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@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 this:

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

"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".

Articles

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:

Public

This is the most stable and supported code. It has the fewest bugs and should be used for critical databases.

Monthly

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.

Overnight

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:

NORMAL EXIT

acedb program exitted normally.

ABNORMAL EXIT

acedb program did not crash, but rather detected an error such as "database not found" and so could not continue.

CRASH

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

~acedb/RELEASE.DEVELOPMENT

External users

http://www.acedb.org/Software/Downloads/monthly.shtml

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

!*! Please note changed venue !*!