update February 20, 2005
birchdb - Database for documentation distributed
All BIRCH documentation is organized
into two databases, managed using ACeDB found in the following
- The database for documentation files included as part of the BIRCH
- 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
documentation for locally-installed programs.
FILE NAMING CONVENTIONS
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
documentation for $local/doc/staden/manual_unix.pdf would be
File names can also be URLs pointing to documentation anywhere on the
Internet. In this case, the URL is also used for the hypertext link.
For example, the file object for the NCBI Cn3D program is named
'http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.html", which is also
the URL to that document.
In summary, htmldoc.py creates URLs by either taking the full
name of the File object, if it begins with 'http://' or 'file://', or
if the name begins with '$', the '$' is replaced with the URL prefix
for your BIRCH site.
Dr. Brian Fristensky
Department of Plant Science
University of Manitoba
Winnipeg, MB Canada R3T 2N2