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In this months newsletter: new help files, read-only databases, bug fixes and something you need to know about "parse".
Some of the discussions from the Acedb2000 meeting are beginning to filter through to the code, xml dumping is being added, the new AcePerl that talks directly to the socket server is on the way.
A report of what happened at Acedb2000 is now on the acedb web site (http://www.acedb.org/winfo/Conferences/acedb2000/) - with photos !
Courtesy of Jo Dicks we have some new help files for Comparative maps, so acedb administrators should get a new copy of the whelp directory to pick up these files (they are called whelp/Comparative_Maps_*).
There are two new dump options, -k and -K, these act like -j -J except data types are written as below:
int -> #Int
float -> #Float
txt -> #Text
date -> #Date
BOOL -> #BOOL
dates are written in native acedb form YYYY-MM-DD_HH:MM:SS
(with truncations allowed)
These apply to commands "list", "show", "table-maker", "aql" and "select".
Its now possible to set a new option, READONLY_DATABASE
in wspec/serverconfig.wrm that allows the administrator to set unix file
permissions for the entire database directory to "read only". The server
will not write any logging information and the database cannot be altered
by any user. This allows administrators to more securely set up "read only" databases
for web access. But note that the server will not record any logs of connecting clients
or requests.
If you have used the parse command from tace, or its equivalent
from xace you will probably be aware that you can choose either to stop at the
first error in the your ace file or to continue to the end of the file. What you may not
have realised is that if you choose to stop at the first error, then any objects/updates
parsed in before that error will have been added to the database. But what if you
didn't want those changes made (i.e. you either wanted all the updates made or,
if there was an error, none of them) ??
In fact when you parse an ace file, the database is only updated in your programs local copy of the database held in memory, not the actual database held on disk. This means that you can avoid making permanent updates to the database by simply quitting the program without saving any of your changes.
Future versions of acedb (see last months newsletter) may offer transaction support which would mean that changes like this could be reversed without having to quit the program. But for now you should make sure that you quit without saving if you want the "all or nothing" style of database update via ace file parsing.
Both aceserver and saceserver log all requests, this is fine for commands but not good when the request is raw ace data because the amount of data can be very large which makes the logs grow alarmingly. This has been fixed so that the log file records that ace data has been parsed to the server but the data itself is not stored in the log.
Two bugs have been fixed in the parse/pparse commands:
"parse <filename>" - previously aceclient would ignore
the filename and wait for input from the terminal, this has been corrected.
The filename will now be recognised and ace data read from the file. Input is
only taken from the terminal if you just type "parse".
"pparse <filename>" - should report all errors encountered
in parsing the file, this got broken in acedb 4_8c, it's fixed now.
You will only have noticed this bug if you used the development (4_8c) version of aceserver. The bug prevented any clients being authorised to connect. The bug is fixed in the July monthly build (see below for where to get this).
This bug affects xace 4_7l code on Solaris 5.7 machines. There is an xace bug whereby the entire X server seems to freeze if the acedb main window is covered and then uncovered. The cause of the bug has been found and we now have a fix for it, it will be applied to 4_7l but shouldn't be a problem in 4_8 code. The fix should be available from the acedb ftp site in the next week or so, if you need it more urgently than that please contact either Jean Thierry-Mieg <mieg@ray.nlm.nih.gov> or Ed Griffiths <edgrif@sanger.ac.uk>.
Sylvia Martinelli's acedb course was run again in June in the HGMP, this was the first course that included material on the new socket client/server. See the acedb home page for future courses.
You can pick up the monthly builds from:
Sanger users: ~acedb/RELEASE.DEVELOPMENT
External users: ftp://ftp.sanger.ac.uk/pub/acedb/Sanger-release.2000_07_14.tar.gz