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 $BIRCH/local. This directory is a starting point for
installing additional programs, documents, datafiles and database to
BIRCH.
<>$BIRCH/local-generic/public_html/birchdb
- Empty database for locally-installed documentation files.
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:
- $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.