Website:Application overview

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Revision as of 12:48, 17 January 2008 by Tharris (talk | contribs) (→‎Widgets)
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Directory Structure

-rw-rw-r--    Changes
-rw-rw-r--    Makefile.PL
-rw-rw-r--    README
drwxrwxr-x    build
  Staging directory for building third party libraries.  Current releases should be symlinked to the correct unpacked source.

drwxrwxr-x    conf
  Application and third-party library configuration.

drwxrwxr-x    design
  Design elements and ideas.

drwxrwxr-x    extlib
  Directory containing builds of third party libraries.

drwxrwxr-x    lib
  The core application modules.

drwxrwxr-x    logs
drwxrwxr-x    private
  Docs and presentations.

drwxrwxr-x   root
  /root contains static files and templates.

drwxrwxr-x   script
  Helper scripts and the stand-alone server.

drwxrwxr-x   sql
  SQL statements for various databases.

drwxrwxr-x   src
  Third party sources.

drwxrwxr-x   t
  Application test suite.

-rw-rw-rw-  wormbase.yml
  Application-wide default configurations.

-rw-rw-r--   wormbase_local.yml.template
  Template for local configuration.  Entries here will override defaults.


Catalyst offers a powerful configuration system. We use it to provide application-wide, per-page, and per-session configuration. In addition, local configuration files can be used to override any configuration option for production or development deployment.

Here, $ROOT refers to the document root of your application.


This file contains the default configuration for the application. The application defaults to using remote data sources. If you would like to override this, see wormbase_local.yml.


Move this template file to wormbase_local.yml and edit values to locally override the default configuration variables. This file is maintainted in SVN as a template so that individual development preferences are not obliterated by an inadvertent svn commit.

Quick Overview

The general structure of the application mirrors the organization in Acedb. Separate Model::* packages correspond to classes in Acedb.


Pages are composed of widgets, in turn composed of fields.


Widgets are small segments of a page comprised of a series of fields. Widgets roughly correspond to sections of the old WormBase site.

The widgets available for any page are specified in the primary configuration file. They are comprised of:

  • a Controller action named after the widget.
  • a template file (if required).


Individual sections of each widget are referred to as fields. They are comprised of:

  • a Controller method implementing a chained action. This calls a...
  • a Model method(s) that collect and massage the appropriate data. The primary method should correspond to the name of the field.
  • a template file (if required). The name of the field corresponds to it's section name in the presentation layer.
  • field names are: stash keys (dynamic), controller actions (dynamic), template filenames (static), section names in templates.
  • fields are also URL and REST targets.



Access a widget called identification that collects together the fields that comprise the widget.


Access the ncbi field of the identification widget. Note that it is not necessary to know the containing widget.


Problem: Objects must be fetched for each widget.

Solution: Have a gateway search that redirects to page where widgets are loaded by their ID, or cache the current object the first time it is fetched.


  • Each action becomes its own URL target opening up many possibilities for presentation.
  • Can I make these REST services, too?

Implementation Questions

Q: Does it make sense to forward to a chained action?

Q: For customizable data, at which point should display decision be made?

If made prior to fetching data, the code will be faster. If made at the display level, the code is slower but easier caching. (NO!) The caching unit should probably be the actual Perl data structures, not HTMLized data.

Dynamic creation of controller actions

The following actions are created dynamically directly from the configuration.

- Each widget is a controller method called "name_widget".

- This method is an action chained to fetch.

- Each field corresponds to a PathPart of a Chained reaction:

     sub description : Chained('fetch') PathPart('description') Args(0) {



Generic Model methods


Generic Controller Actions


Specifying configuration

Required Controller actions

Required Model methods


Creating new Models and Controllers

1. Create your new Model or Controller using the script. This script provides stub formatting, documentation, and test files.

$ROOT/scripts/ model Test


[todd@micos trunk:23]$ ./script/ model Test
exists "/Users/todd/projects/wormbase/website/trunk/script/../lib/WormBase/Model"
exists "/Users/todd/projects/wormbase/website/trunk/script/../t"
created "/Users/todd/projects/wormbase/website/trunk/script/../lib/WormBase/Model/"
created "/Users/todd/projects/wormbase/website/trunk/script/../t/model_Test.t"

2. Add the new files to the SVN repository

svn add lib/WormBase/Model/ t/model_Test.t
svn commit lib/WormBase/Model/ t/model_Test.t