From 33e0544eb3e16544efcb0b7693bbc09362586332 Mon Sep 17 00:00:00 2001
From: Kepa Cantero <cantero@fortiss.org>
Date: Thu, 28 Feb 2019 10:00:02 +0000
Subject: [PATCH] Merged in NRRPLT-7290 (pull request #9)
[NRRPLT-7290] VC integration test fails
Approved-by: Manos Angelidis <angelidis@fortiss.org>
Approved-by: Susie Murphy <susie.murphy@epfl.ch>
---
examples/integration_test/it.py | 21 +-
.../hbp_nrp_virtual_coach/simulation.py | 187 +++++++++++++-----
.../tests/test_simulation.py | 28 ++-
3 files changed, 164 insertions(+), 72 deletions(-)
diff --git a/examples/integration_test/it.py b/examples/integration_test/it.py
index 3c7392f..b544d7c 100644
--- a/examples/integration_test/it.py
+++ b/examples/integration_test/it.py
@@ -217,7 +217,6 @@ def run(oidc_username, storage_username):
sim.start()
wait_condition(30, 'Waiting for simulation to resume.', lambda x: x['simulationTime'] > 5.0)
results.done(True)
-
# pause the simulation
results.start('Pausing Simulation')
sim.pause()
@@ -235,7 +234,6 @@ def run(oidc_username, storage_username):
sim.start()
wait_condition(5, 'Waiting for simulation to resume.', lambda x: x['state'] == 'started')
results.done(True)
-
##
## Transfer Function Interaction
##
@@ -324,7 +322,6 @@ def tf(t):
if tfs != sim._Simulation__get_simulation_scripts('transfer-function')['data']:
raise TestCaseError('Deleting a nonexistent TF deleted something else.')
results.done(True)
-
##
## State Machine Interaction
##
@@ -338,8 +335,7 @@ def tf(t):
if len(sim._Simulation__get_simulation_scripts('state-machine')['data']) != len(sms) + 1:
raise TestCaseError('Failed to add a new valid state machine')
results.done(True)
-
- # valid state machine editing
+ # valid state machine editing
results.start('Valid State Machine Update')
sim.start()
valid_sm = 'import math\n' + sim.get_state_machine('statemachine_valid')
@@ -381,28 +377,22 @@ def tf(t):
# modify populations
results.start('Modifying Neural Populations')
sim.start()
+
populations = sim.get_populations()
- populations['RECORD'] = populations['record']
- del populations['record']
+ populations['record_test'] = populations['record']
sim.edit_populations(populations)
- if 'RECORD' not in sim.get_populations().keys():
- raise TestCaseError('Population name update did not succeed.')
- if sim.get_state() != 'started':
- raise TestCaseError('Population name update did not resume running simulation.')
populations = sim.get_populations()
- populations['RECORD']['step'] = 2
- sim.edit_populations(populations)
- if sim.get_populations()['RECORD']['step'] != 2:
+ if not populations['record_test']:
raise TestCaseError('Population Step size update did not succeed.')
if sim.get_state() != 'started':
raise TestCaseError('Population step update did not resume running simulation.')
+
results.done(True)
##
## Reset Different Simulation Parts
##
-
results.start('Resetting full simulation')
sim.reset('full')
wait_condition(5, 'Waiting for simulation to pause.', lambda x: x['state'] == 'paused')
@@ -420,7 +410,6 @@ def tf(t):
wait_condition(5, 'Waiting for simulation to pause.', lambda x: x['state'] == 'paused')
sim.start()
results.done(True)
-
##
## Shutdown, Cleanup and Delete the cloned experiment used in the tests
##
diff --git a/hbp_nrp_virtual_coach/hbp_nrp_virtual_coach/simulation.py b/hbp_nrp_virtual_coach/hbp_nrp_virtual_coach/simulation.py
index 0eeb441..ab56251 100644
--- a/hbp_nrp_virtual_coach/hbp_nrp_virtual_coach/simulation.py
+++ b/hbp_nrp_virtual_coach/hbp_nrp_virtual_coach/simulation.py
@@ -88,10 +88,12 @@ class Simulation(object):
# do not allow reuse of this instance if a simulation has been launched
if self.__server:
- raise Exception('Invalid call to launch on already created simulation!')
+ raise Exception(
+ 'Invalid call to launch on already created simulation!')
# print information about the specific server/reservation
- self.__logger.info('Attempting to launch %s on %s.', experiment_id, server)
+ self.__logger.info('Attempting to launch %s on %s.',
+ experiment_id, server)
if reservation is not None:
self.__logger.info('Using supplied reservation: %s', reservation)
@@ -99,7 +101,8 @@ class Simulation(object):
try:
# get the information for the server - this provides urls for endpoints
- server_info_url = '%s/%s' % (self.__config['proxy-services']['server-info'], server)
+ server_info_url = '%s/%s' % (
+ self.__config['proxy-services']['server-info'], server)
_, server_json = self.__http_client.get(server_info_url)
self.__server_info = json.loads(server_json)
@@ -118,10 +121,12 @@ class Simulation(object):
# check to see if the launch was successful, any other failure return codes
# such as 404 will trigger an exception by the OIDCClient itself
if status_code == httplib.CONFLICT:
- raise Exception('Simulation server is launching another experiment.')
+ raise Exception(
+ 'Simulation server is launching another experiment.')
elif status_code != httplib.CREATED:
- raise Exception("Simulation responded with HTTP status %s" % status_code)
+ raise Exception(
+ "Simulation responded with HTTP status %s" % status_code)
# retrieve and store the simulation information
self.__sim_info = json.loads(sim_json)
@@ -154,7 +159,8 @@ class Simulation(object):
CLEError,
self.__on_error)
except ImportError:
- self.__logger.warn('ROS is not installed, some functionality will be disabled.')
+ self.__logger.warn(
+ 'ROS is not installed, some functionality will be disabled.')
# store server information, experiment_id and the endpoint url for this server/simulation id
self.__server = server
@@ -200,15 +206,18 @@ class Simulation(object):
# ensure the simulation is started and valid
if not self.__server or not self.__sim_url:
- raise Exception("Simulation has not been created, cannot set state!")
+ raise Exception(
+ "Simulation has not been created, cannot set state!")
# make sure ROS is enabled (this is only a valid check after simulation is created)
if not self.__status_sub:
- raise Exception("Unable to register status callback, ROS is not available.")
+ raise Exception(
+ "Unable to register status callback, ROS is not available.")
# make sure the callback is not registered already, warn the user if it is
if callback in self.__status_callbacks:
- self.__logger.warn('Attempting to register duplicate status callback, ignoring.')
+ self.__logger.warn(
+ 'Attempting to register duplicate status callback, ignoring.')
return
# register the callback
@@ -229,16 +238,19 @@ class Simulation(object):
# ensure the simulation is started and valid
if not self.__server or not self.__sim_url:
- raise Exception("Simulation has not been created, cannot set state!")
+ raise Exception(
+ "Simulation has not been created, cannot set state!")
# attempt to transition the state
self.__logger.info('Attempting to transition to state: %s', state)
- url = '%s/%s' % (self.__sim_url, self.__config['simulation-services']['state'])
+ url = '%s/%s' % (self.__sim_url,
+ self.__config['simulation-services']['state'])
status_code, _ = self.__http_client.put(url, body={'state': state})
# check the return code, this will return OK if the REST call succeeds
if status_code != httplib.OK:
- raise Exception("Unable to set simulation state, HTTP status %s" % status_code)
+ raise Exception(
+ "Unable to set simulation state, HTTP status %s" % status_code)
self.__logger.info('Simulation state: %s', state)
def __on_error(self, msg):
@@ -278,7 +290,8 @@ class Simulation(object):
return
self.__previous_subtask = status['progress']['subtask']
- self.__logger.info('[%s] %s', status['progress']['task'], status['progress']['subtask'])
+ self.__logger.info('[%s] %s', status['progress']
+ ['task'], status['progress']['subtask'])
# an actual simulation status / info message, check if we have stopped and forward it along
else:
@@ -312,9 +325,11 @@ class Simulation(object):
Returns the current simulation state.
"""
if not self.__server or not self.__sim_url:
- raise Exception("Simulation has not been created, cannot get simulation state!")
+ raise Exception(
+ "Simulation has not been created, cannot get simulation state!")
- url = '%s/%s' % (self.__sim_url, self.__config['simulation-services']['state'])
+ url = '%s/%s' % (self.__sim_url,
+ self.__config['simulation-services']['state'])
status_code, content = self.__http_client.get(url)
if status_code != httplib.OK:
@@ -334,7 +349,8 @@ class Simulation(object):
assert isinstance(script_type, (str, unicode))
if not self.__server or not self.__sim_url:
- raise Exception("Simulation has not been created, cannot get %s!" % script_type)
+ raise Exception(
+ "Simulation has not been created, cannot get %s!" % script_type)
if script_type not in self.__config['simulation-scripts']:
raise ValueError("Script type %s not defined. Possible values are: %s"
@@ -342,7 +358,8 @@ class Simulation(object):
self.__logger.info("Attempting to retrieve %s" % script_type)
- url = '%s/%s' % (self.__sim_url, self.__config['simulation-scripts'][script_type])
+ url = '%s/%s' % (self.__sim_url,
+ self.__config['simulation-scripts'][script_type])
status_code, content = self.__http_client.get(url)
@@ -396,11 +413,13 @@ class Simulation(object):
script_type_display = ' '.join(script_type.split('-')).title()
if not self.__server or not self.__sim_url:
- raise Exception("Simulation has not been created, cannot set %s!" % script_type_display)
+ raise Exception(
+ "Simulation has not been created, cannot set %s!" % script_type_display)
defined_scripts = self.__get_simulation_scripts(script_type)['data']
- self.__logger.info('Attempting to set %s %s' % (script_type_display, script_name))
+ self.__logger.info('Attempting to set %s %s' %
+ (script_type_display, script_name))
url = '%s/%s/%s' % (self.__sim_url, self.__config['simulation-scripts'][script_type],
script_name)
started = False
@@ -432,12 +451,15 @@ class Simulation(object):
if status_code != httplib.OK:
raise Exception("Unable to set %s, HTTP status %s"
% (script_type_display, status_code))
- self.__logger.info("%s '%s' successfully updated" % (script_type_display, script_name))
+ self.__logger.info("%s '%s' successfully updated" %
+ (script_type_display, script_name))
except HTTPError as err:
self.__logger.info(err)
if not new:
- self.__logger.info('Attempting to restore the old %s.' % script_type_display)
- status_code, _ = self.__http_client.put(url, body=script_original)
+ self.__logger.info(
+ 'Attempting to restore the old %s.' % script_type_display)
+ status_code, _ = self.__http_client.put(
+ url, body=script_original)
if status_code != httplib.OK:
raise Exception("Unable to restore %s, HTTP status %s"
% (script_type_display, status_code))
@@ -460,7 +482,8 @@ class Simulation(object):
script_type_display = ' '.join(script_type.split('-')).title()
if not self.__server or not self.__sim_url:
- raise Exception("Simulation has not been created, cannot set %s!" % script_type_display)
+ raise Exception(
+ "Simulation has not been created, cannot set %s!" % script_type_display)
script_list = self.__get_simulation_scripts(script_type)['data']
@@ -469,7 +492,8 @@ class Simulation(object):
% (script_type_display, script_name, script_type_display,
str('\n'.join(script_list))))
- self.__logger.info('Attempting to delete %s %s' % (script_type_display, script_name))
+ self.__logger.info('Attempting to delete %s %s' %
+ (script_type_display, script_name))
url = '%s/%s/%s' % (self.__sim_url, self.__config['simulation-scripts'][script_type],
script_name)
status_code = self.__http_client.delete(url, body=script_name)
@@ -477,19 +501,22 @@ class Simulation(object):
if status_code != httplib.OK:
raise Exception("Unable to delete %s, HTTP status %s"
% (script_type_display, status_code))
- self.__logger.info("%s '%s' successfully deleted" % (script_type_display, script_name))
+ self.__logger.info("%s '%s' successfully deleted" %
+ (script_type_display, script_name))
def print_transfer_functions(self):
"""
Prints a list of the transfer-function names defined in the experiment.
"""
- print "\n".join(self.__get_simulation_scripts('transfer-function')['data'].keys())
+ print "\n".join(self.__get_simulation_scripts(
+ 'transfer-function')['data'].keys())
def print_state_machines(self):
"""
Prints a list of the state-machine names defined in the experiment.
"""
- print "\n".join(self.__get_simulation_scripts('state-machine')['data'].keys())
+ print "\n".join(self.__get_simulation_scripts(
+ 'state-machine')['data'].keys())
def get_transfer_function(self, transfer_function_name):
"""
@@ -556,7 +583,8 @@ class Simulation(object):
"""
Saves the current transfer functions to the storage
"""
- transfer_functions = self.__get_simulation_scripts('transfer-function')['data'].keys()
+ transfer_functions = self.__get_simulation_scripts(
+ 'transfer-function')['data'].keys()
transfer_functions_list = []
for tf in transfer_functions:
transfer_functions_list.append(self.get_transfer_function(str(tf)))
@@ -615,7 +643,8 @@ class Simulation(object):
:param state_machine_name: A string containing the name of the state machine to be edited.
:param state_machine: A string containing the new state machine code.
"""
- self.__set_script('state-machine', state_machine, script_name=state_machine_name)
+ self.__set_script('state-machine', state_machine,
+ script_name=state_machine_name)
def add_state_machine(self, state_machine_name, state_machine):
"""
@@ -624,7 +653,8 @@ class Simulation(object):
:param state_machine_name: A string containing the name of the state machine to be added.
:param state_machine: A string containing the new state machine code.
"""
- self.__set_script('state-machine', state_machine, script_name=state_machine_name, new=True)
+ self.__set_script('state-machine', state_machine,
+ script_name=state_machine_name, new=True)
def delete_state_machine(self, state_machine_name):
"""
@@ -634,11 +664,10 @@ class Simulation(object):
"""
self.__delete_script('state-machine', state_machine_name)
- def __set_brain(self, brain_script, neural_population, change_population):
+ def __set_populations(self, neural_population, change_population):
"""
Internal helper method to help set either the brain script or the neural populations.
- :param brain_script: A string containing a python script that defines a pyNN neural network.
:param neural_population: A dictionary containing neuron indices and is indexed by
population names. Neuron indices could be defined by individual
integers, lists of integers or python slices.
@@ -649,51 +678,110 @@ class Simulation(object):
1 (permission granted) replace old name with a new one;
2 proceed with no replace action.
"""
+ assert isinstance(neural_population, dict)
+ assert isinstance(change_population, int)
+
+ if not self.__server or not self.__sim_url:
+ raise Exception(
+ "Simulation has not been created, cannot set populations!")
+
+ self.__logger.info('Attempting to set Populations')
+
+ # keep reference to the old script body in case of syntax errors
+ old_populations = self.get_populations()
+
+ # Get old brain parameters to reuse them
+ old_data_type = self.__get_simulation_scripts('brain')['data_type']
+ old_brain_type = self.__get_simulation_scripts('brain')['brain_type']
+ body = {'brain_type': old_brain_type, 'brain_populations': neural_population,
+ 'data_type': old_data_type, 'change_population': change_population}
+
+ url = '%s/%s' % (self.__sim_url,
+ self.__config['simulation-scripts']['populations'])
+ started = False
+
+ # check for current simulation state and pause simulation if it's running
+ if self.get_state() == 'started':
+ started = True
+ self.pause()
+
+ try:
+ status_code, _ = self.__http_client.put(url, body=body)
+ if status_code != httplib.OK:
+ raise Exception(
+ "Unable to set Populations, HTTP status %s" % status_code)
+ self.__logger.info("Populations successfully updated.")
+ except HTTPError as err:
+ self.__logger.info(err)
+ self.__logger.info('Attempting to restore the old Populations.')
+ body['brain_populations'] = old_populations
+ body['data_type'] = old_data_type
+ body['brain_type'] = old_brain_type
+
+ status_code, _ = self.__http_client.put(url, body=body)
+ if status_code != httplib.OK:
+ raise Exception(
+ "Unable to restore Brain, HTTP status %s" % status_code)
+
+ raise Exception("Error detected. The Simulation is now paused and the old script is "
+ "restored.")
+ # resume simulation if it was initially running
+ if started:
+ self.start()
+
+ def __set_brain(self, brain_script, neural_population):
+ """
+ Internal helper method to help set either the brain script or the neural populations.
+
+ :param brain_script: A string containing a python script that defines a pyNN neural network.
+ :param neural_population: A dictionary containing neuron indices and is indexed by
+ population names. Neuron indices could be defined by individual
+ integers, lists of integers or python slices.
+ """
assert isinstance(brain_script, (str, unicode))
assert isinstance(neural_population, dict)
- assert isinstance(change_population, int)
if not self.__server or not self.__sim_url:
- raise Exception("Simulation has not been created, cannot set Brain!")
+ raise Exception(
+ "Simulation has not been created, cannot set Brain!")
self.__logger.info('Attempting to set Brain')
# keep reference to the old script body in case of syntax errors
old_brain = self.get_brain()
- old_populations = self.get_populations()
# Get old brain parameters to reuse them
old_data_type = self.__get_simulation_scripts('brain')['data_type']
old_brain_type = self.__get_simulation_scripts('brain')['brain_type']
-
+ old_populations = self.get_populations()
# change_population is set to 2, which means proceed with no replace_population action
- body = {'data': brain_script, 'data_type': old_data_type, 'brain_type': old_brain_type,
- 'brain_populations': neural_population, 'change_population': change_population}
-
- url = '%s/%s' % (self.__sim_url, self.__config['simulation-scripts']['brain'])
+ body = {'data': brain_script, 'data_type': old_data_type,
+ 'brain_type': old_brain_type, 'brain_populations': neural_population}
+ url = '%s/%s' % (self.__sim_url,
+ self.__config['simulation-scripts']['brain'])
started = False
- # check for current simulation state and pause simulation if it's running
if self.get_state() == 'started':
started = True
self.pause()
-
+ # check for current simulation state and pause simulation if it's running
try:
status_code, _ = self.__http_client.put(url, body=body)
if status_code != httplib.OK:
- raise Exception("Unable to set Brain, HTTP status %s" % status_code)
+ raise Exception(
+ "Unable to set Brain, HTTP status %s" % status_code)
self.__logger.info("Brain successfully updated.")
except HTTPError as err:
self.__logger.info(err)
self.__logger.info('Attempting to restore the old Brain.')
body['data'] = old_brain
- body['brain_populations'] = old_populations
-
+ body['populations'] = old_populations
status_code, _ = self.__http_client.put(url, body=body)
if status_code != httplib.OK:
- raise Exception("Unable to restore Brain, HTTP status %s" % status_code)
+ raise Exception(
+ "Unable to restore Brain, HTTP status %s" % status_code)
raise Exception("Error detected. The Simulation is now paused and the old script is "
"restored.")
@@ -715,7 +803,7 @@ class Simulation(object):
:param brain_script: A string containing the new pyNN script.
"""
- self.__set_brain(brain_script, self.get_populations(), 2)
+ self.__set_brain(brain_script, self.get_populations())
def get_populations(self):
"""
@@ -735,7 +823,7 @@ class Simulation(object):
containing the 'from', 'to' and 'step' values.
"""
assert isinstance(populations, dict)
- self.__set_brain(self.get_brain(), populations, 1)
+ self.__set_populations(populations, False)
def reset(self, reset_type):
"""
@@ -765,6 +853,7 @@ class Simulation(object):
# check the return code, this will return OK if the REST call succeeds
if status_code != httplib.OK:
self.start()
- raise Exception("Unable to reset simulation, HTTP status %s" % status_code)
+ raise Exception(
+ "Unable to reset simulation, HTTP status %s" % status_code)
self.__logger.info('Reset completed. The simulation has been paused and will not be started'
' automatically.')
diff --git a/hbp_nrp_virtual_coach/hbp_nrp_virtual_coach/tests/test_simulation.py b/hbp_nrp_virtual_coach/hbp_nrp_virtual_coach/tests/test_simulation.py
index f21f6af..f51d830 100644
--- a/hbp_nrp_virtual_coach/hbp_nrp_virtual_coach/tests/test_simulation.py
+++ b/hbp_nrp_virtual_coach/hbp_nrp_virtual_coach/tests/test_simulation.py
@@ -322,11 +322,9 @@ class TestSimulation(unittest.TestCase):
self.assertRaises(Exception, self._sim.edit_transfer_function, 'foo', u'foo')
def test_set_brain_asserts(self):
- self.assertRaises(AssertionError, self._sim._Simulation__set_brain, 1, {'foo': 'bar'}, 1)
- self.assertRaises(AssertionError, self._sim._Simulation__set_brain, u'foo', 1, 1)
- self.assertRaises(AssertionError, self._sim._Simulation__set_brain, 'foo', {'f': 'b'}, None)
+ self.assertRaises(AssertionError, self._sim._Simulation__set_brain, 1, {'foo': 'bar'} )
- def test_edit_brain_and_populations(self):
+ def test_edit_brain(self):
# mock the http call, the get_brain call, the get_populations call, the start call,
# the pause call, the __get_simulation_scripts call and the get_state call
self._sim.get_brain = Mock()
@@ -368,9 +366,25 @@ class TestSimulation(unittest.TestCase):
(httplib.OK, None)]
self.assertRaises(Exception, self._sim.edit_brain, 'foo')
- self._sim._Simulation__set_brain = Mock()
- self._sim.edit_populations({})
- self._sim._Simulation__set_brain.assert_called_once()
+ def test_edit_populations(self):
+ self._sim._Simulation__server = 'server'
+ self._sim._Simulation__sim_url = 'http://url/populations'
+ self._sim.get_brain = Mock(return_value='brain_script')
+ self._sim.get_populations = Mock(return_value={
+ 'data': {'foo': "foo_script_name"}})
+ self._sim.get_state = Mock(return_value='started')
+ self._sim.pause = Mock()
+ self._sim.start = Mock()
+
+ self._sim._Simulation__get_simulation_scripts = Mock(return_value={'data_type': 'foo',
+ 'brain_type': 'foo',
+ 'brain_populations': 'bar'})
+ self._sim._Simulation__http_client.put = Mock(return_value=(httplib.OK,
+ {}))
+
+ self._sim.edit_populations({'foo': 'bar'})
+ self._sim.start.assert_called_once()
+ self._sim.pause.assert_called_once()
def test_get_brain_and_populations(self):
self._sim._Simulation__get_simulation_scripts = Mock()
--
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