IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

Acedb January Newsletter

Ed Griffiths edgrif at sanger.ac.uk
Wed Feb 7 07:08:06 EST 2001

The January Newsletter, slightly late...sorry, you'll have to put it down to New
Year tardiness.

Do remember that contributions to the Newsletter would be most welcome, topic
could be anything from "your favourite tip" to "your favourite bug" to "my wish
list". Just send me a few paragraphs and I'll put it in the next newsletter.

cheers Ed

| Ed Griffiths, Acedb development, Informatics Group,                    |
|               The Sanger Centre, Wellcome Trust Genome Campus,         |
|               Hinxton, Cambridge CB10 1SA, UK                          |
|                                                                        |
| email: edgrif at sanger.ac.uk  Tel: +44-1223-494780  Fax: +44-1223-494919 |


ACEDB User Group Newsletter - January 2001

If you want to have this newsletter mailed to you _or_ you want to make
comments/suggestions about the format/content then send an email to
acedb at sanger.ac.uk.

This is the post-Christmas/not that much has changed report. There are small
but important changes to the acedb database log format, a short article
about the introduction of better web-based downloads for acedb and a number
of bug fixes.

General News

File Chooser and selecting a directory

A number of users didn't see last months newsletter and wanted to know how
to go directly to a directory using the 4_8c file chooser. I'll just repeat
last months item about how to do this:

   * If you want to go directly to a directory using the file chooser
     window, you can do this by typing the directory name in the bottom
     "selection" window and pressing the <tab> key. This will point the file
     chooser to this directory so you can then choose files from there.
   * _Note_ that the <tab> key also does C-shell style filename completion
     just like you get when using an xterm window. So if you type part of a
     directory and press <tab> the rest will be filled in for you (as far as
     this can be done unambiguously).

Hope that's useful.

New Features

Acedb on windows

The acedb locking/write access mechanism now works on Windows 95/98.

Better information for signals

When an internal error happens in acedb or the system runs out of resources
(e.g. program stack space), the operating system may send a "signal" to
acedb which stops the program from running. When this happens acedb runs a
special signal handling routine which attempts to terminate the acedb
program with a message about what has happened.

The message that acedb outputs has been improved in the following ways:

   * The message now includes an operating system defined message that
     identifies the cause of the signal.
   * The text of the message has been changed so more accurately indicate
     whether the signal is likely to have been caused by an acedb error or
     by a system resource error.

So if one of the acedb programs you are using exits with a message like

// ABORT : Fatal error, program received signal....

and you can remember/reproduce the sequence of actions that caused it then
please get in touch with the acedb developers (acedb at sanger.ac.uk).

"Preserve" behaviour restored

Due to popular demand, the "preserve" button has been added back for the
tree window display, selecting this item on a tree window menu will ensure
that the window stays around until explicitly "quit".


Rearrangements to acedb downloads

Its possible to download acedb code in one of two ways:

FTP site
     login to the sanger ftp site and go to /pub/acedb
Web site
     visit http://www.acedb.org/Software/Downloads/

We've introduced the web pages to make it easier to navigate the acedb
downloads directories and get the download package you want. On visiting
http://www.acedb.org/Software/Downloads/ you will find there are three
levels of code you can download and a quick summary of the current build
status available at the bottom of the page.

The three levels of code that can be downloaded are:

     This is the most stable and supported code. It has the fewest bugs and
     should be used for critical databases.
     This is a montly build of the development code and will have been
     tested by developers and with the overnight build/test system. This
     code will have most of the latest features/bug fixes in it. The code is
     widely used within the Sanger Centre and should be fairly bug free, if
     you find a bug in this code please report it as soon as possible.
     This code is the very latest and is not guaranteed to compile/run or
     anything, its there only to allow other developers to see the latest
     acedb code and perhaps to allow some users to try out very new
     features. You shouldn't use this code without talking to the acedb
     developers first.

If you visit the page for one of these levels of code you will see that
there are various packages that can be downloaded ranging from the source
code, to precompiled binaries for various platforms to a demonstration
database. If you find any problems with any aspect of the download pages
then please let the acedb developers know.

Bugs Fixed

Drawing performance bug

Drawing of some fmap/gmap displays was very slow because a bug in the acedb
code was causing the displays to be drawn twice. This should now be fixed
for all acedb displays, please email the acedb developers if this is not so
in the latest monthly build code.

A another smaller bug was that gmap code would try to map loci or regions
even if they had no given map coordinates, this has also been fixed. In this
case the loci/regions are displayed in a text window.

Objects missing from active keyset after rename

Where a simple rename of an object was done via parsing an acefile, the
object was not left in the active keyset. Now the renamed object will be in
the active keyset allowing a quick check of renames.

Log entries in database/log.wrm

Logging information in acedb was not complete because although the start of
a new user session was recorded, the end of the session was not. This meant
that if acedb failed in a way that could not be caught by the error handling
routines, there was no record in the log that this had happened.

Now all session starts/ends shouid be bracketed by:

<date/time> <machine> <process>  SESSION_START - <user/program details>

<date/time> <machine> <process>  session information

<date/time> <machine> <process>  SESSION_END - <session end type>

where "session end type" can be one of:

     acedb program exitted normally.
     acedb program did not crash, but rather detected an error such as
     "database not found" and so could not continue.
     acedb detected an unrecoverable error such as an internal programming
     fault, or the system running out of memory.

If a SESSION_START is found in the log without a corresponding SESSION_END,
this means (assuming the acedb program is no longer running) that acedb
crashed severely in a way that it could not detect (e.g. if the program was
killed with "kill -9" or on some systems if it ran out of stack space). This
type of crash _may_ have left the database corrupted if the program crashed
while updating the database, and certainly if the database does become
corrupted you should look in the log for either a SESSION_END - CRASH or an
unmatched SESSION_START.

Note that a little care is required in parsing the log file for these paired
starts and ends, process ids can be reused by the operating system. This
means that you need to first find the "SESSION_START/machine/process_id" and
then look for both a new "SESSION_START/machine/same_process_id" and a
"SESSION_END/machine/process_id". If you find the former, or don't find the
latter it means the acedb program crashed severely.

January monthly build now available.

You can pick up the monthly builds from:

Sanger users
External users

Next User Group Meeting - D319, 2.30pm, Thursday 15th February 2001

!*! Please note changed venue !*!
Ed Griffiths <edgrif at sanger.ac.uk>
Last modified: Tue Feb 6 12:55:14 GMT 2001

More information about the Acedb mailing list

Send comments to us at biosci-help [At] net.bio.net