update February 20, 2005
lgbirchdb - Empty database for to be used for locally-installed documentation

This script is primarily for use by the BIRCH Administrator at the master BIRCH site at the Univ. of Manitoba. When creating a new BIRCH site, the directory $BIRCH/local-generic is renamed to $BIRCH/local. This directory is a starting point for installing additional programs, documents, datafiles and database to BIRCH.
lgbirchdb launches the xace interface for the database in $BIRCH/local-generic/public_html/birchdb. lgbirchdb is used for creating the empty local birchdb database. Initially, this database is populated with Category and Platform objects, that can be referred to in the local customized birchdb database.

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:
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.

htmldoc.py, birchdb, lbirchdb
Dr. Brian Fristensky
Department of Plant Science
University of Manitoba
Winnipeg, MB  Canada R3T 2N2