Running and writing tests

The following guidelines apply to tests in both the Java and Python test components. However, some of the presented options apply to only one or the other.

The default build target does not compile all the required testing resources. You should run test-compile (or build-dev if you are using Eclipse) first:

./build.py build-default test-compile

You must rebuild the test-compile target if you subsequently modify any of the Java tests.

Note

The OMERO C++ components and tests are under heavy development, and are not compiled or run by the targets mentioned on this page.

Running tests

Running unit tests

Starting from version 5.5, components have been migrated to their own repository.

The following repositories use Gradle to run the unit tests:

The following repositories use pytest to run the unit tests:

Running integration tests

Integration testing is a bit more complex because of the reliance on a database, which is not easily mockable. All Hibernate-related classes are tested in integration mode.

The tests require a fast computer. Running all the integration tests places several restrictions on the environment:

There must be a running OMERO database.
An OMERO.server instance must be running.

Integration tests assume that:

ICE_CONFIG has been properly set. The contents of the etc/ice.config file should be enough to configure a running server for integration testing. This means that code creating a client connection as outlined in Developing OMERO clients should execute without errors.
An OMERO.server instance is running on the host and port specified in the ICE_CONFIG file.

If any of the tests fail with a user authentication exception (or omero.client throws an exception), a new ice.config file can be created and pointed to by the ICE_CONFIG environment variable. Most likely the first settings that will have to be put there will be omero.user and omero.pass.

Running all tests

To run all the integration tests, use

./build.py test-integration

Note that some Python tests are excluded by default, see Using markers in OmeroPy tests for more details.

Component tests

Running an integration test suite for an individual component can be done explicitly via:

./build.py -f components/<component>/build.xml integration

Results are placed in components/<component>/target/reports.

Individual tests

Warning

Some integration tests leak file descriptors. If many tests are run then they may start to fail after the system’s open files limit is reached. Depending on your system the limit may be checked or adjusted using ulimit -n and /etc/login.conf or /etc/security/limits.conf.

Running Java tests

Individual tests

Alternatively, you can run individual tests which you may currently be working on using the --tests parameter. The test class must be provided in the fully qualified name form.

cd components/tools/OmeroJava
gradle test --tests "integration.gateway.AdminFacilityTest"

Individual test class methods

Individual OmeroJava test class methods can be run using the --tests parameter. The test method must be provided in the fully qualified name form.

cd components/tools/OmeroJava
gradle test --tests "integration.chgrp.AnnotationMoveTest.testMoveTaggedImage"

Individual test groups

To run individual OmeroJava test groups the --tests parameter.

cd components/tools/OmeroJava
gradle test --tests "integration.*"

Using Eclipse to run tests

To facilitate importing OMERO components into Eclipse, there are .project and .classpath-template files stored in each component directory (e.g. tools/OmeroJava’s .project and .classpath-template).

There are also top-level .classpath and .project files which allow for importing all components as a single project, but this approach requires more memory and does not clearly differentiate the classpaths, and so can lead to confusion.

Before importing any component as a project into Eclipse, a successful build has to have taken place:

./build.py

This is for two reasons. Firstly, the Eclipse projects are not configured to perform the code generation needed. The build.py command creates the directory:

<component>/target

which will be missing from any Eclipse project you open before building the source.

Secondly, Ivy is used to copy all the jar dependencies from OMERO_SOURCE_PREFIX/lib/repository to <component>/target/libs, which is then used in the Eclipse .classpath files.

If Eclipse ever gets out of sync after the first build, ./build.py build-eclipse can be used to quickly synchronize.

A prerequisite of running unit and integration tests in the Eclipse UI is having the TestNG plug-in installed and working (help available on the TestNG site).

Running the unit tests under Eclipse requires no extra settings and is as easy as navigating to the package or class context menu Run As or Debug As, then selecting TestNG.

Integration tests require the ICE_CONFIG environment variable to be available for the Eclipse-controlled JVM. This can be done by editing Debug/Run configurations in Eclipse. After navigating to the Debug (or Run) Configurations window, the Environment tab needs to be selected. After clicking New, ICE_CONFIG can be defined as a path to the ice.config file. This setting needs to be defined per package, class or method.

By using the “debug” target from templates.xml, it is possible to have OMERO listen on port 8787 for a debugging connection.

omero admin stop
omero admin start debug

Then in Eclipse, you can create a new “Debug” configuration by clicking on Remote Java Application, and setting the port to 8787. These values are arbitrary and can be changed locally.

Keep in mind:

The server will not start up until you have connected with Eclipse. This is due to the “suspend=y” clause in templates.xml. If you would like the server to start without you connecting, use “suspend=n”.
If you take too much time examining your threads, your calls may throw timeout exceptions.

Running Python tests

Using markers in OmeroPy tests

Tests under OmeroPy can be included or excluded according to markers defined in the tests. This can be done by using the -DMARK option. For example, to run all the integration tests marked as broken:

./build.py -f components/tools/OmeroPy/build.xml integration -DMARK=broken

By default tests marked as broken are excluded so the following two builds are equivalent:

./build.py -f components/tools/OmeroPy/build.xml integration
./build.py -f components/tools/OmeroPy/build.xml integration -DMARK="not broken"

In order to run all tests, including broken, an empty marker must be used:

./build.py -f components/tools/OmeroPy/build.xml integration -DMARK=

Running tests directly

When writing tests it can be more convenient, flexible and powerful to run the tests from https://github.com/ome/openmicroscopy/tree/develop/components/tools/OmeroPy or https://github.com/ome/openmicroscopy/tree/develop/components/tools/OmeroWeb using pytest. Since Python is interpreted, tests can be written and then run without having to rebuild or restart the server. A few basic options are shown below.

First create a python virtual environment as described on the OMERO Python page, including omero-py and omero-web if you want to run OmeroWeb tests. Some tests also require the installation of PyTables.

Then install some additional test dependencies:

$ pip install pytest pytest-mock pyyaml tables

# for Omeroweb tests
$ pip install pytest-django

Run tests directly with pytest, setting the ICE_CONFIG as described above. Also set OMERODIR to point to the OMERO.server:

export ICE_CONFIG=/path/to/openmicroscopy/etc/ice.config
export OMERODIR=/path/to/OMERO.server-x.x.x-ice36-bxx

cd components/tools/OmeroPy
pytest test/integration/test_admin.py

# OR for OmeroWeb tests:
cd components/tools/OmeroWeb

pytest test/integration/test_annotate.py

-k <string>

This option will run all integration tests containing the given string in their names. For example, to run all the tests under test/integration with permissions in their names:

pytest test/integration -k permissions

This option can also be used to run a named test within a test module:

pytest test/integration/test_admin.py -k testGetGroup

-m <marker>

This option will run integration tests depending on the markers they are decorated with. Available markers can be listed using the pytest --markers option. For example, to run all integration tests excluding those decorated with the marker broken:

pytest test/integration -m "not broken"

--markers

This option lists available markers for decorating tests:

pytest --markers

-s

This option allows the standard output to be shown on the console:

pytest test/integration/test_admin.py -s

-h, --help

This option displays the full list of available options:

pytest -h

See https://docs.pytest.org/en/latest/how-to/usage.html for more help in running tests.

Failing tests

The test.with.fail ant property is set to false by default, which prevents test failures from failing the build. However, it can instead be set to true to allow test failures to fail the build. For example:

./build.py -Dtest.with.fail=true integration

Some components might provide individual targets for specific tests (e.g. OmeroJava provides the broken target for running broken tests). The build.xml file is the reference in each component.

Writing tests

Writing Java tests

For more information on writing tests in general see https://testng.org/. For a test to be an “integration” test, place it in the “integration” TestNG group. If a test is temporarily broken, add it to the “broken” group:

@Test(groups = {"integration", "broken"}
public void testMyStuff() {

}

Tests should be of the Acceptance Test form. The ticket number for which a test is being written should be added in the TestNG annotation:

@Test(groups = "ticket:60")

This works at either the method level (see SetsAndLinksTest.java) or the class level (see UniqueResultTest.java).

The tests under https://github.com/ome/openmicroscopy/tree/develop/components/tools/OmeroJava/test will be the starting point for most Java-client developers coming to OMERO. An example skeleton for an integration test looks similar to

@Test(groups = "integration")
public class MyTest {

  omero.client client;

  @BeforeClass
  protected void setup() throws Exception {
    client = new omero.client();
    client.createSession();
  }

  @AfterClass
  protected void tearDown() throws Exception {
    client.closeSession();
  }

  @Test
  public void testSimple() throws Exception {
    client.getSession().getAdminService().getEventContext();
  }

}

Writing Python tests

To write and run Python tests you first need to install pytest:

pip install pytest

For more information on writing tests in general see https://pytest.org/.

Unit tests can be found in various repositories such as omero-py, omero-web, and omero-dropbox.

Integration tests which require OMERO.server to run are found in the openmicroscopy repository. See: https://github.com/ome/openmicroscopy/tree/develop/components/tools/OmeroPy/test, https://github.com/ome/openmicroscopy/tree/develop/components/tools/OmeroWeb/test and https://github.com/ome/openmicroscopy/tree/develop/components/tools/OmeroFS/test.

The file names must begin with test_ for the tests to be found by pytest.

import omero.clients

class TestExample(object)

  def setup_method(self, method):
    client = new omero.client()
    client.createSession()

  def teardown_method(self, method):
    client.closeSession()

  def testSimple():
    ec = client.getSession().getAdminService().getEventContext()
    assert ec, "No EventContext!"

Marking OmeroPy tests

Methods, classes and functions can be decorated with pytest markers to allow for the selection of tests. pytest provides some predefined markers and markers can be simply defined as they are used. However, to centralize the use of custom markers they should be defined in https://github.com/ome/openmicroscopy/tree/develop/components/tools/pytest.ini.

To view all available markers the pytest --markers option can be used with pytest or py.test as detailed in Running tests directly.

There is one custom marker defined:

broken: Used to mark broken tests. These are tests that fail consistently with no obvious quick fix. Broken tests are excluded from the main integration builds and instead are run in a separate daily build. broken markers should have a reason, an associated Trac ticket number or both. If there are multiple associated tickets then a comma-separated list should be used.

import pytest

class TestExample2(object):

    @pytest.mark.broken(reason="Asserting false", ticket="12345,67890")
    def testBroken():
        assert False, "Bound to fail"

Using the Python test library

The OMERO Python test library defines an abstract ITest class that implements the connection set up as well as many methods shared amongst all Python integration tests.

Each concrete instance of the ITest will initiate a connection to the server specified by the ICE_CONFIG environment variable at the setup_class() level. The following objects are created by ITest.setup_class() and shared by all test methods of this class:

self.root is a client for the root user
self.group is a new group which permissions are set to ITest.DEFAULT_PERMS by default. Overriding DEFAULTS_PERMS in a subclass of ITest means the group will be created with the new permissions.
self.user is a new user and member of self.group
self.client is a client for the self.user created at class setup.

Additionally, for the self.client object, different shortcuts are available:

self.sf is the non-root client session
self.update is the update service for the non-root client session
self.query is the query service for the non-root client session
self.ctx is the event context for the non-root client session. Note this corresponds to the context at creation time and should be refreshed if the context is modified.

The example below inherits the ITest class and would create a read-write group by default

from omero.testlib import ITest

class TestExample(ITest):

    DEFAULT_PERMS = 'rwrw--'  # Override default permissions
    def test1():
        doAction(self.sf)

New user and groups can be instantiated by individual tests using the ITest.new_user() and ITest.new_group() methods:

def testNewGroupOwner():
    new_group = self.new_group(perms='rwa---')
    new_owner = self.new_use(group=new_group, owner=True)
    assert new_owner.id.val, "No EventContext!"

New clients can be instantiated by individual tests using the ITest.new_client() or ITest.new_client_and_user() methods:

def testNewClient():
    new_client = self.new_user_and_client()
    ec = new_client.getSession().getAdminService().getEventContext()
    assert ec, "No EventContext!"

Images can be imported using the ITest.import_fake_file() method:

def testFileset():
    # 2 images sharing a fileset
    images = self.import_fake_file(2)
    assert len(images) == 2

Writing OMERO.web tests

For OMERO.web integration tests, the OMERO.web test library defines an abstract IWebTest class that inherits from ITest and also implements Django clients at the class setup using the Django testing tools.

On top of the elements created by ITest.setup_class(), the IWebTest class creates:

self.django_root_client is a Django test client for the root user
self.django_client is a client for the new user created at the class setup.

from omeroweb.testlib import IWebTest

class TestExample(IWebTest):
    def testSimple():
        self.django_client.post('/login/', {'username': 'john'})

New Django test clients can be instantiated by individual tests using the IWebTest.new_django_client() method:

def testNewDjangoClient():
    new_user = self.new_user()
    omeName = new_user.omeName.val
    new_django_client = self.new_django_client(omeName, omeName)