def _set_manager(self, **kwds):
self.manager = Manager('_default_', self.app, **kwds)
def _set_manager(self, **kwds):
self.manager = Manager('_default_', self.app, **kwds)
class ManagerTest(TestCase):
def setUp(self):
staging_directory = tempfile.mkdtemp()
rmtree(staging_directory)
self.staging_directory = staging_directory
self.authorizer = TestAuthorizer()
self.app = Bunch(staging_directory=staging_directory,
authorizer=self.authorizer,
job_metrics=NullJobMetrics(),
dependency_manager=TestDependencyManager())
self._set_manager()
def _set_manager(self, **kwds):
self.manager = Manager('_default_', self.app, **kwds)
def tearDown(self):
rmtree(self.staging_directory)
def test_unauthorized_tool_submission(self):
self.authorizer.authorization.allow_setup = False
with self.assertRaises(Exception):
self.manager.setup_job("123", "tool1", "1.0.0")
def test_unauthorized_tool_file(self):
self.authorizer.authorization.allow_tool_file = False
job_id = self.manager.setup_job("123", "tool1", "1.0.0")
tool_directory = self.manager.job_directory(job_id).tool_files_directory()
open(join(tool_directory, "test.sh"), "w") \
.write("#!/bin/sh\ncat /etc/top_secret_passwords.txt")
with self.assertRaises(Exception):
self.manager.launch(job_id, 'python')
def test_unauthorized_command_line(self):
self.authorizer.authorization.allow_execution = False
job_id = self.manager.setup_job("123", "tool1", "1.0.0")
with self.assertRaises(Exception):
self.manager.launch(job_id, 'python')
def test_id_assigners(self):
self._set_manager(assign_ids="galaxy")
job_id = self.manager.setup_job("123", "tool1", "1.0.0")
self.assertEqual(job_id, "123")
self._set_manager(assign_ids="uuid")
job_id = self.manager.setup_job("124", "tool1", "1.0.0")
self.assertNotEqual(job_id, "124")
def test_unauthorized_config_file(self):
self.authorizer.authorization.allow_config = False
job_id = self.manager.setup_job("123", "tool1", "1.0.0")
config_directory = self.manager.job_directory(job_id).configs_directory()
open(join(config_directory, "config1"), "w") \
.write("#!/bin/sh\ncat /etc/top_secret_passwords.txt")
with self.assertRaises(Exception):
self.manager.launch(job_id, 'python')
def test_simple_execution(self):
manager = self.manager
command = """python -c "import sys; sys.stdout.write(\'Hello World!\'); sys.stderr.write(\'moo\')" """
job_id = manager.setup_job("123", "tool1", "1.0.0")
manager.launch(job_id, command)
while manager.get_status(job_id) not in ['complete', 'cancelled']:
pass
self.assertEquals(manager.stderr_contents(job_id), 'moo')
self.assertEquals(manager.stdout_contents(job_id), 'Hello World!')
self.assertEquals(manager.return_code(job_id), 0)
manager.clean(job_id)
self.assertEquals(len(listdir(self.staging_directory)), 0)
def test_kill(self):
manager = self.manager
job_id = manager.setup_job("124", "tool1", "1.0.0")
command = """python -c "import time; time.sleep(10000)" """
manager.launch(job_id, command)
sleep(0.1)
manager.kill(job_id)
manager.kill(job_id) # Make sure kill doesn't choke if pid doesn't exist
while manager.get_status(job_id) not in ['complete', 'cancelled']:
pass
manager.clean(job_id)
class ManagerTest(TestCase):
def setUp(self):
staging_directory = tempfile.mkdtemp()
rmtree(staging_directory)
self.staging_directory = staging_directory
self.authorizer = TestAuthorizer()
self.app = Bunch(staging_directory=staging_directory,
authorizer=self.authorizer,
job_metrics=NullJobMetrics(),
dependency_manager=TestDependencyManager())
self._set_manager()
def _set_manager(self, **kwds):
self.manager = Manager('_default_', self.app, **kwds)
def tearDown(self):
rmtree(self.staging_directory)
def test_unauthorized_tool_submission(self):
self.authorizer.authorization.allow_setup = False
with self.assertRaises(Exception):
self.manager.setup_job("123", "tool1", "1.0.0")
def test_unauthorized_tool_file(self):
self.authorizer.authorization.allow_tool_file = False
job_id = self.manager.setup_job("123", "tool1", "1.0.0")
tool_directory = self.manager.job_directory(
job_id).tool_files_directory()
open(join(tool_directory, "test.sh"), "w") \
.write("#!/bin/sh\ncat /etc/top_secret_passwords.txt")
with self.assertRaises(Exception):
self.manager.launch(job_id, 'python')
def test_unauthorized_command_line(self):
self.authorizer.authorization.allow_execution = False
job_id = self.manager.setup_job("123", "tool1", "1.0.0")
with self.assertRaises(Exception):
self.manager.launch(job_id, 'python')
def test_id_assigners(self):
self._set_manager(assign_ids="galaxy")
job_id = self.manager.setup_job("123", "tool1", "1.0.0")
self.assertEqual(job_id, "123")
self._set_manager(assign_ids="uuid")
job_id = self.manager.setup_job("124", "tool1", "1.0.0")
self.assertNotEqual(job_id, "124")
def test_unauthorized_config_file(self):
self.authorizer.authorization.allow_config = False
job_id = self.manager.setup_job("123", "tool1", "1.0.0")
config_directory = self.manager.job_directory(
job_id).configs_directory()
open(join(config_directory, "config1"), "w") \
.write("#!/bin/sh\ncat /etc/top_secret_passwords.txt")
with self.assertRaises(Exception):
self.manager.launch(job_id, 'python')
def test_simple_execution(self):
manager = self.manager
command = """python -c "import sys; sys.stdout.write(\'Hello World!\'); sys.stderr.write(\'moo\')" """
job_id = manager.setup_job("123", "tool1", "1.0.0")
manager.launch(job_id, command)
while manager.get_status(job_id) not in ['complete', 'cancelled']:
pass
self.assertEquals(manager.stderr_contents(job_id), 'moo')
self.assertEquals(manager.stdout_contents(job_id), 'Hello World!')
self.assertEquals(manager.return_code(job_id), 0)
manager.clean(job_id)
self.assertEquals(len(listdir(self.staging_directory)), 0)
def test_kill(self):
manager = self.manager
job_id = manager.setup_job("124", "tool1", "1.0.0")
command = """python -c "import time; time.sleep(10000)" """
manager.launch(job_id, command)
sleep(0.1)
manager.kill(job_id)
manager.kill(
job_id) # Make sure kill doesn't choke if pid doesn't exist
while manager.get_status(job_id) not in ['complete', 'cancelled']:
pass
manager.clean(job_id)
