# 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:

  - https://github.com/ome/omero-model

  - https://github.com/ome/omero-common

  - https://github.com/ome/omero-romio

  - https://github.com/ome/omero-renderer

  - https://github.com/ome/omero-server

  - https://github.com/ome/omero-blitz

  - https://github.com/ome/omero-gateway-java

The following repositories use pytest to run the unit tests:

  - https://github.com/ome/omero-py

  - https://github.com/ome/omero-web

### 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=

See also

Marking OmeroPy tests

#### 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)

See also

test_simple.py

  Example test class using the OMERO.web test library methods