galaxy/doc/source/dev/writing_tests.md

Writing Tests for Galaxy

:depth: 1
:local:

{#other_sources}

Other Sources of Documentation

Over the last several years, the most up-to-date documentation on the structure and running of Galaxy tests has been in the help text for run_tests.sh script shipped with Galaxy (./run_tests.sh --help). High-level information on Galaxy's CI process can be found in the Galaxy Code Architecture Slides and the corresponding YouTube playlist. Some more specifics on running and writing Galaxy client unit tests can be found in client/README.md of the Galaxy codebase.

{#overview}

An Overview of Galaxy Tests

Galaxy has many test suites and frameworks. A potentially overwhelming question at first is, where does a given test belong? What testing suite or framework should it be added to? The following questions may be able to help find the right documentation for a given test one wishes to write.

Does this test require a running server and database to execute?

• No

  If no, this test should probably be implemented as a Galaxy unit test. Unit tests generally, and Galaxy ones specifically, are especially useful for complex components that are well architected to be tested in isolation. The best unit tests are unit tests that shield a lot of their potential complexity from their consumers and components that do not have a lot of dependencies - especially on the database or a web server.

  Is the component under test a client (ES6) or backend (Python) component?

  • Client/ES6

    These tests should be placed in client/src directly and executed via Vitest. Checkout Frontend/ES6 Unit Tests below for more information.

  • Backend/Python

    These tests should be placed in test/unit or doctests and executed via pytest. Checkout Backend/Python Unit Tests below for more information.

• Yes

  In this case you're looking at some sort of functional test that requires a running Galaxy server and the Galaxy database. All of these tests are currently implemented in Python.

  Does this test require the Galaxy web interface?

  • No

    Most of the time, we have found that these tests work best when they use the Galaxy API to drive the test. These tests are all Python tests executed by pytest. The testing frameworks provide everything you need to spin up a Galaxy instance, communicate with its API to invoke the component under test, and write expectations about the outcome of the test. There are three different (but very related) frameworks to do this and the choice between which is appropriate comes down to the following questions.

    Does this test require a special configuration of Galaxy?

    • No

      Does this test check only functionalities of Galaxy tools?

      • Yes

        In this case you do not actually need to deal with the Galaxy API directly and you can just create a Galaxy tool test to check that the required functionality does work as expected. These are called Galaxy tool framework tests and are located in test/functional/tools/. Checkout Tool Framework Tests below for more information.

      • No

        In this case Galaxy API tests are likely the most appropriate way to implement the desired test. These tests are located in lib/galaxy_test/api. Checkout API Tests below for more information.

    • Yes

      Tests that require a custom Galaxy with a very specific configuration are called Galaxy integration tests and are located in test/integration. Checkout Integration Tests below for more information.

  • Yes

    The tests that exercise the Galaxy user interface and require a functional Galaxy server use Selenium to drive interaction with the Galaxy web interface. There are two frameworks or suites available for building tests like this and they both provide high level access to the Galaxy API like the tests above. The frameworks also take care of starting the Galaxy server.

    The choice between these two different frameworks comes down to the answer to the following question.

    Does this test require a special configuration of Galaxy?

    • No

      These tests should be placed into lib/galaxy_test/selenium and implemented using the Selenium Tests framework describe below.

    • Yes

      Tests that require both a very specific Galaxy configuration as well as the ability to drive a running Galaxy web interface should be placed into test/integration_selenium. Checkout the Selenium Integration Tests information below for more information.

{#python_unit}

Backend/Python Unit Tests

These are Python unit tests either defined inside of test/unit or via doctests within a Python component. These should generally not require a Galaxy instance and should quickly test just a component or a few components of Galaxy's backend code.

doctests to stand-alone tests?

doctests tend to be more brittle and more restrictive. I (@jmchilton) would strongly suggest writing stand-alone unit testing files separate from the code itself unless the tests are so clean and so isolated they serve as high-quality documentation for the component under test.

Slow 'Unit' Tests

There are tests in Galaxy that test integration with external sources that do not require a full Galaxy server. While these aren't really "unit" tests in a traditional sense, they are unit tests from a Galaxy perspective because they do not depend on a Galaxy server.

These tests should be marked with the @external_dependency_management decorator, and can then be tested with tox -e mulled.

Continuous Integration

The Python unit tests are run against each pull request to Galaxy using CircleCI. If any of these tests fail, the pull request will be marked red. This test suite is moderately prone to having tests fail that are unrelated to the pull request being tested; if this test suite fails on a pull request with changes that seem to be unrelated to the pull request - ping the Galaxy committers on the pull request and request a re-run. The CircleCI test definition for these tests is located in .circleci/config.yml below Galaxy's root.

{#es6_unit}

Frontend/ES6 Unit Tests

Detailed information on writing Galaxy client tests can be found in client/README.md.

Continuous Integration

The client tests are run against each pull request to Galaxy using GitHub actions. If any of these tests fail, the pull request will be marked red. This test suite is moderately prone to having tests fail that are unrelated to the pull request being tested; if this test suite fails on a pull request with changes that seem to be unrelated to the pull request - ping the Galaxy committers on the pull request and request a re-run. The GitHub actions workflow definition for these tests is located in .github/workflows/client-unit.yaml below Galaxy's root.

{#framework}

Tool Framework Tests

A great deal of the complexity and interface exposed to Galaxy plugin developers comes in the form of Galaxy tool wrapper definition files. Likewise, a lot of the legacy behavior Galaxy needs to maintain is maintained for older tool definitions. For this reason, a lot of Galaxy's complex internals can just be tested by simply running a tool test. Obviously Galaxy is much more complex than this, but a surprising amount of Galaxy's tests are simply tool tests. This suite of tools that have their tests exercised is called the "Tool Framework Tests" or simply "Framework Tests".

Adding a tool test is as simple as finding a related tool in the sample tools (test/functional/tools) and adding a test block to that file or adding a new tool to this directory and referencing it in the sample tool configuration XML (test/functional/tools/sample_tool_conf.xml).

General information on writing Galaxy Tool Tests can be found in Planemo's documentation - for instance in the Test-Driven Development section.

Continuous Integration

The Tool framework tests are run against each pull request to Galaxy using GitHub actions. If any of these tests fail, the pull request will be marked red. This test suite is fairly stable and typically there are not transiently failed tests unrelated to the pull request being tested. The GitHub actions workflow definition for these tests is located in .github/workflows/framework.yaml below Galaxy's root.

{#api}

API Tests

These tests are located in lib/galaxy_test/api and test various aspects of the Galaxy API, as well as general backend aspects of Galaxy using the API.

An Example: lib/galaxy_test/api/test_roles.py

This test file shows a fairly typical API test. It demonstrates the basic structure of a test, how to GET and POST against the API, and how to use both typical user and admin user-only functionality.

Common Code for Populating Fixture Data

The galaxy_test.base.populators module contains detailed docstrings describing the concept and implementation of "Populators" that can be used for this purposes.

The test_roles.py example creates a DatasetPopulator object that it uses to get some common information from the configured Galaxy server under test.

Populators are used extensively throughout API tests as well as integration and Selenium tests to both populate data to test (histories, workflows, collections, libraries, etc..) as well as access information from the Galaxy server (e.g. fetch information from datasets, users, Galaxy's configuration, etc.).

Populators and API tests in general make heavy use of the requests library for Python.

API Test Assertions

The galaxy_test.base.api_asserts module contains common assertion functions used to check API request status codes, dictionary content, and Galaxy specific error messages.

See galaxy_test.base.api_asserts documentation for details on each function and information on verifying Galaxy API error codes.

Continuous Integration

The API tests are run against each pull request to Galaxy using GitHub actions. If any of these tests fail, the pull request will be marked red. This test suite is fairly stable and typically there are not transiently failed tests unrelated to the pull request being tested. The GitHub actions workflow definition for these tests is located in .github/workflows/api.yaml below Galaxy's root.

{#integration}

Integration Tests

These tests are located in test/integration. These tests have access to all the same API utilities as API tests described above, but can access Galaxy internals and may define hooks for configuring Galaxy in certain ways during startup.

Galaxy integration tests in some ways are more powerful than API tests - they can both control Galaxy's configuration and can access Galaxy's internals. However, this power comes at a real cost - each test case must spin up its own Galaxy server (a relatively expensive operation) and the tests cannot be executed against external Galaxy servers (it wouldn't make sense to, given these custom hooks during configuration of the server). For these reasons, we bundle up Galaxy API tests for use in deployment testing of production setups. Therefore Galaxy API tests are generally preferred, while integration tests should be implemented only when an API test is not possible or practical.

Integration tests can make use of dataset populators and API assertions as described above in the API test documentation. It is worth reviewing that documentation before digging into integration examples.

An Example: test/integration/test_quota.py

This is a really simple example that does some testing with the Quotas API of Galaxy. This API is off by default so it must be enabled for the test. The top of the test file demonstrates both how to create an integration test and how to modify Galaxy's configuration for the test.

#...
from galaxy_test.driver import integration_util


class QuotaIntegrationTestCase(integration_util.IntegrationTestCase):
    require_admin_user = True

    @classmethod
    def handle_galaxy_config_kwds(cls, config):
        config["enable_quotas"] = True

    #...

Integration test cases extend the IntegrationTestCase class defined in the galaxy_test.driver.integration_util module (located in lib/galaxy_test/driver/integration_uti.py below Galaxy's root).

The require_admin_user option above tell the test framework that the default user configured for API interactions must be an admin user.

This example overrides Galaxy's configuration using the handle_galaxy_config_kwds class method. This method is called before a Galaxy server is created, and is passed the testing server's default configuration as the config argument to that class method. This config object is effectively the Python representation of the Galaxy configuration file (galaxy.yml) used to start the Python server. Almost anything you can do in galaxy.yml, you can modify the Galaxy server to do using the same keys. Examples of various ways integration tests have modified this dictionary include setting up custom object stores (e.g. objectstore/test_mixed_store_by.py), setting up non-local job runners (e.g. test_cli_runners.py), setting up custom job destinations (e.g. test_job_recovery.py), and configuring Galaxy for tool shed operations (e.g. test_repository_operations.py).

There may be cases where an integration test is used not to allow some custom configuration of Galaxy but to access Galaxy's internals. Integration tests have direct access to Galaxy's app object via self._app and direct access to the database as a result. An example of such a test is test_workflow_refactoring.py. This test required accessing the way workflow steps are stored in the database and not just how they are serialized by the API, so it tests database models directly. Generally though, this type of usage should be avoided.

Continuous Integration

The Integration tests are run against each pull request to Galaxy using GitHub actions. If any of these tests fail, the pull request will be marked red. This test suite is moderately prone to having tests fail that are unrelated to the pull request being tested; if this test suite fails on a pull request with changes that seem to be unrelated to the pull request - ping the Galaxy committers on the pull request and request a re-run. The GitHub actions workflow definition for these tests is located in .github/workflows/integration.yaml below Galaxy's root.

{#selenium}

Selenium Tests

These are full stack tests meant to test the Galaxy UI with real browsers and are located in lib/galaxy_test/selenium.

Jupyter + Selenium

Jupyter can leveraged to develop Selenium test cases interactively, checkout out the galaxy_test.selenium.jupyter documentation for more a full discussion of this.

Continuous Integration

The Selenium tests are run against each pull request to Galaxy using GitHub actions. If any of these tests fail, the pull request will be marked red. This test suite is moderately prone to having tests fail that are unrelated to the pull request being tested; if this test suite fails on a pull request with changes that seem to be unrelated to the pull request - ping the Galaxy committers on the pull request and request a re-run. The GitHub actions workflow definition for these tests is located in .github/workflows/selenium.yaml below Galaxy's root.

{#selenium_integration}

Selenium Integration Tests

These tests are located in test/integration_selenium and simply combine the capabilities of Selenium tests and Integration tests (both described above) into test cases that can do both. There are no new capabilities or gotchas of this test suite beyond what is described above in these sections.

A quintessential example is test/integration_selenium/test_upload_ftp.py. Testing the FTP capabilities of the user interface requires both Selenium to drive the test case and a custom Galaxy configuration that mocks out an FTP directory and points the Galaxy server at it with various options (ftp_upload_dir, ftp_upload_site).

Continuous Integration

The Selenium integration tests are run against each pull request to Galaxy using GitHub actions. If any of these tests fail, the pull request will be marked red. This test suite is moderately prone to having tests fail that are unrelated to the pull request being tested; if this test suite fails on a pull request with changes that seem to be unrelated to the pull request - ping the Galaxy committers on the pull request and request a re-run. The GitHub actions workflow definition for these tests is located in .github/workflows/selenium_integration.yaml below Galaxy's root.

{#running_tests}

Running Python Tests

The best information about how to run Galaxy's Python tests can be found in the help output of run_tests.sh --help.

:literal: