Bradford Condon PhD

Bioinformatics, Web & Mobile Development


Testing in Tripal Core

This guide is for developers looking to contribute code to the core Tripal project. It introduces the testing philosophy and guidelines for Tripal core. Tripal uses Tripal Test Suite, which brings bootstraps your Tripal site for PHPUnit. It also provides conveniences like namespacing, seeders, transactions, and data factories.

Tripal Logo

Tripal Test Suite

For a basic introduction of Tripal Testing, please see the Test Suite repo.

Installation

After cloning the Tripal github repo, you will need to install the developer dependencies required to run tests locally. To do this, you’ll need to install Composer, and then execute composer install in your project root.

Testing criteria

For facilitate accepting your pull requests, your code should include tests. The tests should meet the following guidelines:

  • All tests pass
  • Tests pass in all environments (Travis)
  • Tests don’t modify the database (use transactions or clean up after yourself)
  • Tests are properly organized (see organization section below)
  • Tests run quietly

Test organization

Tests should be placed in tests/. This root directory contains the following files:

  • bootstrap.php - Test directory configuration. Don’t modify this.
  • DatabasSeeders/ - Database seeders, for filling Chado with permanent test data
  • DataFactory.php - Data factories, for providing test-by-test Chado data.
  • example.env - An example environment file. Configure this to match your development site and save as .env.

Tests must end with Test.php to be recognized by PHPUnit. The tests themselves should be organized by submodule, and category.

Submodules
  • tripal
  • tripal_bulk_loader
  • tripal_chado
  • tripal_chado_views
  • tripal_daemon
  • tripal_ds
  • tripal_ws
Categories
  • API
  • theme
  • views
  • drush
  • fields
  • entities
  • admin

So for example, tests for the file tripal/api/tripal.jobs.api.inc should go in tests/tripal/api/TripalJobsAPITest.php. tests that don’t fit in any of these categories should be placed in tests/[submodule]/.

In order for tests to run locally, you’ll need an environmental file tests/.env with the project root, base url, and locale. See tests/example.env for an example.

Writing tests

When doing test driven development, you might be running tests over and over. To speed you along, you can assign your tests a unique @group tag, ie @group failing. Then specify your novel group when you run phpunit, ie phpunit --group failing.

You should also tag your test with relevant groups. For example, our Tripal Chado API tests should be tagged with @group api. We don’t tag it with @group chado because it is in the testsuite (the submodule folder) Chado.

Defining the test class

Once you’ve identified where your test will go, we can start writing our test.

Tripal Test suite provides a convenient way to start writing a test class: tripaltest make:test TestName. From the project root, our example ./vendor/bin/tripaltest make:test tripal_chado/api/TripalChadoOrganismAPITest. This will generate a test stub file with namespacing.

The test class file should extend StatonLab\TripalTestSuite\TripalTestCase instead of TestCase to take advantage of the Tripal Test Suite tools. For example, to wrap our tests in a database transaction (so we can indescriminately insert and modify without having to revert consider how to clean up the database after), we use StatonLab\TripalTestSuite\DBTransaction;. Your test class name should match the file.

use StatonLab\TripalTestSuite\DBTransaction;
use StatonLab\TripalTestSuite\TripalTestCase;

class TripalChadoOrganismAPITest extends TripalTestCase {
	use DBTransaction;

You typically will want at least one test per public method in your file or class. In the below test class, I define a single test: test_tripal_get_organism(). The test should start with test_, otherwise it wont run by default in PHPUnit (you can also declare that it is a test in the method documentation using @test.

An ideal test operates independently of other tests: by default, unit tests run in random order. How, then, do we provide our test with relevant data? We use Factories, which you can read about on the Tripal Test Suite repo. In the below example, we create an organism with known information, and assert that we can retrieve it with the Chado API functions.


namespace Tests\tripal_chado\api;

use StatonLab\TripalTestSuite\DBTransaction;
use StatonLab\TripalTestSuite\TripalTestCase;

class TripalChadoOrganismAPITest extends TripalTestCase {

  use DBTransaction;

  /**
   * Test tripal_get_organism.
   *
   * @group api
   */
  public function test_tripal_get_organism() {

    $genus_string = 'a_genius_genus';
    $species_string = 'fake_species';

    $organism = factory('chado.organism')->create([
      'genus' => $genus_string,
      'species' => $species_string,
    ]);

    $results = [];

    $results[] = tripal_get_organism(['organism_id' => $organism->organism_id]);
    $results[] = tripal_get_organism([
      'genus' => $genus_string,
      'species' => $species_string,
    ]);

    foreach ($results as $result) {
      $this->assertNotFalse($result);
      $this->assertNotNull($result);
      $this->assertObjectHasAttribute('genus', $result);
      $this->assertEquals($genus_string, $result->genus);
    }
  }

  public function test_tripal_get_organism_fails_gracefully() {
    $result = tripal_get_organism([
      'genus' => uniqid(),
      'species' => uniqid(),
    ]);

    $this->assertNull($result);
  }

Testing quietly

Code may output errors when failing intentionally, or as part of job progress. This can clutter the test environment, so you should wrap the offending methods. If the output goes to standard out, you can use ob_start() and ob_end_clean().


    ob_start();//dont display the job message
    $bool = tripal_chado_publish_records($values);
    ob_end_clean();

If the message comes from the Tripal error reporter, you must use "TRIPAL_SUPPRESS_ERRORS=TRUE" to suppress the tripal error reporter message.


  /**
   * Test chado_publish_records returns false given bad bundle.
   *
   * @group api
   */
  public function test_tripal_chado_publish_records_false_with_bad_bundle() {
    putenv("TRIPAL_SUPPRESS_ERRORS=TRUE");//this will fail, so we suppress the tripal error reporter
    $bool = tripal_chado_publish_records(['bundle_name' => 'never_in_a_million_years']);
    $this->assertFalse($bool);
    putenv("TRIPAL_SUPPRESS_ERRORS");//unset
  }

Testing Entities and Fields

Coming soon.