birchdb - Database for documentation distributed with BIRCH

All BIRCH documentation is organized into two databases, managed using ACeDB found in the following directories:

$BIRCH/public_html/birchdb - The database for documentation files included as part of the BIRCH distribution
$BIRCH/local/public_html/birchdb - The database for locally-installed documentation files.

birchdb launches the xace interface for the database in $BIRCH/public_html/birchdb. The BIRCH administrator can use xace to update the database. birchdb is primarily for use at the master BIRCH site at the Univ. of Manitoba for updating the documentation. Changes made using birchdb at other sites will be lost the next time BIRCH is updated. Instead, use lbirchdb to maintain documentation for locally-installed programs.

Each documentation file is represented in the database by a File object. For data objects of the type "File", the name of the data object is identical to the path of the file. All file paths must begin with the name of a birch environment variable, which corresponds a birch directory:

$dat - The $BIRCH/dat directory
$doc - The $BIRCH/doc directory
$local - The $BIRCH/local directory
$tutorials - The $BIRCH/tutorials directory

For example, the file $doc/fsap/numseq.txt would be represented in birchdb as a file object with the name '$doc/fsap/numseq.txt'. When htmldoc.py creates a documentation page for the numseq program, it will include a hypertext link to this file. The prefix for the URL will be taken from the file $BIRCH/local/newstr.param. This file contains lines used by customdoc.py to construct URLs to BIRCH documentation. On the U. of Manitoba BIRCH site, the path to all BIRCH documentation is listed in this file as 'http\://home.cc.umanitoba.ca/~psgendb'. The URL for $doc/fsap/numseq.txt would therefore be 'http\://home.cc.umanitoba.ca/~psgendb/doc/fsap/numseq.txt'.The documentation for $local/doc/staden/manual_unix.pdf would be http\://home.cc.umanitoba.ca/~psgendb/local/doc/staden/manual_unix.pdf'.

File names can also be URLs pointing to documentation anywhere on the Internet. In this case, the URL is also used for the hypertext link. For example, the file object for the NCBI Cn3D program is named 'http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.html", which is also the URL to that document.

In summary, htmldoc.py creates URLs by either taking the full name of the File object, if it begins with 'http://' or 'file://', or if the name begins with '$', the '$' is replaced with the URL prefix for your BIRCH site.