def run(self, input, output=None):
if input is None:
raise ACQUAChemistryError("Missing input.")
self._parser = InputParser(input)
self._parser.parse()
driver_return = self._run_driver_from_parser(self._parser, False)
if driver_return[0] == ACQUAChemistry._DRIVER_RUN_TO_HDF5:
logger.info('No further process.')
return {'printable': [driver_return[1]]}
data = run_algorithm(driver_return[1], driver_return[2], True)
if not isinstance(data, dict):
raise ACQUAChemistryError(
"Algorithm run result should be a dictionary")
if logger.isEnabledFor(logging.DEBUG):
logger.debug('Algorithm returned: {}'.format(
json.dumps(data, indent=4)))
convert_json_to_dict(data)
lines, result = self._format_result(data)
logger.info('Processing complete. Final result available')
result['printable'] = lines
if output is not None:
with open(output, 'w') as f:
for line in lines:
print(line, file=f)
return result
def test_load_from_dict(self):
json_dict = self.parser.to_JSON()
p = InputParser(json_dict)
p.parse()
dict1 = json.loads(json.dumps(self.parser.to_dictionary()))
dict2 = json.loads(json.dumps(p.to_dictionary()))
self.assertEqual(dict1, dict2)
def test_save(self):
save_path = self._get_resource_path('output.txt')
self.parser.save_to_file(save_path)
p = InputParser(save_path)
p.parse()
os.remove(save_path)
dict1 = json.loads(json.dumps(self.parser.to_dictionary()))
dict2 = json.loads(json.dumps(p.to_dictionary()))
self.assertEqual(dict1, dict2)
def _run_drive(self, input, save_json_algo_file):
if input is None:
raise ACQUAChemistryError("Missing input.")
self._parser = InputParser(input)
self._parser.parse()
driver_return = self._run_driver_from_parser(self._parser,
save_json_algo_file)
driver_return[1]['input'] = driver_return[2].to_params()
driver_return[1]['input']['name'] = driver_return[2].configuration[
'name']
return driver_return[1]
def test_is_modified(self):
json_dict = self.parser.to_JSON()
p = InputParser(json_dict)
p.parse()
p.set_section_property('optimizer', 'maxfun', 1002)
self.assertTrue(p.is_modified())
self.assertEqual(p.get_section_property('optimizer', 'maxfun'), 1002)
def load_file(self,filename):
if filename is None:
return []
try:
self._parser = InputParser(filename)
self._parser.parse()
uipreferences = UIPreferences()
if uipreferences.get_populate_defaults(True):
self._parser.validate_merge_defaults()
self._parser.commit_changes()
return self._parser.get_section_names()
except:
self._parser = None
raise
def delete_section_property(self, section_name, property_name):
if self._parser is None:
raise ACQUAChemistryError('Input not initialized.')
self._parser.delete_section_property(section_name, property_name)
if InputParser.is_pluggable_section(section_name) and property_name == InputParser.NAME:
self._parser.delete_section_properties(section_name)
def new(self):
try:
dict = {}
jsonfile = os.path.join(os.path.dirname(__file__), 'input_template.json')
with open(jsonfile) as json_file:
dict = json.load(json_file)
self._parser = InputParser(dict)
self._parser.parse()
uipreferences = UIPreferences()
if uipreferences.get_populate_defaults(True):
self._parser.validate_merge_defaults()
self._parser.commit_changes()
return self._parser.get_section_names()
except:
self._parser = None
raise
def test_validate(self):
json_dict = self.parser.to_JSON()
p = InputParser(json_dict)
p.parse()
try:
p.validate_merge_defaults()
except Exception as e:
self.fail(str(e))
p.set_section_property('optimizer', 'dummy', 1002)
self.assertRaises(ACQUAChemistryError, p.validate_merge_defaults)
class TestInputParser(QISKitAcquaChemistryTestCase):
"""InputParser tests."""
def setUp(self):
filepath = self._get_resource_path('test_input_parser.txt')
self.parser = InputParser(filepath)
self.parser.parse()
def test_save(self):
save_path = self._get_resource_path('output.txt')
self.parser.save_to_file(save_path)
p = InputParser(save_path)
p.parse()
os.remove(save_path)
dict1 = json.loads(json.dumps(self.parser.to_dictionary()))
dict2 = json.loads(json.dumps(p.to_dictionary()))
self.assertEqual(dict1, dict2)
def test_load_from_dict(self):
json_dict = self.parser.to_JSON()
p = InputParser(json_dict)
p.parse()
dict1 = json.loads(json.dumps(self.parser.to_dictionary()))
dict2 = json.loads(json.dumps(p.to_dictionary()))
self.assertEqual(dict1, dict2)
def test_is_modified(self):
json_dict = self.parser.to_JSON()
p = InputParser(json_dict)
p.parse()
p.set_section_property('optimizer', 'maxfun', 1002)
self.assertTrue(p.is_modified())
self.assertEqual(p.get_section_property('optimizer', 'maxfun'), 1002)
def test_validate(self):
json_dict = self.parser.to_JSON()
p = InputParser(json_dict)
p.parse()
try:
p.validate_merge_defaults()
except Exception as e:
self.fail(str(e))
p.set_section_property('optimizer', 'dummy', 1002)
self.assertRaises(ACQUAChemistryError, p.validate_merge_defaults)
def set_section_property(self, section_name, property_name, value):
if self._parser is None:
raise ACQUAChemistryError('Input not initialized.')
self._parser.set_section_property(section_name,property_name,value)
if InputParser.is_pluggable_section(section_name) and property_name == InputParser.NAME:
properties = self._parser.get_section_default_properties(section_name)
if isinstance(properties,dict):
properties[ InputParser.NAME] = value
self._parser.delete_section_properties(section_name)
for property_name,property_value in properties.items():
self._parser.set_section_property(section_name,property_name,property_value)
def get_operator_section_names(self):
problem_name = None
if self._parser is not None:
problem_name = self.get_section_property(InputParser.PROBLEM,InputParser.NAME)
if problem_name is None:
problem_name = self.get_property_default_value(InputParser.PROBLEM,InputParser.NAME)
if problem_name is None:
return local_chemistry_operators()
operator_names = []
for operator_name in local_chemistry_operators():
problems = InputParser.get_operator_problems(operator_name)
if problem_name in problems:
operator_names.append(operator_name)
return operator_names
def get_pluggable_section_names(self,section_name):
if not Model.is_pluggable_section(section_name):
return []
if InputParser.ALGORITHM == section_name:
problem_name = None
if self._parser is not None:
problem_name = self.get_section_property(InputParser.PROBLEM,InputParser.NAME)
if problem_name is None:
problem_name = self.get_property_default_value(InputParser.PROBLEM,InputParser.NAME)
if problem_name is None:
return local_pluggables(InputParser.ALGORITHM)
algo_names = []
for algo_name in local_pluggables(InputParser.ALGORITHM):
problems = InputParser.get_algorithm_problems(algo_name)
if problem_name in problems:
algo_names.append(algo_name)
return algo_names
return local_pluggables(section_name)
def is_pluggable_section(section_name):
return InputParser.is_pluggable_section(section_name)
def setUp(self):
filepath = self._get_resource_path('test_input_parser.txt')
self.parser = InputParser(filepath)
self.parser.parse()
class Model(object):
def __init__(self):
"""Create Model object."""
self._configuration_mgr = ConfigurationManager()
self._parser = InputParser()
def is_empty(self):
return self._parser is None or len(self._parser.get_section_names()) == 0
def new(self):
try:
dict = {}
jsonfile = os.path.join(os.path.dirname(__file__), 'input_template.json')
with open(jsonfile) as json_file:
dict = json.load(json_file)
self._parser = InputParser(dict)
self._parser.parse()
uipreferences = UIPreferences()
if uipreferences.get_populate_defaults(True):
self._parser.validate_merge_defaults()
self._parser.commit_changes()
return self._parser.get_section_names()
except:
self._parser = None
raise
def load_file(self,filename):
if filename is None:
return []
try:
self._parser = InputParser(filename)
self._parser.parse()
uipreferences = UIPreferences()
if uipreferences.get_populate_defaults(True):
self._parser.validate_merge_defaults()
self._parser.commit_changes()
return self._parser.get_section_names()
except:
self._parser = None
raise
def get_filename(self):
if self._parser is None:
return None
return self._parser.get_filename()
def is_modified(self):
if self._parser is None:
return False
return self._parser.is_modified()
def save_to_file(self,filename):
if self.is_empty():
raise ACQUAChemistryError("Empty input data.")
self._parser.save_to_file(filename)
def get_dictionary(self):
if self.is_empty():
raise ACQUAChemistryError("Empty input data.")
return self._parser.to_dictionary()
def export_dictionary(self,filename):
if self.is_empty():
raise ACQUAChemistryError("Empty input data.")
self._parser.export_dictionary(filename)
def get_section_names(self):
if self._parser is None:
return []
return self._parser.get_section_names()
def get_property_default_values(self,section_name,property_name):
if self._parser is None:
return None
return self._parser.get_property_default_values(section_name,property_name)
def section_is_text(self,section_name):
if self._parser is None:
return False
return self._parser.section_is_text(section_name)
def get_section_text(self,section_name):
if self._parser is None:
return ''
return self._parser.get_section_text(section_name)
def get_section_data(self,section_name):
if self._parser is None:
return None
return self._parser.get_section_data(section_name)
def get_section_properties(self,section_name):
if self._parser is None:
return {}
return self._parser.get_section_properties(section_name)
def get_section_properties_with_substitution(self,section_name):
properties = self.get_section_properties(section_name)
result_tuples = self._parser.check_if_substitution_key(section_name,list(properties.keys()))
properties_with_substitution = {}
for result_tuple in result_tuples:
properties_with_substitution[result_tuple[0]] = (properties[result_tuple[0]],result_tuple[1])
return properties_with_substitution
def default_properties_equals_properties(self,section_name):
if self.section_is_text(section_name):
return self.get_section_default_properties(section_name) == self.get_section_data(section_name)
default_properties = self.get_section_default_properties(section_name)
properties = self.get_section_properties(section_name)
if not isinstance(default_properties,dict) or not isinstance(properties,dict):
return default_properties == properties
if InputParser.NAME in properties:
default_properties[InputParser.NAME] = properties[InputParser.NAME]
if len(default_properties) != len(properties):
return False
substitution_tuples = self._parser.check_if_substitution_key(section_name,list(properties.keys()))
for substitution_tuple in substitution_tuples:
property_name = substitution_tuple[0]
if property_name not in default_properties:
return False
if not substitution_tuple[1]:
if default_properties[property_name] != properties[property_name]:
return False
return True
def get_section_property(self,section_name,property_name):
if self._parser is None:
return None
return self._parser.get_section_property(section_name,property_name)
def get_section(self,section_name):
return self._parser.get_section(section_name) if self._parser is not None else None
def set_section(self,section_name):
if self._parser is None:
raise ACQUAChemistryError('Input not initialized.')
self._parser.set_section(section_name)
value = self._parser.get_section_default_properties(section_name)
if isinstance(value,dict):
for property_name,property_value in value.items():
self._parser.set_section_property(section_name,property_name,property_value)
# do one more time in case schema was updated
value = self._parser.get_section_default_properties(section_name)
for property_name,property_value in value.items():
self._parser.set_section_property(section_name,property_name,property_value)
else:
if value is None:
types = self._parser.get_section_types(section_name)
if 'null' not in types:
if 'string' in types:
value = ''
elif 'object' in types:
value = {}
elif 'array' in types:
value = []
self._parser.set_section_data(section_name,value)
def set_default_properties_for_name(self,section_name):
if self._parser is None:
raise ACQUAChemistryError('Input not initialized.')
name = self._parser.get_section_property(section_name,InputParser.NAME)
self._parser.delete_section_properties(section_name)
if name is not None:
self._parser.set_section_property(section_name,InputParser.NAME,name)
value = self._parser.get_section_default_properties(section_name)
if isinstance(value,dict):
for property_name,property_value in value.items():
if property_name != InputParser.NAME:
self._parser.set_section_property(section_name,property_name,property_value)
else:
if value is None:
types = self._parser.get_section_types(section_name)
if 'null' not in types:
if 'string' in types:
value = ''
elif 'object' in types:
value = {}
elif 'array' in types:
value = []
self._parser.set_section_data(section_name,value)
@staticmethod
def is_pluggable_section(section_name):
return InputParser.is_pluggable_section(section_name)
def get_operator_section_names(self):
problem_name = None
if self._parser is not None:
problem_name = self.get_section_property(InputParser.PROBLEM,InputParser.NAME)
if problem_name is None:
problem_name = self.get_property_default_value(InputParser.PROBLEM,InputParser.NAME)
if problem_name is None:
return local_chemistry_operators()
operator_names = []
for operator_name in local_chemistry_operators():
problems = InputParser.get_operator_problems(operator_name)
if problem_name in problems:
operator_names.append(operator_name)
return operator_names
def get_pluggable_section_names(self,section_name):
if not Model.is_pluggable_section(section_name):
return []
if InputParser.ALGORITHM == section_name:
problem_name = None
if self._parser is not None:
problem_name = self.get_section_property(InputParser.PROBLEM,InputParser.NAME)
if problem_name is None:
problem_name = self.get_property_default_value(InputParser.PROBLEM,InputParser.NAME)
if problem_name is None:
return local_pluggables(InputParser.ALGORITHM)
algo_names = []
for algo_name in local_pluggables(InputParser.ALGORITHM):
problems = InputParser.get_algorithm_problems(algo_name)
if problem_name in problems:
algo_names.append(algo_name)
return algo_names
return local_pluggables(section_name)
def delete_section(self, section_name):
if self._parser is None:
raise ACQUAChemistryError('Input not initialized.')
self._parser.delete_section(section_name)
def get_default_sections(self):
if self._parser is None:
raise ACQUAChemistryError('Input not initialized.')
return self._parser.get_default_sections()
def get_section_default_properties(self,section_name):
if self._parser is None:
raise ACQUAChemistryError('Input not initialized.')
return self._parser.get_section_default_properties(section_name)
def allows_additional_properties(self,section_name):
if self._parser is None:
raise ACQUAChemistryError('Input not initialized.')
return self._parser.allows_additional_properties(section_name)
def get_property_default_value(self,section_name,property_name):
if self._parser is None:
raise ACQUAChemistryError('Input not initialized.')
return self._parser.get_property_default_value(section_name,property_name)
def get_property_types(self,section_name,property_name):
if self._parser is None:
raise ACQUAChemistryError('Input not initialized.')
return self._parser.get_property_types(section_name,property_name)
def set_section_property(self, section_name, property_name, value):
if self._parser is None:
raise ACQUAChemistryError('Input not initialized.')
self._parser.set_section_property(section_name,property_name,value)
if InputParser.is_pluggable_section(section_name) and property_name == InputParser.NAME:
properties = self._parser.get_section_default_properties(section_name)
if isinstance(properties,dict):
properties[ InputParser.NAME] = value
self._parser.delete_section_properties(section_name)
for property_name,property_value in properties.items():
self._parser.set_section_property(section_name,property_name,property_value)
def delete_section_property(self, section_name, property_name):
if self._parser is None:
raise ACQUAChemistryError('Input not initialized.')
self._parser.delete_section_property(section_name, property_name)
if InputParser.is_pluggable_section(section_name) and property_name == InputParser.NAME:
self._parser.delete_section_properties(section_name)
def set_section_text(self, section_name, value):
if self._parser is None:
raise ACQUAChemistryError('Input not initialized.')
self._parser.set_section_data(section_name, value)
def delete_section_text(self, section_name):
if self._parser is None:
raise ACQUAChemistryError('Input not initialized.')
self._parser.delete_section_text(section_name)
class ACQUAChemistry(object):
"""Main entry point."""
KEY_HDF5_OUTPUT = 'hdf5_output'
_DRIVER_RUN_TO_HDF5 = 1
_DRIVER_RUN_TO_ALGO_INPUT = 2
def __init__(self):
"""Create an ACQUAChemistry object."""
self._configuration_mgr = ConfigurationManager()
self._parser = None
self._core = None
def get_effective_logging_level(self):
"""
Returns the logging level being used by ACQUA Chemistry
"""
levels = get_logger_levels_for_names(
['qiskit_acqua_chemistry', 'qiskit_acqua'])
return levels[0]
def set_logging(self, level=logging.INFO):
"""Sets logging output of the logging messages.
Sets the output of logging messages (above level `level`) by
configuring the logger accordingly.
Disables logging if set to logging.NOTSET
Params:
level (int): minimum severity of the messages that are displayed.
"""
logging_config = build_logging_config(
['qiskit_acqua_chemistry', 'qiskit_acqua'], level)
preferences = Preferences()
preferences.set_logging_config(logging_config)
preferences.save()
set_logger_config(logging_config)
def run(self, input, output=None):
if input is None:
raise ACQUAChemistryError("Missing input.")
self._parser = InputParser(input)
self._parser.parse()
driver_return = self._run_driver_from_parser(self._parser, False)
if driver_return[0] == ACQUAChemistry._DRIVER_RUN_TO_HDF5:
logger.info('No further process.')
return {'printable': [driver_return[1]]}
data = run_algorithm(driver_return[1], driver_return[2], True)
if not isinstance(data, dict):
raise ACQUAChemistryError(
"Algorithm run result should be a dictionary")
if logger.isEnabledFor(logging.DEBUG):
logger.debug('Algorithm returned: {}'.format(
json.dumps(data, indent=4)))
convert_json_to_dict(data)
lines, result = self._format_result(data)
logger.info('Processing complete. Final result available')
result['printable'] = lines
if output is not None:
with open(output, 'w') as f:
for line in lines:
print(line, file=f)
return result
def save_input(self, input_file):
"""Save the input of a run to a file.
Params:
input_file (string): file path
"""
if self._parser is None:
raise ACQUAChemistryError("Missing input information.")
self._parser.save_to_file(input_file)
def run_drive_to_jsonfile(self, input, jsonfile):
if jsonfile is None:
raise ACQUAChemistryError("Missing json file")
data = self._run_drive(input, True)
if data is None:
logger.info('No data to save. No further process.')
return
logger.debug('Result: {}'.format(
json.dumps(data, sort_keys=True, indent=4)))
with open(jsonfile, 'w') as fp:
json.dump(data, fp, sort_keys=True, indent=4)
print("Algorithm input file saved: '{}'".format(jsonfile))
def run_algorithm_from_jsonfile(self, jsonfile, output=None):
with open(jsonfile) as json_file:
return self.run_algorithm_from_json(json.load(json_file), output)
def run_algorithm_from_json(self, params, output=None):
ret = run_algorithm(params, None, True)
if not isinstance(ret, dict):
raise ACQUAChemistryError(
"Algorithm run result should be a dictionary")
logger.debug('Algorithm returned: {}'.format(json.dumps(ret,
indent=4)))
convert_json_to_dict(ret)
print('Output:')
if isinstance(ret, dict):
for k, v in ret.items():
print("'{}': {}".format(k, v))
else:
print(ret)
return ret
def _format_result(self, data):
lines, result = self._core.process_algorithm_result(data)
return lines, result
def run_drive(self, input):
return self._run_drive(input, False)
def _run_drive(self, input, save_json_algo_file):
if input is None:
raise ACQUAChemistryError("Missing input.")
self._parser = InputParser(input)
self._parser.parse()
driver_return = self._run_driver_from_parser(self._parser,
save_json_algo_file)
driver_return[1]['input'] = driver_return[2].to_params()
driver_return[1]['input']['name'] = driver_return[2].configuration[
'name']
return driver_return[1]
def _run_driver_from_parser(self, p, save_json_algo_file):
if p is None:
raise ACQUAChemistryError("Missing parser")
p.validate_merge_defaults()
#logger.debug('ALgorithm Input Schema: {}'.format(json.dumps(p.to_JSON(), sort_keys=True, indent=4)))
experiment_name = "-- no &NAME section found --"
if InputParser.NAME in p.get_section_names():
name_sect = p.get_section(InputParser.NAME)
if 'data' in name_sect:
experiment_name = name_sect['data']
logger.info('Running chemistry problem from input file: {}'.format(
p.get_filename()))
logger.info('Experiment description: {}'.format(
experiment_name.rstrip()))
driver_name = p.get_section_property(InputParser.DRIVER,
InputParser.NAME)
if driver_name is None:
raise ACQUAChemistryError(
'Property "{0}" missing in section "{1}"'.format(
InputParser.NAME, InputParser.DRIVER))
hdf5_file = p.get_section_property(InputParser.DRIVER,
ACQUAChemistry.KEY_HDF5_OUTPUT)
section = p.get_section(driver_name)
if 'data' not in section:
raise ACQUAChemistryError(
'Property "data" missing in section "{0}"'.format(driver_name))
if driver_name not in self._configuration_mgr.module_names:
raise ACQUAChemistryError(
'Driver "{0}" missing in local drivers'.format(driver_name))
work_path = None
input_file = p.get_filename()
if input_file is not None:
work_path = os.path.dirname(os.path.realpath(input_file))
driver = self._configuration_mgr.get_driver_instance(driver_name)
driver.work_path = work_path
molecule = driver.run(section)
if work_path is not None and hdf5_file is not None and not os.path.isabs(
hdf5_file):
hdf5_file = os.path.abspath(os.path.join(work_path, hdf5_file))
molecule.log()
if hdf5_file is not None:
molecule._origin_driver_name = driver_name
molecule._origin_driver_config = section['data']
molecule.save(hdf5_file)
text = "HDF5 file saved '{}'".format(hdf5_file)
logger.info(text)
if not save_json_algo_file:
logger.info('Run ended with hdf5 file saved.')
return ACQUAChemistry._DRIVER_RUN_TO_HDF5, text
# Run the Hamiltonian to process the QMolecule and get an input for algorithms
self._core = get_chemistry_operator_instance(
p.get_section_property(InputParser.OPERATOR, InputParser.NAME))
self._core.init_params(p.get_section_properties(InputParser.OPERATOR))
input_object = self._core.run(molecule)
logger.debug('Core computed substitution variables {}'.format(
self._core.molecule_info))
result = p.process_substitutions(self._core.molecule_info)
logger.debug('Substitutions {}'.format(result))
params = {}
for section_name, section in p.get_sections().items():
if section_name == InputParser.NAME or \
section_name == InputParser.DRIVER or \
section_name == driver_name.lower() or \
section_name == InputParser.OPERATOR or \
'properties' not in section:
continue
params[section_name] = copy.deepcopy(section['properties'])
if InputParser.PROBLEM == section_name and \
InputParser.ENABLE_SUBSTITUTIONS in params[section_name]:
del params[section_name][InputParser.ENABLE_SUBSTITUTIONS]
return ACQUAChemistry._DRIVER_RUN_TO_ALGO_INPUT, params, input_object
def __init__(self):
"""Create Model object."""
self._configuration_mgr = ConfigurationManager()
self._parser = InputParser()
