# ACEDB User Group Newsletter - January 2002

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.

## General News

A short newsletter but a busy month, we are currently working hard on SMap, a replacement for the conversion routines in the FMap code that build virtual sequences and their features. Next months newsletter will contain a full article on SMap.

## New Features

### Smap is coming

After a long, long time we are very close to completely replacing the existing fmap routines that construct virtual sequences with some new routines that use a new set of tags to mark up sequences. the new tags form part of the SMap system which will completely replace the Structure tags of the current Sequence class:

    	  Structure  From	Source UNIQUE ?Sequence
    				Source_Exons Int UNIQUE Int // start at 1
    		     Subsequence ?Sequence XREF Source UNIQUE Int UNIQUE Int

The new SMap system will provide a much more powerful and flexible system for building up sequence/feature relationships. There will be a full article on this in the February newsletter and the code will be generally available in the February release.

## Articles

### Irritating dialogs

Recently a user reported that every time they clicked on an "object" field in the "update" tree window an annoying dialog popped up telling them to "Select an object by double-clicking as though you were going to display it.", they then had to click on the "Remove" button in this window to get rid of it.

By default acedb shows these popup windows whenever the user has selected an option that requires an answer before they can proceed, it's a warning really to say "you must answer this before you can carry on.". You can disable this via your user preferences, you need to turn on the "NO_MESSAGE_WHEN_DISPLAY_BLOCK" preference. You can get to the preferences menu from the "Admin" menu on the main window. When turned on this preference tells acedb not to bother showing these warning popup messages.

### Using pfetch to get EMBL entries for homologies in fmap

When you right click on a homolgy in fmap you get a menu that includes options to show alignments and also to efetch the EMBL entry for the homolgy. There is now an extra option which allows you to use pfetch instead of efetch to get the EMBL entry. pfetch will become the preferred option for retrieving these entries at the Sanger Centre in the future.

### A new "-reopen" option for acedb log files

There are a number of Unix utilities (e.g. "rotatelogs") that provide general log file handling services. These usually rely on the programs that create and use the logs to have an option to close and then reopen the log file. This allows the utility to rename the open logfile, tell the program to close and reopen the file, with the result that the program will now be writing to a new log file and the utility is free to operate on the old log file.

A new "-reopen" option has been added to the "newlog" and "Serverlog" commands which simply closes and reopens the log files. This allows acedb logs to then be handled by the Unix log utilities.

### Reinitialising the Database

Previously the following tests have been applied to say whether you could reinitialise an acedb database:

1. Your real and effective unix userids must be the same, this will only affect you if your versions of the acedb programs have a setuid or setgid bit set.
2. The `wspec/passwd.wrm` file must exist and be readable.
3. You must own the `wspec/passwd.wrm` file.
4. Your userid must be listed in `wspec/passwd.wrm`.

This creates a problem if there are a group of you working on a database and you would like to be able to reinitialise the database without having to `"su"` to the userid of the owner of `wspec/passwd.wrm`.

To get round this a new `"GROUP_ADMIN"` option has been added to the `wspec/database.wrm` file. When this option is uncommented in this file then any user who is in the unix group for the `wspec/database.wrm` will also be able to reinitialise the database.

In other words step 3 above will now be:

- You must own the `wspec/passwd.wrm` file or if the GROUP_ADMIN option was set in `wspec/database.wrm` you must be in the unix group for the password file.

Note that the permissions for the database/ subdirectory of your database must be set to "rws" for the group if this is to work. That is, the group must have read, write and execute permissions for the subdirectory and in addition the sticky bit for group permissions on the directory must also be set. This will ensure that all files created in the subdirectory will have the same group as the subdirectory itself.

For example, assuming that "joe" owns the database and "bloggs" is the group then an "ls -l" of the database should show the following permissions for the database/ subdirectory:

      drwxrwsr-x   6 joe      bloggs      8192 Feb 13 12:51 database

## Developers Corner

If you wish to make comments/suggestions about any of the below, please mail them to acedb@sanger.ac.uk

### Another banal file pathname function

Another banal pathname function has been added to filsubs, this one returns the base filename part of a given path:

      Given   "/some/load/of/directories/filename.something.ext"
    returns   "filename.something"

i.e. it lops off the directory and the _last_ extension.

## No January monthly build

Due to problems with our build system and some large scale and unfinished changes to introduce Smap (see February issue) we were not able to produce a January monthly build. Sorry !

## Next User Group Meeting - D319, 2.30pm, Thursday, 14th February 2002

Last modified: Wed Feb 13 16:14:53 GMT 2002