def mock_delivery(cmd):
project_id = f"snpseq{random.randint(0, 10**10):010d}"
dds_output = f"""Current user: bio
Project created with id: {project_id}
User forskare was associated with Project {project_id} as Owner=True. An e-mail notification has not been sent.
Invitation sent to [email protected]. The user should have a valid account to be added to a
project"""
log.debug(f"Mock is called with {cmd}")
shell = False
if any(cmd[0].endswith(delivery_prgm)
for delivery_prgm in ['dds', 'moverinfo', 'to_outbox']):
new_cmd = ['sleep', str(self.mock_duration)]
if cmd[0].endswith('dds') and 'project' in cmd:
new_cmd += ['&&', 'echo', f'"{dds_output}"']
new_cmd = " ".join(new_cmd)
shell = True
else:
new_cmd = cmd
log.debug(f"Running mocked {new_cmd}")
p = Subprocess(new_cmd,
stdout=PIPE,
stderr=PIPE,
stdin=PIPE,
shell=shell)
return Execution(pid=p.pid, process_obj=p)
def run(self, cmd):
if self.throw:
raise Exception("Test the exception handling...")
mock_process = mock.MagicMock()
execution = Execution(pid=random.randint(1, 1000),
process_obj=mock_process)
return execution
def setUp(self):
self.staging_order1 = StagingOrder(id=1,
source='/test/this',
staging_target='/foo',
status=StagingStatus.pending)
self.mock_general_project_repo = mock.MagicMock()
stdout_mimicing_rsync = """
Number of files: 1 (reg: 1)
Number of created files: 0
Number of deleted files: 0
Number of regular files transferred: 1
Total file size: 207,707,566 bytes
Total transferred file size: 207,707,566 bytes
Literal data: 207,707,566 bytes
Matched data: 0 bytes
File list size: 0
File list generation time: 0.001 seconds
File list transfer time: 0.000 seconds
Total bytes sent: 207,758,378
Total bytes received: 35
sent 207,758,378 bytes received 35 bytes 138,505,608.67 bytes/sec
total size is 207,707,566 speedup is 1.00
"""
mock_process = mock.MagicMock()
mock_execution = Execution(pid=random.randint(1, 1000),
process_obj=mock_process)
self.mock_external_runner_service = mock.create_autospec(
ExternalProgramService)
self.mock_external_runner_service.run.return_value = mock_execution
@coroutine
def wait_as_coroutine(x):
return ExecutionResult(stdout=stdout_mimicing_rsync,
stderr="",
status_code=0)
self.mock_external_runner_service.wait_for_execution = wait_as_coroutine
mock_staging_repo = mock.MagicMock()
mock_staging_repo.get_staging_order_by_id.return_value = self.staging_order1
mock_staging_repo.create_staging_order.return_value = self.staging_order1
self.mock_runfolder_repo = mock.MagicMock()
mock_db_session_factory = mock.MagicMock()
self.staging_service = StagingService(
staging_dir="/tmp",
external_program_service=self.mock_external_runner_service,
staging_repo=mock_staging_repo,
runfolder_repo=self.mock_runfolder_repo,
session_factory=mock_db_session_factory,
project_dir_repo=self.mock_general_project_repo)
self.staging_service.io_loop_factory = MockIOLoop
super(TestStagingService, self).setUp()
def run(cmd):
"""
Run a process and do not wait for it to finish
:param cmd: the command to run as a list, i.e. ['ls','-l', '/']
:return: A instance of Execution
"""
p = Subprocess(cmd, stdout=PIPE, stderr=PIPE, stdin=PIPE)
return Execution(pid=p.pid, process_obj=p)
def setUp(self):
example_mover_stdout = """TestCase_31-ngi2016001-1484739218"""
example_moverinfo_stdout = """Delivered: Jan 19 00:23:31 [1484781811UTC]"""
self.mock_mover_runner = create_autospec(ExternalProgramService)
mock_process = MagicMock()
mock_execution = Execution(pid=random.randint(1, 1000),
process_obj=mock_process)
self.mock_mover_runner.run.return_value = mock_execution
@coroutine
def wait_as_coroutine(x):
return ExecutionResult(stdout=example_mover_stdout,
stderr="",
status_code=0)
self.mock_mover_runner.wait_for_execution = wait_as_coroutine
self.mock_moverinfo_runner = create_autospec(ExternalProgramService)
@coroutine
def mover_info_wait_as_coroutine(x):
return ExecutionResult(stdout=example_moverinfo_stdout,
stderr="",
status_code=0)
self.mock_moverinfo_runner.run_and_wait = MagicMock(
wraps=mover_info_wait_as_coroutine)
self.mock_staging_service = MagicMock()
self.mock_delivery_repo = MagicMock()
self.delivery_order = DeliveryOrder(id=1,
delivery_source="/foo",
delivery_project="TestProj")
self.mock_delivery_repo.create_delivery_order.return_value = self.delivery_order
self.mock_delivery_repo.get_delivery_order_by_id.return_value = self.delivery_order
self.mock_session_factory = MagicMock()
self.mock_path_to_mover = "/foo/bar/"
self.mover_delivery_service = MoverDeliveryService(
external_program_service=None,
staging_service=self.mock_staging_service,
delivery_repo=self.mock_delivery_repo,
session_factory=self.mock_session_factory,
path_to_mover=self.mock_path_to_mover)
# Inject separate external runner instances for the tests, since they need to return
# different information
self.mover_delivery_service.mover_external_program_service = self.mock_mover_runner
self.mover_delivery_service.moverinfo_external_program_service = self.mock_moverinfo_runner
super(TestMoverDeliveryService, self).setUp()
def setUp(self):
example_dds_project_ls_stdout = """[
{
"Last updated": "Thu, 03 Mar 2022 11:46:31 CET",
"PI": "Dungeon master",
"Project ID": "snpseq00001",
"Size": 26956752654,
"Status": "In Progress",
"Title": "Bullywug anatomy"
},
{
"Last updated": "Thu, 03 Mar 2022 10:34:05 CET",
"PI": "matas618",
"Project ID": "snpseq00002",
"Size": 0,
"Status": "In Progress",
"Title": "Site admins project"
}
]
"""
self.mock_mover_runner = create_autospec(ExternalProgramService)
mock_process = MagicMock()
mock_execution = Execution(pid=random.randint(1, 1000), process_obj=mock_process)
self.mock_mover_runner.run.return_value = mock_execution
@coroutine
def wait_as_coroutine(x):
return ExecutionResult(stdout=example_dds_project_ls_stdout, stderr="", status_code=0)
self.mock_mover_runner.wait_for_execution = wait_as_coroutine
self.mock_staging_service = MagicMock()
self.mock_delivery_repo = MagicMock()
self.mock_dds_project_repo = MagicMock()
self.delivery_order = DeliveryOrder(
id=1,
delivery_source="/staging/dir/bar",
delivery_project="snpseq00001",
)
self.mock_delivery_repo.create_delivery_order.return_value = self.delivery_order
self.mock_delivery_repo.get_delivery_order_by_id.return_value = self.delivery_order
self.mock_session_factory = MagicMock()
self.mock_dds_config = {
'log_path': '/foo/bar/log',
}
self.dds_service = DDSService(
external_program_service=ExternalProgramService(),
staging_service=self.mock_staging_service,
staging_dir='/foo/bar/staging_dir',
delivery_repo=self.mock_delivery_repo,
dds_project_repo=self.mock_dds_project_repo,
session_factory=self.mock_session_factory,
dds_conf=self.mock_dds_config
)
# Inject separate external runner instances for the tests, since they need to return
# different information
self.dds_service.mover_external_program_service = self.mock_mover_runner
super(TestDDSService, self).setUp()