Directory Structure

-rw-rw-r--    Changes
-rw-rw-r--    Makefile.PL
-rw-rw-r--    README

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.conf
  Application-wide default configurations.

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

Quick Overview

The code that powers the website is divided into two main components: the code responsible for the website (henceforth "the web application") and a series of external models in the WormBase::API namespace.

External Model (aka WormBase::API)

The WormBase::API is an external model and abstraction layer that rests on top of AcePerl/AceDB. It's structure resembles classes in AceDB; however, models often cross class boundaries when aggregating data.

The external model implements a number of globally shared methods that can be used across classes (for example, collating references).

See the API documentation for additional details.

The Web Application

The Web Application follows the Model-View-Controller design pattern.

Configuration

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. View-specific configuration (for example, external URLs) is maintained in Template::Toolkit configuration files.

See the Configuration documentation for details.

Model

The Web Application Model is a thin adaptor that pastes in the external model. There's not much to see and even less to do.

See the Model documentation for additional details.

View

The interface is a hybrid of server- and client-side processing powered by extensive Javascript, REST, and Template::Toolkit.

See the View documentation for additional details.

Controller

Controllers handle interactions with the user. Controllers implement authorization/authentication, caching, and complete RESTful interface to the entire database.

See the Controller documentation for additional details.

General Page Structure

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

Page

Each page is specific in configuration (see below).
A generic template renders the page and inserts appropriate widgets by XHR.

Widgets

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. The architecture of a widget consists of:

suitable configuration in wormbase.conf.
a (generic) REST controller action that...
...calls methods in the external model that correspond to each component field.
and (usually) a template file.

Fields

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

a Controller method implementing a chained action. This calls a...
.. an external model method(s) that collates the appropriate data. The method name must match the name of the field.
field names are used as: stash keys and section names in templates.
each field is both a plain URL as well as REST target.

Example

http://localhost/reports/gene/*/overview

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

http://localhost/reports/gene/*/ncbi

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

Setting up a new page

Add Configuration

Add configuration specifying the name of the page, the order widgets should be loaded, and each widget and the fields it contains to wormbase.conf:

<pages>
    <account_details>
         widget_order profile
         widget_order address
         <widgets>
               <profile>
                     name profile
                     title Account Profile
                     fields id
                     fields nickname
                     fields email
                </profile>
                <address>
                      name address
                      title Address
                      fields street
                      fields city
                      fields state
                      fields zip
                </address>
        </widgets>
    </account_details>
</pages>

See wormbase.conf and the documentation on configuration for full details.

Create your WormBase::API::Object::* methods

Remember: The names of these methods should correspond to the names of your widget fields! If they do not, your template stash will not be populated.

Create templates (if necessary)

Create templates as necessary. These should be located in:

The widget template: root/templates/classes/$class/$your_widget_name.tt2

Caching

To ease server load and accelerate page load times, the web application implements a number of caching mechanisms.

File cache of computationally intensive methods

Required modules

Catalyst::Plugin::Cache
CHI
CHI::Driver::File

Usage

 # Check the cache for the presence of your data.
 # my_cache_id can be any string you want (see below for details).

 # $cache_id is the provided string with the current version of WormBase appended
 # $cached_data is data returned from the cache, if any
 my ($cache_id,$cached_data) = $c->check_cache("my_cache_id");

 unless ($cached_data) {
     my $data = some_computationally_expensive_method();
     $c->set_cache($cache_id,$data);
  }

Cache ID

When using the check_cache/set_cache approach, the initial cache ID that you provide will have the current version of WormBase appended to it. This lets us automatically expire entries when a new version of the database is released. Note that this ONLY works if you use both check_cache() and set_cache(). You should always follow this strategy as checking the cache is extremely efficient.

Here's an example from the REST controller for widgets:

sub widget_GET {
    my ($self,$c,$class,$name,$widget) = @_; 
			     
    # Does the data for this widget already exist in the cache?
    my ($cache_id,$cached_data) = $c->check_cache($class,$widget,$name);

    # The cache ONLY includes the field data for the widget, nothing else.
    # This is because most backend caches cannot store globs.
    if ($cached_data) {
	$c->stash->{fields} = $cached_data;
    } else {
  
	# Load the stash with the field contents for this widget.
	my @fields;

	# Widgets accessible by name
	if (ref $c->config->{pages}->{$class}->{widgets}->{$widget}->{fields} ne "ARRAY") {
	    @fields = ($c->config->{pages}->{$class}->{widgets}->{$widget}->{fields});
	} else {
	    @fields = @{ $c->config->{pages}->{$class}->{widgets}->{$widget}->{fields} };
	}
       		
	foreach my $field (@fields) {
	    my $data = {};
	    $data = $object->$field if defined $object->$field;
	    
	    # Conditionally load up the stash (for now) for HTML requests.
	    # Alternatively, we could return JSON and have the client format it.
	    $c->stash->{fields}->{$field} = $data; 
	}
		
	# Cache the field data for this widget.
	$c->set_cache($cache_id,$c->stash->{fields});
    }
    
    $self->status_ok($c, entity => {
	class   => $class,
	name    => $name,
	uri     => "$uri"
		     }
	);
}

Types of data to store in the cache

In the REST widget() example, we cache all data drawn from the database necessary for the widget. We do not cache generated HTML (template processing is very efficient). Should we deem it necessary, we can exploring caching of generated HTML using Template::Plugin::Cache.

Note that it is not possible to cache data structures containing globs.

Cache Duration/Expiry

Caching is enabled for *all* installations. This enables us to test the caching mechanism in development.

Cached items in development installations are set to 4 seconds to ensure that code changes are reflected in page reloads. Cached items in production installations are set to expire after 4 weeks. These values can be modified in lib/WormBase/Web.pm.

Cache Location

The cache is written to /tmp/wormbase/file_cache_chi. This is specified during in Web.pm during application setup.

NFS?

Component and page-level caching via reverse proxy

Production websites site behind a caching reverse proxy. This proxy caches many (but not all) dynamically generated content as well. Due to performance considerations, the front end proxy cache expires sooner than that of the back end application cache. See documentation on squid3 elsewhere on this wiki.

Caching references

The following sources contain useful information on cache options for Catalyst apps.

Website:Application overview

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