Note

This documentation is for OMERO 5.2. This version is now in maintenance mode and will only be updated in the event of critical bugs or security concerns. OMERO 5.3 is expected in the first quarter of 2017.

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

The unit testing framework is fairly simple. Only methods which contain logic written within OMERO are tested. This means that framework functionality like remoting or the Hibernate layer is not tested. This is a part of integration testing (see below).

You can run the unit tests for any component from its directory by entering:

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

The same can be done for all components using:

./build.py test-unit

Note that for tests written in Python the package pytest must be installed, see Writing Python tests. Also note that some Python tests are excluded by default, see Using markers in OmeroPy tests for more details.

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

Alternatively, you can run individual tests which you may currently be working on. This can be done using the test target. For example:

./build.py -f components/tools/OmeroJava/build.xml test -DTEST=integration/chown/PermissionsTest
./build.py -f components/tools/OmeroPy/build.xml test -DTEST=test/integration/test_admin.py

Running Java tests

Individual test class methods

Individual OmeroJava test class methods (or a comma-separated list of methods) can be run using the -DMETHODS parameter together with the test target. The test method must be provided in the fully qualified name form (-Dpackage.class.method).

./build.py -f components/tools/OmeroJava/build.xml test -DMETHODS=integration.chgrp.AnnotationMoveTest.testMoveTaggedImage

Individual test groups

To run individual OmeroJava test groups (or comma-separated sets of groups) of tests, the -DGROUPS parameter can be used together with the test target

./build.py -f components/tools/OmeroJava/build.xml test -DGROUPS=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. common’s .classpath and common’s .project).

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.

bin/omero admin stop
bin/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 long_running and broken are excluded and 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 (long_running or broken)"

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

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

See also

Marking OmeroPy tests

Running tests directly

When writing tests it can be more convenient, flexible and powerful to run the tests from components/tools/OmeroPy using setup.py test. 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.

-t <test_path>, --test-path <test_path>

This option specifies the test suite to run. For instance to run a single test file:

cd components/tools/OmeroPy
./setup.py test -t test/integration/test_admin.py

Or to run all tests under a given folder:

cd components/tools/OmeroPy
./setup.py test -t test/integration/clitest

-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:

./setup.py test -t test/integration -k permissions

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

./setup.py test -t 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 --markers option. For example, to run all integration tests excluding those decorated with the marker long_running:

./setup.py test -t test/integration -m "not long_running"

--markers

This option lists available markers for decorating tests:

./setup.py test --markers

-s

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

./setup.py test -t test/integration/test_admin.py -s

-h, --help

This option displays the full list of available options:

./setup.py test -h

To make use of the more advanced options available in pytest that are not accessible using setup.py test, the py.test script can be used directly. To use this PYTHONPATH must contain the path to the OMERO Python libraries, see OMERO Python language bindings as well as the path to the OMERO Python test library. Alternatively, the pytest plugin pytest-pythonpath can be used to add paths to PYTHONPATH specifically for pytest.

--repeat <number>

This option allows to repeat tests for number occurences:

py.test --repeat 20 test/unit/fstest

-h, --help

This option displays the full list of options:

py.test --help

and http://pytest.org/latest/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 http://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 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 http://pytest.org.

Similar to the OmeroJava tests, the tests under components/tools/OmeroPy/test, components/tools/OmeroFS/test and components/tools/OmeroWeb/test will be the starting point for most Python-client developers coming to OMERO. Integration tests should be placed under the integration subfolders. The file names must begin with test_ for the tests to be found by pytest.

import omero

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 components/tools/pytest.ini.

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

There are a small number of custom markers defined:

long_running

Used to mark tests as long running. These are tests that typically take 10 minutes or more and are excluded from the daily integration builds.

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.

intermittent

Used to mark tests that fail intermittently. intermittent 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. Tests marked as intermittent are included in the daily integration builds.

import pytest

class TestExample2(object):

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

    @pytest.mark.long_running
    def testLongRunning():
        self.somePotentiallyLongCall()

    @pytest.mark.intermittent(reason="Occasionally times out", ticket="98765")
    def testIntermittent():
        self.somePotentiallyIntermittentCall()

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 library 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.importSingleImage() or ITest.importSingleImageWithCompanion() or ITest.importMIF() methods:

def testImportMIF():
    images = self.importMIF(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 weblibrary 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)

See also

test_simple.py

Example test class using the OMERO.web test library methods