Chado Tables to Wiki
The process described on this page is obsolete. The process described on Chado Schema Documentation HOWTO is the the current one. This page should be deleted once the new process has been fully adopted.
The postgresql_autodoc script uses template files to create HTML documentation of Postgres schemas. To create table documentation for this Wiki you will use one template file to create the documentation for the entire Chado schema (as in this Chado Tables page, where all links are internal to the page) and another template to create table documentation for a module (e.g. Chado Organism Module, where all links go to the Chado Tables page). A simple Perl script converts the HTML to Wiki text.
First, the Chado tables or schema that you want to document has to be installed in Postgres. Then:
- Install postgresql_autodoc (http://www.rbt.ca/autodoc/)
- Save this text as html.tmpl if you want to create table documentation for the entire schema
- Save this text as html.tmpl if you want to create table documentation for a single module
- Run the postgresql_autodoc script in the same directory as the html.tmpl file. The command will be something like this (substitute your own user name, password, and database name):
>postgresql_autodoc -f chado -u user -d chado --password=passwd -l .
- This should create an HTML file called chado.html
- Run this Perl script to convert the HTML to Wiki text (this script will work with the Chado v. 1.6 schema)
- If you're creating table documentation for the entire schema the command will look something like this:
>print-wiki-tables.pl -all > allmodules.wiki
- If you're creating table documentation for a module the command will look something like this:
>print-wiki-tables.pl -m cv > cv.wiki
Then copy and paste.
If you have added new tables then you will need to modify the
print-wiki-tables.pl script. Notice that there's a hash in that script that uses module name as key and table names as values. The reason that this is necessary is that Postgres has no internal definition of a related subset of tables like Chado modules.