.

Page building: Dynamic pages

Preamble

Script handler calls

• Plug in directories
• ENSEMBL_ROOT/perl/default
• ENSEMBL_ROOT/perl/common
• ENSEMBL_ROOT/perl/multi

Building a page with Document::WebPage

package geneview;

use EnsEMBL::Web::Document::WebPage;
simple_with_redirect( 'Gene' );

(simple_with_redirect create an object of type "Gene")

Renderers, output types and document types

Renderers

WebPage renderers are of the EnsEMBL::Web::Document::Renderer family of classes and dictate the destination of any output generated by WebPage and its components. The default, EnsEMBL::Web::Document::Renderer::Apache, sends the output as a response to a request from a browser, via Apache. Renderers usually accept output via one or more print methods. (Other example EnsEMBL::Web::Document::Renderer::GZfile).

Output types

Output types determine the format of the response set to a final destination by the Renderer. The default is a particular flavour of HTML.

Document types

WebPage uses an object from the EnsEMBL::Web::Document family to setup and configure the content of the output. This is usually (but not necessarily) coupled with an output type. The default for dynamic pages is (unsurprisingly) EnsEMBL::Web::Document::Dynamic. Other examples include EnsEMBL::Web::Document::Pop-Up and EnsEMBL::Web::Document::Common. (Common has the components which are needed for the static, dynamic and pop-up pages and EnsEMBL::Web::Document::Dynamic inherits from this).

The WebPage build pipeline

  START
    ↓
  Initialise output 
    ↓
  Setup common output components
    ↓
  Retrieve data
    ↓
  Setup data specific output components
    ↓
  Collate and render
    ↓
  Delivery

START

The pipeline starts with a call from the view script (e.g. perl/default/geneview) to WebPage::simple_with_redirect(). A single parameter is provided which informs WebPage of the type of page to create. In effect, this parameter (Gene, in the case of GeneView) configures which data objects to create, and how they are to be configured and collated for the final deliverable content.

Initialise output

WebPage then initialises the various components necessary to produce output: the renderer (e.g. Apache), the output type (e.g. HTML) and the document type (e.g. Dynamic). In addition, a SpeciesDefs object is created. This object plays an important part in configuring Ensembl, and is made available to all other layout and data objects created by WebPage. It is discussed in more detail on the Configuration and sessions page. A timer is also set up for debugging and profiling.

Setup common output components

Almost all types of output (especially HTML) require a certain amount of common content. These output components are independent of the data requested, and include items such as:


• The XML DOCTYPE statement
• Common headers
• HTML meta tags
• Stylesheet includes
• Javascript includes
• Common look and feel elements
• Common menus
• Copyright notices

For GeneView, as it is a dynamic HTML page, the WebPage::new calls EnsEMBL::Web::Document::Dynamic::_initialize_HTML which by default contains all these and more. The templates for each section of the webpage are in an ordered array which is passed to the add_body_elements function. The common output components can be expanded, edited or removed using the Ensembl plugin system ¹.

At the end of this stage, an output template has been established based on a collection of components, optionally configured and tweaked by the plugins. It has not yet been constructed (for example, the HTML has not yet been collated ready for delivery), but is ready to be populated with additional data content.

Retrieve data

The retrieval of data in Ensembl is also compartmentalised and distributed between a collection of Perl modules. The EnsEMBL::Web::Document::Dynamic document type object is attached to the WebPage's page parameter for easy access of other page components, and it is the WebPage that proceeds to retrieve data from the Ensembl databases.

The methods by which data is retrieved from an EnsEMBL database is separated from the methods by which that data is rendered and delivered back from the user. In effect, the classes and methods that retrieve and represent the data can be reused in other projects relatively easily. When a new WebPage is created, a new object of the Factory family is created. This Factory is responsible for creating the appropriate data objects for the page², and is configured using the original page type provided at the start of the pipeline (for example, 'Gene'). The CGI object containing the parameters passed to the page in the URL is passed along to the Factory allowing it to retrieve and configure the necessary data objects for display.

Once the data objects have been retrieved, additional data-specific components are added to the output. The actual data output will be added in the Collate and Render stage.

Setup data specific output components

At this stage, additional output components which display data are configured. For example, menu items can be added or removed, or the mast head for a page can be updated to reflect the data within it.

Collate and render

Now that all the data and layout components have been retrieved and configured, the page output is collated. Any images are drawn (and optionally cached), and the output is rendered for delivery.

Delivery

Once rendered, the output is delivered to a final destination. In most cases this is served back to the user's browser via Apache, but it could also be sent to a gzip file for archival, to another server as a response to a web service, or returned over an alternate transport protocol for communication between processes.

Building other responses with Document::WebPage

Footnotes

• 1. The document type for a page configures the appropriate set of common output components (such as those listed above) based on the output type (for example, GeneView defaults to calling _initialize_HTML). Once a default set of components has been established, the installed plugins are queried for updates to that default set. Any plugins wishing to extend the default output components should implement one or both of:
  
  
  • MyPlugin::modules::EnsEMBL::MyPlugin::Document::Configure::common_page_elements()
  • MyPlugin::modules::EnsEMBL::MyPlugin::Document::Configure::dynamic_page_elements()
  
  These methods can then make use of such calls as add_body_element(), add_body_element_after() and replace_body_element(). Check the e! doc for EnsEMBL::Web::Document::Page for more information. ↑

• 2. In effect, the Factory created is an EnsEMBL::Web::Proxy::Factory, which in turn creates the correct Factory type, determined by the original page type provided at the start of the pipeline. For example, in the case of GeneView, an EnsEMBL::Web::Factory::Gene would be created. This is also so the Factory can cope with the plug-in code looping through each Factory in the plug-ins directory.
  
  This Factory then creates the appropriate EnsEMBL::Web::Object::Gene, EnsEMBL::Web::Configuration::Gene and EnsEMBL::Web::Component::Gene objects, which provide data, configuration and layout view information respectively. ↑

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