Adding Data to a Widget (Example)

Introduction

A common form of feature request is adding some data to be displayed on a page.

Here is an example that illustrates work flow required to add some data to a widget.

Issue #2551 required showing the data under the "Former_designating_laboratory" field on the widget "Overview" of a "Gene class" (the Gene class "daf" for example).

Using the data flow graph

Widget Loading

we can see that data goes through 4 stages from the database to the UI - Rest, Conf, API and Template. Usually our work doesn't involve the Rest stage, but it sure does involve modifying the .conf (the configuration), .pm (the API) and .tt2 (the template) files.

Let's go back to our example. If you go to the "daf" page [1], you can view the database you are going to be working on by going to Tools -> Tree Display using the menu on the left side of the page. Our field "Former_designating_laboratory" has two data objects under it, a time "19 Mar 2014 14:41:19" and a link to the lab "DR". In this example we are only going to care about displaying the time on the "Overview" widget (if you can't see a widget you can show it by clicking on it from the side menu).

Modify configuration file

The wormbase.conf file, which you can find under the main website directory contains default configurations for the WormBase application.

Now under the "overview" element of the "gene_class" section add the Former Designating Laboratory field "fields former_laboratory". <gene_class> <overview> name overview title Overview display report tooltip Gene class (eg Unc) overview. fields name fields other_names fields description fields laboratory fields former_laboratory fields remarks </overview> </gene_class>

Add a subroutine to the API module

We are going to add a subroutine to the API of the Gene class object in order to grab the data from the database. You can find the API file we need to fix in lib/WormBase/API/Object/, then find the Gene_class object.

We are going to add a subroutine and call it former_laboratory:

sub former_laboratory {

   my $self = shift;
   my $object    = $self->object;
   # Access the field Former_designating_laboratory
   my $former_lab_time = $object->Former_designating_laboratory;
    
    
   return   { description => 'Former_designating_laboratory', data =>  "$former_lab_time" || undef };
                      }

Return a hash that contains the description of the field and the former lab time. The value of the "data" key should be "undef" if there is no data in the "Former_designating_laboratory" field. If the "data" is "undef" the template won't show a "Former designating laboratory" field on the UI.

Edit template: for displaying data

A template - with the file extension .tt2 - is responsible of view the data grabbed from the database on the the UI. Every widget in an object has its own separate template. So if you go to this directory root/templates/classes/gene_class/ which contains all the Gene class widgets you will find a template for the Overview widget with the name overview.tt2.

We are going to add a new WRAPPER for our field. The key parameter should match our subroutine name that we made in the API file - which was "former_laboratory" -.

WRAPPER $field_block title="$title"||'Former Designating Laboratory' key="former_laboratory";

    #Access the value of the "data" key returned from the former_laboratory subroutine
    fields.former_laboratory.data;

END;

You can check out how "$field_block" works from the page_elements.tt2 template. "$field_block" looks of the data returned from former_laboratory if "undef" or not. If it is "undef" - which means there is no data in the that field - it disables the element of the field, and it isn't going to show on the UI.

Formal Testing

It's a good idea to include some test cases for your modification.

Here we focuse on API Tests, which check that an API module (the subroutine it has) successfully retrieves values from the database.

API Tests are located at t/api_tests/ with the extension .t. A .t script usually test a single API module, such as one of the .pm file under lib/WormBase/API/Object/. It has a file name that matches the API module, which it tests. This convention helps with locating a test file, making it easier to add new test case.

1. To add a test case, locate the test file as described above. Create one if you cannot find one by:
   1. Copy the template.t, a sample test file, and name it according to which API module is being tested

In this example what we need to test is the API because we need to know if the "former_laboratory" subroutine in the Gene_classes API is grabbing the data properly from the database or not. There is a standard template "template.t" you can find in the directory t/api_tests/ , and you can use for your API tests.

So you are going to make a copy of the template - using the command "cp t/api_tests/template.t t/api_tests/gene_class.t" - and modify it. Let's call the new test file "gene_class.t". This is how the original template looks like this:

1. !/usr/bin/env perl

1. 1. gene_class

{

   package template;

   use strict;

   use Test::More;

   my $api;

   sub config {
       $api = $_[0];
   }
   
   # This is a test that checks whether former_laboratory attribute is correctly returned
   # related to #2551
   sub test_former_designating_laboratory {
       my $gene_class = $api->fetch({ class => 'Gene_class', name => 'daf' });

       can_ok('WormBase::API::Object::Gene_class', ('former_laboratory'));

       my $former_designating_laboratory = $gene_class->former_laboratory();

       # Please keep test names/descriptions all lower case.
       isnt($former_designating_laboratory->{'data'}, undef, 'data returned');

is($former_designating_laboratory->{'data'}->{'lab'}->{'id'}, 'DR', 'correct lab returned'); is($former_designating_laboratory->{'data'}{'time'}, '19 Mar 2014 14:41:19', 'correct time returned');

   }

}

1;

Make sure to read the instructions that are inside the template and to add the issue number in the comments.

Test and Commit Changes

The only thing left for you now is to commit your code to git. If you have trouble doing that, it's good to check out Development workflow - webdev.