azul_test_case.py

from abc import (
    ABCMeta,
    abstractmethod,
)
from collections.abc import (
    Set,
)
import contextlib
from contextlib import (
    AbstractContextManager,
)
from functools import (
    partial,
)
import os
from re import (
    escape,
)
from typing import (
    Iterable,
    Optional,
)
from unittest import (
    TestCase,
)
from unittest.mock import (
    PropertyMock,
    patch,
)
import warnings

import boto3.session
from botocore.credentials import (
    Credentials,
)
import botocore.session
from furl import (
    furl,
)
import moto.backends
import moto.core.models

from azul import (
    CatalogName,
    config,
)
from azul.deployment import (
    aws,
)
from azul.indexer import (
    SourceRef,
)
from azul.logging import (
    configure_test_logging,
    get_test_logger,
)
from azul.plugins.repository.dss import (
    DSSSourceRef,
)
from azul.plugins.repository.tdr_hca import (
    TDRSourceRef,
)
from azul.terra import (
    TDRSourceSpec,
)

log = get_test_logger(__name__)


# noinspection PyPep8Naming
def setUpModule():
    configure_test_logging(log)


class AzulTestCase(TestCase):
    _catch_warnings: Optional[AbstractContextManager]
    _caught_warnings: list[warnings.WarningMessage]

    @classmethod
    def setUpClass(cls) -> None:
        super().setUpClass()

        class RE(str):
            pass

        catch_warnings = warnings.catch_warnings(record=True)
        # Use tuple assignment to modify state atomically
        cls._catch_warnings, cls._caught_warnings = catch_warnings, catch_warnings.__enter__()
        permitted_warnings_ = {
            ResourceWarning: {
                RE(r'.*<ssl\.SSLSocket.*>'),
                RE(r'.*<socket\.socket.*>'),
            },
            DeprecationWarning: {
                RE(r'Call to deprecated method .*\. \(DOS support will be removed\)'),

                'Call to deprecated method fetch_bundle_manifest',

                'ProjectContact.contact_name is deprecated',
                'File.file_format is deprecated',
                'ProjectPublication.publication_title is deprecated',
                'ProjectPublication.publication_url is deprecated',
                'CellLine.cell_line_type is deprecated',
                'CellSuspension.selected_cell_type is deprecated',
                'CellSuspension.total_estimated_cells is deprecated',
                'DonorOrganism.biological_sex is deprecated',
                'DonorOrganism.disease is deprecated',
                'LibraryPreparationProtocol.library_construction_approach is deprecated',
                'SpecimenFromOrganism.disease is deprecated',
                'SpecimenFromOrganism.organ_part has been removed',
                'Project.laboratory_names is deprecated',
                'Project.project_shortname is deprecated',
                'Project.insdc_project_accessions is deprecated',
                'Project.geo_series_accessions is deprecated',
                'Project.array_express_accessions is deprecated',
                'Project.insdc_study_accessions is deprecated',

                RE(r'.*humancellatlas\.data\.metadata\.api\.DissociationProcess'),
                RE(r'.*humancellatlas\.data\.metadata\.api\.EnrichmentProcess'),
                RE(r'.+humancellatlas\.data\.metadata\.api\.LibraryPreparationProcess'),
                RE(r'.*humancellatlas\.data\.metadata\.api\.SequencingProcess'),

                # FIXME: https://github.com/DataBiosphere/azul/issues/2758
                'OpenJDK 64-Bit Server VM warning: Option UseConcMarkSweepGC was deprecated',

                RE(r'.*Fielddata access on the _uid field is deprecated, use _id instead'),
                RE(r'.*Accessing variable \[_aggs\]'),
                RE(r'.*Accessing variable \[_agg\]'),

                # FIXME: furl.fragmentstr raises deprecation warning
                #        https://github.com/DataBiosphere/azul/issues/2848
                'furl.fragmentstr is deprecated',

                (
                    "Using or importing the ABCs from 'collections' instead of from "
                    "'collections.abc' is deprecated since Python 3.3, and in 3.9 "
                    "it will stop working"
                ),

                'Call to deprecated function (or staticmethod) patch_source_cache',

                # FIXME: DeprecationWarning for ES body parameter
                #        https://github.com/DataBiosphere/azul/issues/5912
                #
                RE(
                    'The \'body\' parameter is deprecated for the \'.*\' API '
                    'and will be removed in .*. Instead use .*'
                ),

                # FIXME: DeprecationWarning for datetime methods in Python 3.12
                #        https://github.com/DataBiosphere/azul/issues/5953
                'datetime.datetime.utcnow() is deprecated',
                'datetime.datetime.utcfromtimestamp() is deprecated',
            },
            UserWarning: {
                'https://github.com/DataBiosphere/azul/issues/2114',
            }
        }
        for warning_class, message_patterns in permitted_warnings_.items():
            for message_pattern in message_patterns:
                if isinstance(message_pattern, tuple):
                    message_pattern, module_name = message_pattern
                else:
                    module_name = ''
                if not isinstance(message_pattern, RE):
                    message_pattern = escape(message_pattern)
                if not isinstance(module_name, RE):
                    module_name = escape(module_name)
                warnings.filterwarnings('ignore',
                                        message=message_pattern,
                                        category=warning_class,
                                        module=module_name)

    @classmethod
    def tearDownClass(cls) -> None:
        if cls._catch_warnings is not None:
            cls._catch_warnings.__exit__(None, None, None)
            caught_warnings = cls._caught_warnings
            # Use tuple assignment to modify state atomically
            cls._catch_warnings, cls._caught_warnings = None, []
            if caught_warnings:
                # Running a single test method in PyCharm somehow doesn't print
                # anything when the assertion below is raised. To account for
                # that we additionally log each warning. Note that PyCharm
                # sometimes (non-deterministically) dumps these log messages
                # above the log messages emitted by the actual tests, even
                # though these messages are emitted afterwards, when the class
                # is torn down.
                for warning in caught_warnings:
                    log.error('Caught unexpected warning: %s', warning)
                assert False, list(map(str, caught_warnings))
        super().tearDownClass()

    def assertIsSubset(self, subset: Set, superset: Set):
        """
        More useful than using :meth:`assertTrue` and :meth:`set.issubset`
        because the offending elements are shown.
        """
        self.assertEqual(set(), subset - superset)

    def assertIsDisjoint(self, set1: Set, set2: Set):
        """
        More useful than using :meth:`assertTrue` and :meth:`set.isdisjoint`
        because the offending elements are shown.
        """
        self.assertEqual(set(), set1 & set2)

    @classmethod
    def addClassPatch(cls, instance: patch) -> None:
        instance.start()
        cls.addClassCleanup(instance.stop)

    def addPatch(self, instance: patch) -> None:
        # Moto mock's stop() method has the drastic effect of resetting the
        # model class attributes that are used to track model instances so that
        # they can later be cleaned up when the backend is reset.
        if isinstance(instance, moto.core.models.MockAWS):
            cleanup = partial(instance.stop, remove_data=False)
        else:
            cleanup = instance.stop
        instance.start()
        self.addCleanup(cleanup)

    @contextlib.contextmanager
    def stacked_patches(self, patches: Iterable[patch]):
        with contextlib.ExitStack() as context:
            for cm in patches:
                context.enter_context(cm)
            yield


class AlwaysTearDownTestCase(TestCase):
    """
    AlwaysTearDownTestCase makes sure that tearDown / cleanup methods are always
    run when they should be.

    This means that

    - if a KeyboardInterrupt is raised in a test, then tearDown, tearDownClass,
      and tearDownModule will all still run
    - if any exception is raised in a setUp, then tearDown, tearDownClass,
      and tearDownModule will all still run

    Caveats:

    - All tearDown methods should pass even if their corresponding setUps don't
      run at all, as in the case of a KeyboardInterrupt or other exception.
    - If an exception is raised in setUpClass or setUpModule, the corresponding
      tearDown will not be run.
    """

    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self.setUp = self._cleanup_wrapper(self.setUp, BaseException)

    def run(self, result=None):
        test_method = getattr(self, self._testMethodName)
        wrapped_test = self._cleanup_wrapper(test_method, KeyboardInterrupt)
        setattr(self, self._testMethodName, wrapped_test)
        return super().run(result)

    def _cleanup_wrapper(self, method, exception_cls):
        def wrapped(*args, **kwargs):
            try:
                return method(*args, **kwargs)
            except exception_cls:
                self.tearDown()
                self.doCleanups()
                raise

        return wrapped


class AzulUnitTestCase(AzulTestCase):

    @classmethod
    def setUpClass(cls) -> None:
        super().setUpClass()
        cls._patch_aws_account()
        cls._patch_aws_credentials()
        cls._patch_aws_region()
        cls._patch_dss_query_prefix()
        cls._patch_lambda_env()

    def setUp(self) -> None:
        super().setUp()
        # Moto backends are reset to ensure no mock resources are left over if
        # a test fails to clean up after itself.
        self._reset_moto()

    def _reset_moto(self):
        # Note that we don't use moto.core.models.moto_api_backend.reset() here
        # because it resets all backends and therefore requires that all Moto
        # extras are installed. The backends listed here need to match the
        #  extras specified for the `moto` dependency in `requirements.dev.txt`.
        for name in ('s3', 'sqs', 'sns', 'dynamodb', 'iam'):
            backends = moto.backends.get_backend(name)
            for region_name, backend in backends.items():
                backend.reset()

    _aws_account_name = 'test-hca-dev'

    @classmethod
    def _patch_aws_account(cls):
        # Set AZUL_AWS_ACCOUNT_ID to what the Moto is using. This circumvents
        # assertion errors in azul.deployment.aws.account.
        cls.addClassPatch(patch.dict(os.environ,
                                     AZUL_AWS_ACCOUNT_ID=moto.core.models.DEFAULT_ACCOUNT_ID,
                                     azul_aws_account_name=cls._aws_account_name))

    @classmethod
    def _patch_aws_credentials(cls):
        # Discard cached Boto3/botocore clients, resources and sessions
        def reset():
            aws.clear_caches()
            aws.discard_all_sessions()

        reset()
        cls.addClassCleanup(reset)

        # Save and then reset the default boto3session. This overrides any
        # session customizations such as those performed by envhook.py which
        # interfere with moto patchers, rendering them ineffective.
        cls.addClassPatch(patch.object(boto3, 'DEFAULT_SESSION', None))

        # This ensures that we don't accidentally use actual cloud resources in
        # unit tests. Furthermore, `boto3` and `botocore` cache credentials
        # which can lead to credentials from an unmocked use of boto3 in one
        # test to leak into a mocked use of boto3. The latter was the reason for
        # https://github.com/DataBiosphere/azul/issues/668.

        def dummy_get_credentials(_self):
            # These must match what `moto` uses to mock the instance metadata
            # response (see InstanceMetadataResponse.metadata_response() in
            # moto.instance_metadata.responses).
            return Credentials(access_key='test-key',
                               secret_key='test-secret-key',
                               token='test-session-token')

        cls.addClassPatch(patch.object(botocore.session.Session,
                                       'get_credentials',
                                       dummy_get_credentials))

        cls.addClassPatch(patch.object(boto3.session.Session,
                                       'get_credentials',
                                       dummy_get_credentials))

    # We almost certainly won't have access to this region
    _aws_test_region = 'us-gov-west-1'

    @classmethod
    def _patch_aws_region(cls):
        # Ensure that mock leakages fail by targeting a region we don't have
        # access to. Subclasses can override the selected region if moto rejects
        # the default one.
        cls.addClassPatch(patch.dict(os.environ,
                                     AWS_DEFAULT_REGION=cls._aws_test_region))

    dss_query_prefix = ''

    @classmethod
    def _patch_dss_query_prefix(cls):
        cls.addClassPatch(patch.object(target=type(config),
                                       attribute='dss_query_prefix',
                                       new_callable=PropertyMock,
                                       return_value=cls.dss_query_prefix))

    @classmethod
    def _patch_lambda_env(cls):
        cls.addClassPatch(patch.dict(os.environ,
                                     AWS_LAMBDA_FUNCTION_NAME='unit-tests'))


class CatalogTestCase(AzulUnitTestCase, metaclass=ABCMeta):
    catalog: CatalogName = 'test'
    source: SourceRef

    @classmethod
    @abstractmethod
    def catalog_config(cls) -> dict[CatalogName, config.Catalog]:
        raise NotImplementedError

    @classmethod
    def setUpClass(cls) -> None:
        super().setUpClass()
        cls._patch_catalogs()
        cls._patch_replicas_enabled()
        cls._patch_deployment()

    @classmethod
    def _patch_catalogs(cls):
        # Reset the cached properties
        try:
            # noinspection PyPropertyAccess
            del config.catalogs
        except AttributeError:
            pass
        try:
            # noinspection PyPropertyAccess
            del config.default_catalog
        except AttributeError:
            pass
        try:
            # noinspection PyPropertyAccess
            del config.integration_test_catalogs
        except AttributeError:
            pass
        # Patch the catalog property to use a single fake test catalog.
        cls.addClassPatch(patch.object(target=type(config),
                                       attribute='catalogs',
                                       new_callable=PropertyMock,
                                       return_value=cls.catalog_config()))
        assert cls.catalog_config()[cls.catalog]
        # Ensure that derived cached properties are affected
        assert config.default_catalog == cls.catalog
        assert config.integration_test_catalogs == {}

    @classmethod
    def _patch_replicas_enabled(cls):
        cls.addClassPatch(patch.object(type(config),
                                       'enable_replicas',
                                       return_value=True))

    @classmethod
    def _patch_deployment(cls):
        cls.addClassPatch(patch.object(type(config),
                                       'deployment_stage',
                                       new_callable=PropertyMock,
                                       return_value=config.deployment.test_name))


class DSSTestCase(CatalogTestCase, metaclass=ABCMeta):
    """
    A mixin for test cases that depend on certain DSS-related environment
    variables.
    """

    @classmethod
    def setUpClass(cls):
        super().setUpClass()
        cls._patch_source()
        cls._patch_source_cache()
        cls._patch_drs_domain()

    source = DSSSourceRef.for_dss_source('https://fake_dss_instance/v1:/2')

    @classmethod
    def _patch_source(cls):
        cls.addClassPatch(patch.dict(os.environ,
                                     AZUL_DSS_SOURCE=str(cls.source.spec)))

    @classmethod
    def _patch_source_cache(cls):
        from service import (
            patch_source_cache,
        )
        cls.addClassPatch(patch_source_cache())

    # With DSS as the repository, which doesn't support DRS, Azul acts as a
    # partial DRS implementation, proxying DSS. The REST endpoints making up
    # that partial implementaton are exposed by the Azul service. Optionally, a
    # CNAME alias for the canonical service endpoint can be set up. When the
    # repository is DSS and if the alias is enabled by configuring
    # AZUL_DRS_DOMAIN_NAME, all DRS URIs emitted by the service reference that
    # alias instead of the service's canonical endpoint. In a unit test, the
    # canonical service endpoint is 'localhost:' followed by some ephemeral
    # port. Since many cans hard-code DRS URIs we need a predictable value for
    # the DRS endpoint, so we patch AZUL_DRS_DOMAIN_NAME to achieve that.

    _drs_domain_name = 'mock_drs_domain.lan'

    @classmethod
    def _patch_drs_domain(cls):
        cls.addClassPatch(patch.dict(os.environ,
                                     AZUL_DRS_DOMAIN_NAME=cls._drs_domain_name))


class DCP1TestCase(DSSTestCase):

    @classmethod
    def catalog_config(cls) -> dict[CatalogName, config.Catalog]:
        return {
            cls.catalog: config.Catalog(name=cls.catalog,
                                        atlas='hca',
                                        internal=False,
                                        plugins=dict(metadata=config.Catalog.Plugin(name='hca'),
                                                     repository=config.Catalog.Plugin(name='dss')),
                                        sources={str(cls.source.spec)})
        }


class TDRTestCase(CatalogTestCase, metaclass=ABCMeta):

    @classmethod
    def setUpClass(cls):
        super().setUpClass()
        cls._patch_tdr_service_url()
        cls._patch_source_cache()

    mock_tdr_service_url = furl('https://mock_tdr.lan')

    @classmethod
    def _patch_tdr_service_url(cls):
        cls.addClassPatch(patch.object(type(config),
                                       'tdr_service_url',
                                       new=PropertyMock(return_value=cls.mock_tdr_service_url)))

    _drs_domain_name = str(mock_tdr_service_url.netloc)

    @classmethod
    def _sources(cls):
        return {str(cls.source.spec)}

    @classmethod
    def _patch_source_cache(cls):
        from service import (
            patch_source_cache,
        )
        cls.addClassPatch(patch_source_cache(hit=[cls.source.id]))


class DCP2TestCase(TDRTestCase):
    source = TDRSourceRef(id='d8c20944-739f-4e7d-9161-b720953432ce',
                          spec=TDRSourceSpec.parse('tdr:bigquery:gcp:test_hca_project:hca_snapshot:/2'))

    @classmethod
    def catalog_config(cls) -> dict[CatalogName, config.Catalog]:
        return {
            cls.catalog: config.Catalog(name=cls.catalog,
                                        atlas='hca',
                                        internal=False,
                                        plugins=dict(metadata=config.Catalog.Plugin(name='hca'),
                                                     repository=config.Catalog.Plugin(name='tdr_hca')),
                                        sources=cls._sources())
        }


class AnvilTestCase(TDRTestCase):
    source = TDRSourceRef(id='6c87f0e1-509d-46a4-b845-7584df39263b',
                          spec=TDRSourceSpec.parse('tdr:bigquery:gcp:test_anvil_project:anvil_snapshot:/2'))

    @classmethod
    def catalog_config(cls) -> dict[CatalogName, config.Catalog]:
        return {
            cls.catalog: config.Catalog(name=cls.catalog,
                                        atlas='anvil',
                                        internal=False,
                                        plugins=dict(metadata=config.Catalog.Plugin(name='anvil'),
                                                     repository=config.Catalog.Plugin(name='tdr_anvil')),
                                        sources={str(cls.source.spec)})
        }


class Hidden:
    # Keep this test case out of the main namespace

    class TracingTestCase:
        """A test case which traces its calls."""

        def __init__(self, events):
            super().__init__('test')
            self.events = events

        # noinspection PyPep8Naming
        def setUp(self):
            self.events.append('setUp')

        def test(self):
            self.events.append('test')

        # noinspection PyPep8Naming
        def tearDown(self):
            self.events.append('tearDown')


class TestAlwaysTearDownTestCase(AzulUnitTestCase):

    def test_regular_execution_order(self):
        expected = ['setUp', 'test', 'tearDown', 'setUp', 'test', 'tearDown']
        for test_class, expected_events in [(TestCase, expected),
                                            (AlwaysTearDownTestCase, expected)]:
            with self.subTest(test_class=test_class, expected_events=expected_events):
                events = []

                class TC(Hidden.TracingTestCase, test_class):
                    pass

                TC(events).run()
                TC(events).run()
                self.assertEqual(events, expected_events)

    def test_keyboard_interrupt_in_test(self):
        expected = ['setUp', 'test']
        for test_class, expected_events in [(TestCase, expected),
                                            (AlwaysTearDownTestCase, expected + ['tearDown'])]:
            with self.subTest(test_class=test_class, expected_events=expected_events):
                events = []

                class TC(Hidden.TracingTestCase, test_class):

                    def test(self):
                        super().test()
                        raise KeyboardInterrupt

                with self.assertRaises(KeyboardInterrupt):
                    TC(events).run()
                self.assertEqual(events, expected_events)
                self.assertEqual(events, expected_events)

    def test_exception_in_setup(self):
        expected = ['setUp']
        for test_class, expected_events in [(TestCase, expected),
                                            (AlwaysTearDownTestCase, expected + ['tearDown'])]:
            with self.subTest(test_class=test_class, expected_events=expected_events):
                events = []

                class TC(Hidden.TracingTestCase, test_class):

                    def setUp(self):
                        super().setUp()
                        raise RuntimeError('Exception in setUp')

                TC(events).run()
                self.assertEqual(events, expected_events)

    def test_keyboard_interrupt_in_setup(self):
        expected = ['setUp']
        for test_class, expected_events in [(TestCase, expected),
                                            (AlwaysTearDownTestCase, expected + ['tearDown'])]:
            with self.subTest(test_class=test_class, expected_events=expected_events):
                events = []

                class TC(Hidden.TracingTestCase, test_class):

                    def setUp(self):
                        super().setUp()
                        raise KeyboardInterrupt

                with self.assertRaises(KeyboardInterrupt):
                    TC(events).run()
                self.assertEqual(events, expected_events)