def test_slots_override( self ):
# Set local_slots in job destination to specify slots for
# local job runner.
self.job_wrapper.job_destination.params[ "local_slots" ] = 3
self.job_wrapper.command_line = '''echo $GALAXY_SLOTS'''
runner = local.LocalJobRunner( self.app, 1 )
runner.queue_job( self.job_wrapper )
assert self.job_wrapper.stdout.strip() == "3"
def test_metadata_gets_set_if_embedded( self ):
self.job_wrapper.job_destination.params[ "embed_metadata_in_job" ] = "True"
# Kill off cruft for _handle_metadata_externally and make sure job stil works...
self.job_wrapper.external_output_metadata = None
self.app.datatypes_registry.set_external_metadata_tool = None
runner = local.LocalJobRunner( self.app, 1 )
runner.queue_job( self.job_wrapper )
assert os.path.exists( self.job_wrapper.mock_metadata_path )
def test_stopping_job(self):
self.job_wrapper.command_line = '''python -c "import time; time.sleep(15)"'''
runner = local.LocalJobRunner(self.app, 1)
def queue():
runner.queue_job(self.job_wrapper)
t = threading.Thread(target=queue)
t.start()
external_id = self.job_wrapper.wait_for_external_id()
assert psutil.pid_exists(external_id)
runner.stop_job(self.job_wrapper)
t.join(1)
assert not psutil.pid_exists(external_id)
def test_stopping_job_at_shutdown(self):
self.job_wrapper.command_line = '''python -c "import time; time.sleep(15)"'''
runner = local.LocalJobRunner(self.app, 1)
self.app.config.monitor_thread_join_timeout = 15
def queue():
runner.queue_job(self.job_wrapper)
t = threading.Thread(target=queue)
t.start()
external_id = self.job_wrapper.wait_for_external_id()
assert psutil.pid_exists(external_id)
runner.shutdown()
t.join(1)
assert not psutil.pid_exists(external_id)
assert "job terminated by Galaxy shutdown" in self.job_wrapper.fail_message
def test_stopping_job(self):
self.job_wrapper.command_line = '''python -c "import time; time.sleep(15)"'''
runner = local.LocalJobRunner(self.app, 1)
def queue():
runner.queue_job(self.job_wrapper)
t = threading.Thread(target=queue)
t.start()
external_id = self.job_wrapper.wait_for_external_id()
mock_job = bunch.Bunch(
get_external_output_metadata=lambda: None,
get_job_runner_external_id=lambda: str(external_id),
get_id=lambda: 1)
assert psutil.pid_exists(external_id)
runner.stop_job(mock_job)
t.join(1)
assert not psutil.pid_exists(external_id)
def test_stopping_job(self):
self.job_wrapper.command_line = '''python -c "import time; time.sleep(15)"'''
runner = local.LocalJobRunner(self.app, 1)
def queue():
runner.queue_job(self.job_wrapper)
t = threading.Thread(target=queue)
t.start()
while True:
if self.job_wrapper.external_id:
break
time.sleep(.01)
external_id = self.job_wrapper.external_id
mock_job = bunch.Bunch(
get_external_output_metadata=lambda: None,
get_job_runner_external_id=lambda: str(external_id),
get_id=lambda: 1)
runner.stop_job(mock_job)
t.join(1)
def test_metadata_gets_set( self ):
runner = local.LocalJobRunner( self.app, 1 )
runner.queue_job( self.job_wrapper )
assert os.path.exists( self.job_wrapper.mock_metadata_path )
def test_exit_code( self ):
self.job_wrapper.command_line = '''sh -c "exit 4"'''
runner = local.LocalJobRunner( self.app, 1 )
runner.queue_job( self.job_wrapper )
assert self.job_wrapper.exit_code == 4
def test_default_slots( self ):
self.job_wrapper.command_line = '''echo $GALAXY_SLOTS'''
runner = local.LocalJobRunner( self.app, 1 )
runner.queue_job( self.job_wrapper )
assert self.job_wrapper.stdout.strip() == "1"
def test_galaxy_lib_on_path( self ):
self.job_wrapper.command_line = '''python -c "import galaxy.util"'''
runner = local.LocalJobRunner( self.app, 1 )
runner.queue_job( self.job_wrapper )
assert self.job_wrapper.exit_code == 0
def test_run( self ):
self.job_wrapper.command_line = "echo HelloWorld"
runner = local.LocalJobRunner( self.app, 1 )
runner.queue_job( self.job_wrapper )
assert self.job_wrapper.stdout.strip() == "HelloWorld"
def test_shutdown_no_jobs(self):
self.app.config.monitor_thread_join_timeout = 5
runner = local.LocalJobRunner(self.app, 1)
runner.shutdown()
