. For
   example usages see the scripts in the BioCoRE Help project.
* Control Panel: Scripting - Added methods to retrieve a particular
   project tab based on its name or the project id.
* Control Panel: Minor addition to previous commit that allowed multi
   line pasting. It wasn't working for private chats (which you can get
   by clicking on someone's name in the user list, or doing /msg userName
   message you want to say.

* Fixed a bug in XML parsing that was causing it to incorrectly handle
   documents with line breaks in the tag name.

* Scripting: Revised set of who can delete notebook entries to include
   author and project administrator.

Kirby Vandivort                      Theoretical and
Senior Research Programmer            Computational Biophysics
Email:          3051 Beckman Institute    University of Illinois
Phone: (217) 244-5711                405 N. Mathews Ave
Fax  : (217) 244-6078                Urbana, IL  61801, USA
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