def test_feature_extraction(
server_setup,
get_interface_params,
discoverable_plugins,
ond_config_with_feature_extraction,
):
"""
Test feature extraction.
Args:
server_setup (tuple): Tuple containing url and result directory
get_interface_params (tuple): Tuple to configure par interface
discoverable_plugins (dict): Dictionary with the plugins
ond_config_with_feature_extraction (str): Path to json file
Return:
None
"""
config_directory, config_name = get_interface_params
par_interface = ParInterface(config_name, config_directory)
ond = SailOn(discoverable_plugins, "", par_interface,
ond_config_with_feature_extraction)
ond.run_protocol()
local_interface = LocalInterface(config_name, config_directory)
SailOn(discoverable_plugins, "", local_interface,
ond_config_with_feature_extraction)
ond.run_protocol()
def test_initialize(server_setup, get_interface_params, discoverable_plugins,
ond_config):
"""
Test ond protocol initialization.
Args:
server_setup (tuple): Tuple containing url and result directory
get_interface_params (tuple): Tuple to configure par interface
discoverable_plugins (dict): Dictionary with the plugins
ond_config (str): Path to json file
Return:
None
"""
config_directory, config_name = get_interface_params
par_interface = ParInterface(config_name, config_directory)
SailOn(discoverable_plugins, "", par_interface, ond_config)
local_interface = LocalInterface(config_name, config_directory)
SailOn(discoverable_plugins, "", local_interface, ond_config)
def test_reaction_baseline(
server_setup,
get_ar_interface_params,
discoverable_plugins,
ond_config_with_reaction_baseline,
):
"""
Test reaction baseline with a detector.
Args:
server_setup (tuple): Tuple containing url and result directory
get_ar_interface_params (tuple): Tuple to configure par interface
discoverable_plugins (dict): Dictionary with the plugins
ond_config_with_reaction_baseline(str): Path to json file
Return:
None
"""
config_directory, config_name = get_ar_interface_params
local_interface = LocalInterface(config_name, config_directory)
ond = SailOn(discoverable_plugins, "", local_interface,
ond_config_with_reaction_baseline)
ond.run_protocol()
def run_protocol(
self, config: Dict[str, Any],
extra_plugins: Dict[str, Any] = dict()) -> None:
"""Run the protocol by printout out the config.
Args:
Config passed in uses 3 parameters to control the launching of the protocols
- protocol: either 'ond' or 'condda' to define which protocol to run
- harness: either 'local' or 'par' to define which harness to use
- workdir: a directory to save all the information from the run including
- Config
- Output of algorithm
Example:
>>> from sailon_tinker_launcher.main import *
>>> dpath = ub.ensure_app_cache_dir('tinker/tests')
>>> config = get_debug_config()
>>> self = LaunchSailonProtocol()
>>> self.run_protocol(config)
>>> assert(self.working_folder.exists())
>>> ub.delete(str(self.working_folder), verbose=False)
"""
# Setup working folder and create new config for this run
self.working_folder, working_config_fp, privileged_config, config = self.setup_experiment(
config)
# Now experiment setup, start a new logger for this
fh = logging.FileHandler(
self.working_folder /
f'{datetime.now().strftime("%Y_%m_%d-%I_%M_%S_%p")}.log')
fh.setLevel(logging.DEBUG)
formatter = logging.Formatter(
'[%(asctime)s][%(name)s][%(levelname)s] - %(message)s')
fh.setFormatter(formatter)
logging.getLogger().addHandler(fh)
log.info(f'Config Filepath: {working_config_fp}')
log.info(f'Config: \n{json.dumps(config, indent=4)}')
# Load the harness
# This config is not used but will throw error if not pointed at
harnness_config_path = Path(protocol_folder.__file__).parent
if privileged_config['harness'] == 'local':
log.info('Loading Local Harness')
harness = LocalInterface('configuration.json',
str(harnness_config_path))
harness.result_directory = config['detectors']['csv_folder']
harness.file_provider.results_folder = config['detectors'][
'csv_folder']
elif privileged_config['harness'] == 'par':
log.info('Loading Par Harness')
harness = ParInterface('configuration.json',
str(harnness_config_path))
harness.folder = config['detectors']['csv_folder']
else:
raise AttributeError(
f'Valid harnesses "local" or "par". '
f'Given harness "{privileged_config["harness"]}" ')
# Get the plugins
plugins = ub.dict_union(discoverable_plugins('tinker'), extra_plugins)
log.debug('Plugins found:')
log.debug(plugins)
# Load the protocol
if privileged_config['protocol'] == 'ond':
log.info('Running OND Protocol')
run_protocol = OND(discovered_plugins=plugins,
algorithmsdirectory='',
harness=harness,
config_file=str(working_config_fp))
elif privileged_config['protocol'] == 'condda':
log.info('Running Condda Protocol')
run_protocol = Condda(discovered_plugins=plugins,
algorithmsdirectory='',
harness=harness,
config_file=str(working_config_fp))
else:
raise AttributeError(
f'Please set protocol to either "ond" or "condda". '
f'"{privileged_config["protocol"]}" in the config files')
# Run the protocol
run_protocol.run_protocol()
log.info('Protocol Finished')
logging.getLogger().removeHandler(fh)