def test_metrics_and_conditions_to_json():
"""
Test for the metrics_to_json and conditions_to_json methods.
Returns
----------
boolean : result of the test.
"""
# Parse yaml file
yaml_obj = yp.YamlParser(ARGS_1, vf.VALID_FLAGS_PLATFORM)
yaml_obj.read()
# Build interaction restrictions
interaction_restrictions = ir.InteractionRestrictionsBuilder()
interaction_restrictions.parse_interaction_restrictions(
PDB_FILE, yaml_obj.interaction_restrictions)
errors = []
# Check metrics json output
metrics = interaction_restrictions.metrics_to_json()
expected_metrics_output = open(EXPECTED_METRICS, "r").read()
if not metrics == expected_metrics_output:
errors.append(
f"Error in metrics json: {metrics} == {expected_metrics_output} ")
# Check conditions json output
conditions = interaction_restrictions.conditions_to_json()
expected_conditions_output = open(EXPECTED_CONDITIONS, "r").read()
if not conditions == expected_conditions_output:
errors.append(
f"conditions json assert: {conditions} == {expected_conditions_output} "
)
# assert no error message has been registered, else print messages
assert not errors
def run_platform(input_yaml):
'''
High level function to run a PELE job. It will:
1) Parse the input.yaml
2) Launch job
3) Return job parametrs
'''
yaml_obj = yp.YamlParser(input_yaml, vf.VALID_FLAGS_PLATFORM)
yaml_obj.read()
job_params = lc.Launcher(yaml_obj).launch()
return job_params
def run_platform(input_yaml):
"""
High level function to run the PELE platform from an input yaml file.
.. todo ::
* In the future we might have other type of runners. We should specify
that this one runs the platform starting from a yaml file. So,
something like run_platform_from_yaml could be more appropriate.
It will:
1) Parse the input.yaml
2) Launch job
3) Return job parameters
Parameters
----------
input_yaml : str
The path pointing to the input yaml file
Returns
-------
job_params : an EnviroBuilder object
The corresponding EnviroBuilder object with the parameters of the
simulation
"""
# Generate the yaml object from the input yaml
from pele_platform.Utilities.Helpers import yaml_parser
from pele_platform.Checker import valid_flags
yaml_obj = yaml_parser.YamlParser(input_yaml,
valid_flags.VALID_FLAGS_PLATFORM)
# Attempt to parse the yaml object
try:
yaml_obj.read()
except AttributeError:
from pele_platform.Errors import custom_errors
raise custom_errors.WrongYamlFile(
"Input file: {}".format(input_yaml)
+ "does not look like a correct yaml file")
# Initialize job launcher
from pele_platform.Utilities.Helpers.launcher import Launcher
launcher = Launcher(yaml_obj)
# Run launcher
job_params = launcher.launch()
# Return job parameters
return job_params
def test_check_SyntaxError_exception(file):
"""
Function to test an input file that should throw a Syntax Error exception.
Parameters
----------
file : Path of the input.yaml file.
"""
# Parse yaml file
yaml_obj = yp.YamlParser(file, vf.VALID_FLAGS_PLATFORM)
yaml_obj.read()
# Build interaction restrictions
interaction_restrictions = ir.InteractionRestrictionsBuilder()
with pytest.raises(SyntaxError):
interaction_restrictions.parse_interaction_restrictions(
PDB_FILE, yaml_obj.interaction_restrictions)
def run_platform_from_yaml(input_yaml):
"""
High level function to run the PELE platform from an input yaml file.
It will:
1) Parse the input.yaml
2) Launch job
3) Return job parameters
Parameters
----------
input_yaml : str
The path pointing to the input yaml file
Returns
-------
job_params : a Parameters object
The corresponding Parameters object with the parameters of the
simulation
"""
# Generate the yaml object from the input yaml
from pele_platform.Utilities.Helpers import yaml_parser
from pele_platform.Checker import valid_flags
yaml_obj = yaml_parser.YamlParser(input_yaml,
valid_flags.VALID_FLAGS_PLATFORM)
# Attempt to parse the yaml object
try:
yaml_obj.read()
except AttributeError:
from pele_platform.Errors import custom_errors
raise custom_errors.WrongYamlFile(
"Input file: {}".format(input_yaml) +
"does not look like a correct yaml file")
# Initialize job launcher
from pele_platform.Utilities.Helpers.launcher import Launcher
launcher = Launcher(yaml_obj)
# Run launcher
job_params = launcher.launch()
# Return job parameters
return job_params
def _read_args(file):
"""
Internal function: parse yaml file and prepare args.
Parameters
----------
file : str
Path of the input.yaml file.
Returns
----------
args : simulation args.
"""
# Parse yaml file
yaml_obj = yp.YamlParser(file, vf.VALID_FLAGS_PLATFORM)
yaml_obj.read()
# Prepare params
launcher = Launcher(yaml_obj)
launcher._define_package_to_run()
return launcher._args