def main():
catalogs = {
'dcp2':
config.Catalog(name='dcp2',
atlas='hca',
internal=False,
plugins=dict(
metadata=config.Catalog.Plugin(name='hca'),
repository=config.Catalog.Plugin(name='tdr')),
sources=set())
}
# To create a normalized OpenAPI document, we patch any
# deployment-specific variables that affect the document.
with patch.object(target=type(config),
attribute='catalogs',
new_callable=PropertyMock,
return_value=catalogs):
assert config.catalogs == catalogs
with patch.object(target=config,
attribute='service_function_name',
return_value='azul_service'):
assert config.service_name == 'azul_service'
with patch.object(target=config,
attribute='service_endpoint',
return_value='localhost'):
assert config.service_endpoint() == 'localhost'
app_module = load_app_module('service')
app_spec = app_module.app.spec()
doc_path = os.path.join(config.project_root,
'lambdas/service/openapi.json')
with write_file_atomically(doc_path) as file:
json.dump(app_spec, file, indent=4)
def test_cached_health(self):
self.storage_service.create_bucket()
# No health object is available in S3 bucket, yielding an error
with self.helper() as helper:
response = requests.get(
str(self.base_url.set(path='/health/cached')))
self.assertEqual(500, response.status_code)
self.assertEqual(
'ChaliceViewError: Cached health object does not exist',
response.json()['Message'])
# A successful response is obtained when all the systems are functional
self._create_mock_queues()
endpoint_states = self._endpoint_states()
app = load_app_module(self.lambda_name(), unit_test=True)
with self.helper() as helper:
self._mock_service_endpoints(helper, endpoint_states)
app.update_health_cache(MagicMock(), MagicMock())
response = requests.get(
str(self.base_url.set(path='/health/cached')))
self.assertEqual(200, response.status_code)
# Another failure is observed when the cache health object is older than 2 minutes
future_time = time.time() + 3 * 60
with self.helper() as helper:
with patch('time.time', new=lambda: future_time):
response = requests.get(
str(self.base_url.set(path='/health/cached')))
self.assertEqual(500, response.status_code)
self.assertEqual(
'ChaliceViewError: Cached health object is stale',
response.json()['Message'])
def load_tests(_loader, tests, _ignore):
root = azul.config.project_root
for module in [
azul, azul.azulclient, azul.collections, azul.doctests, azul.dss,
azul.exceptions, azul.files, azul.indexer.aggregate, azul.json,
azul.json_freeze, azul.objects, azul.openapi, azul.openapi.params,
azul.openapi.responses, azul.openapi.schema,
azul.plugins.metadata.hca.contributor_matrices,
azul.plugins.metadata.hca.full_metadata,
azul.plugins.repository.tdr, azul.plugins.metadata.hca.transform,
azul.service.drs_controller, azul.service.manifest_service,
azul.strings, azul.terra, azul.threads, azul.time, azul.types,
azul.uuids, azul.vendored.frozendict, retorts,
load_app_module('service'),
load_module(root + '/scripts/envhook.py', 'envhook'),
load_module(root + '/scripts/export_environment.py',
'export_environment'),
load_module(root + '/scripts/check_branch.py', 'check_branch'),
load_module(root + '/scripts/velocity.py', 'velocity'),
load_module(root + '/.flake8/azul_flake8.py', 'azul_flake8')
]:
suite = doctest.DocTestSuite(module)
assert suite.countTestCases() > 0, module
tests.addTests(suite)
return tests
def manage_lambdas(self, queues: Mapping[str, Queue], enable: bool):
"""
Enable or disable the readers and writers of the given queues
"""
indexer = load_app_module('indexer', unit_test=True)
functions_by_queue = {
handler.queue: config.indexer_function_name(handler.name)
for handler in indexer.app.handler_map.values()
if hasattr(handler, 'queue')
}
with ThreadPoolExecutor(max_workers=len(queues)) as tpe:
futures = []
def submit(f, *args, **kwargs):
futures.append(tpe.submit(f, *args, **kwargs))
for queue_name, queue in queues.items():
try:
function = functions_by_queue[queue_name]
except KeyError:
assert queue_name in config.fail_queue_names
else:
if queue_name == config.notifications_queue_name():
# Prevent new notifications from being added
submit(self._manage_lambda, config.indexer_name, enable)
submit(self._manage_sqs_push, function, queue, enable)
self._handle_futures(futures)
futures = [tpe.submit(self._wait_for_queue_idle, queue) for queue in queues.values()]
self._handle_futures(futures)
def setUpClass(cls):
super().setUpClass()
# Load the application module without modifying `sys.path` and without
# adding it to `sys.modules`. This simplifies tear down and isolates the
# app modules from different lambdas loaded by different concrete
# subclasses. It does, however, violate this one invariant:
# `sys.modules[module.__name__] == module`
cls.app_module = load_app_module(cls.lambda_name(), unit_test=True)
def setUpClass(cls) -> None:
super().setUpClass()
app_module = load_app_module('service')
app_dir = os.path.dirname(app_module.__file__)
factory = chalice.cli.factory.CLIFactory(app_dir)
config = factory.create_config_obj()
cls.server = factory.create_local_server(app_obj=app_module.app,
config=config,
host=cls.url.host,
port=cls.url.port)
cls.server_thread = threading.Thread(target=cls.server.serve_forever)
cls.server_thread.start()
def load_tests(_loader, tests, _ignore):
root = azul.config.project_root
for module in [
azul,
azul.auth,
azul.azulclient,
azul.bigquery,
azul.caching,
azul.collections,
azul.doctests,
azul.dss,
azul.exceptions,
azul.files,
azul.indexer,
azul.indexer.aggregate,
azul.iterators,
azul.json,
azul.json_freeze,
azul.objects,
azul.openapi,
azul.openapi.params,
azul.openapi.responses,
azul.openapi.schema,
azul.plugins.metadata.hca.contributor_matrices,
azul.plugins.repository.tdr,
azul.plugins.metadata.hca.transform,
azul.service.drs_controller,
azul.service.manifest_service,
azul.service.repository_controller,
azul.strings,
azul.terra,
azul.terraform,
azul.threads,
azul.time,
azul.types,
azul.uuids,
azul.vendored.frozendict,
load_app_module('service', unit_test=True),
load_script('check_branch'),
load_script('envhook'),
load_script('export_environment'),
load_module(root + '/.flake8/azul_flake8.py', 'azul_flake8'),
load_module(root + '/test/test_tagging.py', 'test_tagging'),
load_module(root + '/test/indexer/test_tdr.py', 'test_tdr')
]:
suite = doctest.DocTestSuite(module)
assert suite.countTestCases() > 0, module
tests.addTests(suite)
return tests
def _contribution_lambda_names(cls) -> FrozenSet[str]:
indexer = load_app_module('indexer')
notification_queue_names = {
config.unqual_notifications_queue_name(retry=retry)
for retry in (False, True)
}
def has_notification_queue(handler) -> bool:
try:
queue = handler.queue
except AttributeError:
return False
else:
resource_name, _ = config.unqualified_resource_name(queue)
return resource_name in notification_queue_names
return frozenset((handler.name for handler in vars(indexer).values()
if has_notification_queue(handler)))
def main():
static_dir = os.path.join(parent_dir, 'apidev_static')
web_page = os.path.join(static_dir, 'swagger-editor.html')
host, port = 'localhost', 8787
server_url = f"http://{host}:{port}"
httpd = HTTPServer((host, port), SimpleHTTPRequestHandler)
address = f"{server_url}/{os.path.relpath(web_page)}?url={server_url}/{os.path.relpath(parent_dir)}/{spec_file}"
print(f'Open {address} in browser to validate changes.')
service = load_app_module('service')
event_handler = UpdateHandler(service)
write_specs(service.app)
observer = Observer()
observer.schedule(event_handler,
path=os.path.dirname(service.__file__),
recursive=False)
observer.start()
httpd.serve_forever()
from azul import (
config, )
from azul.modules import (
load_app_module, )
from azul.template import (
emit, )
suffix = '-' + config.deployment_stage
assert config.indexer_name.endswith(suffix)
indexer = load_app_module('indexer')
emit({
"version": "2.0",
"app_name": config.
indexer_name[:-len(suffix)], # Chalice appends stage name implicitly
"api_gateway_stage": config.deployment_stage,
"manage_iam_role": False,
"iam_role_arn": "${var.role_arn}",
"environment_variables": config.lambda_env,
"minimum_compression_size": config.minimum_compression_size,
"lambda_timeout": config.api_gateway_lambda_timeout,
"lambda_memory_size": 128,
"stages": {
config.deployment_stage: {
"lambda_functions": {
indexer.contribute.name: {
"reserved_concurrency":
config.contribution_concurrency(retry=False),
"lambda_memory_size":
256,
def test(self, mock_uuid, mock_helper):
service = load_app_module('service', unit_test=True)
# In a LocalAppTestCase we need the actual state machine name
state_machine_name = config.state_machine_name(service.generate_manifest.name)
with responses.RequestsMock() as helper:
helper.add_passthru(str(self.base_url))
for fetch in (True, False):
with self.subTest(fetch=fetch):
execution_id = '6c9dfa3f-e92e-11e8-9764-ada973595c11'
mock_uuid.return_value = execution_id
format_ = ManifestFormat.compact
filters = Filters(explicit={'organ': {'is': ['lymph node']}},
source_ids={'6aaf72a6-0a45-5886-80cf-48f8d670dc26'})
params = {
'catalog': self.catalog,
'format': format_.value,
'filters': json.dumps(filters.reify(service_config=MagicMock(),
explicit_only=True))
}
path = '/manifest/files'
object_url = 'https://url.to.manifest?foo=bar'
file_name = 'some_file_name'
object_key = f'manifests/{file_name}'
manifest_url = self.base_url.set(path=path,
args=dict(params, objectKey=object_key))
manifest = Manifest(location=object_url,
was_cached=False,
format_=format_,
catalog=self.catalog,
filters=filters,
object_key=object_key,
file_name=file_name)
url = self.base_url.set(path=path, args=params)
if fetch:
url.path.segments.insert(0, 'fetch')
partitions = (
ManifestPartition(index=0,
is_last=False,
file_name=None,
config=None,
multipart_upload_id=None,
part_etags=None,
page_index=None,
is_last_page=None,
search_after=None),
ManifestPartition(index=1,
is_last=False,
file_name=file_name,
config={},
multipart_upload_id='some_upload_id',
part_etags=('some_etag',),
page_index=512,
is_last_page=False,
search_after=('foo', 'doc#bar'))
)
with mock.patch.object(ManifestService, 'get_manifest') as mock_get_manifest:
for i, expected_status in enumerate(3 * [301] + [302]):
response = requests.get(str(url), allow_redirects=False)
if fetch:
self.assertEqual(200, response.status_code)
response = response.json()
self.assertEqual(expected_status, response.pop('Status'))
headers = response
else:
self.assertEqual(expected_status, response.status_code)
headers = response.headers
if expected_status == 301:
self.assertGreaterEqual(int(headers['Retry-After']), 0)
url = furl(headers['Location'])
if i == 0:
state = dict(format_=format_.value,
catalog=self.catalog,
filters=filters.to_json(),
object_key=self.object_key,
authentication=None,
partition=partitions[0].to_json())
mock_helper.start_execution.assert_called_once_with(
state_machine_name,
execution_id,
execution_input=state
)
mock_helper.describe_execution.assert_not_called()
mock_helper.reset_mock()
mock_helper.describe_execution.return_value = {'status': 'RUNNING'}
elif i == 1:
mock_get_manifest.return_value = partitions[1]
state = self.app_module.generate_manifest(state, None)
self.assertEqual(partitions[1],
ManifestPartition.from_json(state['partition']))
mock_get_manifest.assert_called_once_with(
format_=ManifestFormat(state['format_']),
catalog=state['catalog'],
filters=Filters.from_json(state['filters']),
partition=partitions[0],
authentication=None,
object_key=state['object_key']
)
mock_get_manifest.reset_mock()
mock_helper.start_execution.assert_not_called()
mock_helper.describe_execution.assert_called_once()
mock_helper.reset_mock()
# simulate absence of output due eventual consistency
mock_helper.describe_execution.return_value = {'status': 'SUCCEEDED'}
elif i == 2:
mock_get_manifest.return_value = manifest
mock_helper.start_execution.assert_not_called()
mock_helper.describe_execution.assert_called_once()
mock_helper.reset_mock()
mock_helper.describe_execution.return_value = {
'status': 'SUCCEEDED',
'output': json.dumps(
self.app_module.generate_manifest(state, None)
)
}
elif i == 3:
mock_get_manifest.assert_called_once_with(
format_=ManifestFormat(state['format_']),
catalog=state['catalog'],
filters=Filters.from_json(state['filters']),
partition=partitions[1],
authentication=None,
object_key=state['object_key']
)
mock_get_manifest.reset_mock()
mock_helper.start_execution.assert_not_called()
mock_helper.describe_execution.assert_called_once()
expected_url = str(manifest_url) if fetch else object_url
self.assertEqual(expected_url, str(url))
mock_helper.reset_mock()
manifest_states = [
manifest,
CachedManifestNotFound,
CachedManifestSourcesChanged
]
with mock.patch.object(ManifestService,
'get_cached_manifest_with_object_key',
side_effect=manifest_states):
for manifest in manifest_states:
with self.subTest(manifest=manifest):
self.assertEqual(object_key, manifest_url.args['objectKey'])
response = requests.get(str(manifest_url), allow_redirects=False)
if isinstance(manifest, Manifest):
self.assertEqual(302, response.status_code)
self.assertEqual(object_url, response.headers['Location'])
else:
if manifest is CachedManifestNotFound:
cause = 'expired'
elif manifest is CachedManifestSourcesChanged:
cause = 'become invalid due to an authorization change'
else:
assert False
msg = f'GoneError: The requested manifest has {cause}, please request a new one'
self.assertEqual(410, response.status_code)
self.assertEqual(msg, response.json()['Message'])
from azul import (
config, )
from azul.deployment import (
aws, )
from azul.modules import (
load_app_module, )
direct_access_role = config.dss_direct_access_role('service')
service = load_app_module('service')
policy = {
"Version":
"2012-10-17",
"Statement": [
{
"Effect":
"Allow",
"Action": [
"logs:CreateLogGroup", "logs:CreateLogStream",
"logs:PutLogEvents"
],
"Resource":
"arn:aws:logs:*:*:*"
},
{
"Effect":
"Allow",
"Action": [
"es:ESHttpDelete", "es:ESHttpGet", "es:ESHttpHead",
"es:ESHttpPut", "es:ESHttpPost", "es:ESHttpDelete"
],
def on_modified(self, event):
if event.src_path == self.tracked_file:
self.service = load_app_module('service')
write_specs(self.service.app)
print('Spec updated')