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This month includes a tip about what to do if your queries seem not to be working correctly (thanks to Lisa French for raising this), a change to the way acedb programs find their help files, yet more fmap stuff (cascading menus for column configuration) and a change to acedb user group meetings.
The latest monthly release is now available from ~acedb/RELEASE.DEVELOPMENT.
Simon Kelley has added code to help with providing common configuration/help files for multiple databases. Acedb programs will now search in two directories: the database directory itself and an installation-wide directory where default copies of help files and config files and scripts can exist. These are used when the files cannot be found in the database directory.
The database directory is found as before from the command line, or the value of $ACEDB. The installation-wide directory is found on unix from the value of $ACEDB_COMMON, or /usr/share/acedb, or /usr/local/acedb (in that order), on windows it is found from a registry entry set up by the installation program on windows.
This now makes it possible to put common acedb files in to a single directory on the system and find them by setting $ACEDB_COMMON in the users shell environment. This can be used to replace the existing mechanism of maintaining symbolic links within database directories.
The following resources will be searched for in the installation-wide directory if not found in the database:
wspec/wingtkrc
wspec/gtkrc
wspec/winfonts.wrm
wspec/xfonts.wrm
wspec/psfonts.wrm
wspec/acedbrc
wspec/table.menu
wspec/sysclass.wrm
wspec/displays.wrm
wspec/table.menu
wscripts/*
whelp/*
Note that acedb will use only the contents of $ACEDB/whelp or $ACEDB_COMMON/whelp, it won't mix files from both.
The following are searched for only in the database dir.
database/*
rawdata/*
wquery/*
rawdata/*
wgf/*
wspec/layout.wrm
wspec/models.wrm
wspec/constraints.wrm
wspec/subclasses.wrm
wspec/lock.wrm
wspec/serverconfig.wrm
wspec/serverpasswd.wrm
wspec/server.wrm
wspec/datainfo.wrm
wspec/options.wrm
wspec/passwd.wrm
wspec/database.wrm
Simon has also introduced a new command line option to xace which allows you to choose a database when you start xace.
If you type:
xace -promptdb
you will prompted to choose a database directory via the usual "file chooser" type window.
Fmap column configuration via Column pull down menus was covered in the last newsletter but this unfortunately did not work correctly. If several columns of different kinds were drawn over the top of each other, only one of the columns could be manipulated via the pull down menus. This months code fixes this by providing a cascading pull down menu which shows all the columns drawn in one position and allows separate configuration of all those columns. Try it out and if you have problems send mail to acedb@sanger.ac.uk.
Lisa French reported a problem with a number of queries just not working correctly. Investigation showed that the database indexing (which provides rapid accessing of object field/tags) was incorrect, this does not mean the database will lose data but it does mean that queries do not work correctly until the next full reindex of the database.
tace provides a "read models" command optionally with a full reindex, this option has now been added to xace as well (on the main panel, click the "Edit.." button and select the "Read Models and full reindex" option). If you are having problems with queries clearly not working correctly then you should try reindexing the database. Before you do this you should note two points:
This problem shouldn't happen and we hope to fix it soon, you should only suspect that your database is corrupted if reindexing does not fix the problem.
Acedb user group meetings happen every month and are a chance to talk to acedb developers and to other users. Dan Lawson suggested that it would be good if we could have some short overviews in these meetings of various parts of acedb. He has volunteered to start with an overview of "super link" and "link" objects as used in the worm database in Junes user group meeting. If you would like to contribute an overview or would like to see some topic covered then send suggestions to acedb@sanger.ac.uk.