GMOD

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The process described on this page is obsolete.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.

Description

This page shows you how to create the Chado table documentation seen on pages like Chado Tables and Chado Organism Module.

Instructions

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:

  >postgresql_autodoc -f chado -u user -d chado --password=passwd -l .
  >print-wiki-tables.pl -all > allmodules.wiki
 >print-wiki-tables.pl -m cv > cv.wiki

Then copy and paste.

Notes

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.

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