def parse_namelist_files_to_create_a_model_run(self, code_version, description, config_dir,
name, namelist_files, status, user, spinup_in_years):
"""
Ceate a model run
:param code_version: the code version object
:param description: the description fo the model run
:param config_dir: the configuration directory
:param name: name of the model run
:param namelist_files: namelist_files object
:param status: status the model is to have
:param user: the user creating the model run
:param spinup_in_years: the spin up in years, for a science configuration
:return: a model run
"""
model_run = ModelRun()
model_run.name = name
model_run.user = user
model_run.code_version = code_version
model_run.description = description
model_run.status = status
model_run.science_configuration_spinup_in_years = spinup_in_years
model_run.parameter_values = []
log.info("Creating Model Run For: {0} ({1})".format(model_run.name, config_dir))
for namelist_file in namelist_files:
filename = os.path.join(config_dir, namelist_file.filename)
if os.path.exists(filename):
log.info("Parsing: %s" % filename)
nml_dict = self._read_namelist(filename)
model_run.parameter_values.extend(self._create_parameter_values(namelist_file, nml_dict))
return model_run
def duplicate_run_model(self, model_id, user):
"""
Duplicate the run model and all its parameters to a new run model
:param model_id: model run id to duplicate
:param user: the user duplicating the model
:return: nothing
"""
id_for_user_upload_driving_dataset = self._dataset_service.get_id_for_user_upload_driving_dataset()
self.delete_model_run_being_created(user)
with self.transaction_scope() as session:
model_run_to_duplicate = session\
.query(ModelRun)\
.join(ModelRunStatus)\
.outerjoin(ParameterValue)\
.outerjoin(LandCoverAction) \
.filter(ModelRun.id == model_id) \
.filter(or_(
ModelRun.user_id == user.id,
ModelRunStatus.name == constants.MODEL_RUN_STATUS_PUBLISHED,
ModelRunStatus.name == constants.MODEL_RUN_STATUS_PUBLIC,)) \
.options(contains_eager(ModelRun.parameter_values)) \
.options(contains_eager(ModelRun.land_cover_actions)) \
.one()
new_model_run_name = model_run_to_duplicate.name
if self._is_duplicate_name(model_run_to_duplicate.name, session, user):
new_model_run_name = "{} (Copy)".format(model_run_to_duplicate.name)
copy_id = 1
while self._is_duplicate_name(new_model_run_name, session, user):
copy_id += 1
new_model_run_name = "{} (Copy {})".format(model_run_to_duplicate.name, copy_id)
new_model_run = ModelRun()
new_model_run.duplicate_from(model_run_to_duplicate)
new_model_run.name = new_model_run_name
new_model_run.user = user
new_model_run.change_status(session, constants.MODEL_RUN_STATUS_CREATED)
for parameter_value in model_run_to_duplicate.parameter_values:
new_parameter = ParameterValue()
new_parameter.duplicate_from(parameter_value)
new_parameter.model_run = new_model_run
for land_cover_action in model_run_to_duplicate.land_cover_actions:
new_land_cover_action = LandCoverAction()
new_land_cover_action.duplicate_from(land_cover_action)
new_land_cover_action.model_run = new_model_run
session.add(new_model_run)
if model_run_to_duplicate.driving_dataset_id == id_for_user_upload_driving_dataset:
try:
self._job_runner_client.duplicate_uploaded_driving_data(model_run_to_duplicate.id, new_model_run.id)
except ServiceException:
self.delete_model_run_being_created(user)
raise ServiceException("Could not duplicate the model run because "
"the user uploaded data can not be duplicated")
def test_GIVEN_valid_model_WHEN_convert_to_dictionary_THEN_namelist_with_no_representation_are_present(self):
job_runner_client = JobRunnerClient(config)
def _alter_yearly_monthly_output_profiles(params):
return params
def _alter_driving_data_start(params):
return params
job_runner_client.alter_yearly_monthly_output_profiles = _alter_yearly_monthly_output_profiles
job_runner_client.alter_driving_data_start = _alter_driving_data_start
parameter = Parameter(name='param1')
expected_parameter_value = '12'
#There is no parameter value:
parameter.parameter_values = []
namelist = Namelist(name='NAME_LIST')
namelist_file = NamelistFile(filename='filename')
# Need this to run
parameter2 = Parameter(name=constants.JULES_PARAM_LATLON_REGION[1])
parameter2.parameter_values = [ParameterValue(value='.true.')]
namelist2 = Namelist(name=constants.JULES_PARAM_LATLON_REGION[0])
namelist_file = NamelistFile(filename='filename')
namelist2.parameters = [parameter2]
namelist2.namelist_file = namelist_file
namelist.parameters = [parameter]
namelist.namelist_file = namelist_file
model_run = ModelRun()
model_run.id = 101
code_version = CodeVersion(name='Jules v3.4.1')
user = User()
user.id = 1
user.email = "email"
user.username = "******"
model_run.user = user
model_run.code_version = code_version
code_version.parameters = [parameter, parameter2]
result = job_runner_client.convert_model_to_dictionary(model_run, code_version.parameters, [])
namelist_file_result = result[constants.JSON_MODEL_NAMELIST_FILES][0]
assert_that(namelist_file_result[constants.JSON_MODEL_NAMELIST_FILE_FILENAME],
is_(namelist_file.filename), "value is correct")
assert_that(namelist_file_result[constants.JSON_MODEL_NAMELISTS][0][constants.JSON_MODEL_NAMELIST_NAME],
is_(namelist.name), "value is correct")
parameters_result = namelist_file_result[constants.JSON_MODEL_NAMELISTS][0][constants.JSON_MODEL_PARAMETERS]
assert_that(parameters_result, is_({}), "there are no values")
assert_that(len(result[constants.JSON_LAND_COVER]), is_(0))
def test_GIVEN_valid_model_WHEN_convert_to_dictionary_THEN_dictionary_is_correct(self):
job_runner_client = JobRunnerClient(config)
def _alter_yearly_monthly_output_profiles(params):
return params
def _alter_driving_data_start(params):
return params
job_runner_client.alter_yearly_monthly_output_profiles = _alter_yearly_monthly_output_profiles
job_runner_client.alter_driving_data_start = _alter_driving_data_start
parameter = Parameter(name=constants.JULES_PARAM_POINTS_FILE[1])
expected_parameter_value = '51 0.5'
expected_index = 3
#There is only one parameter value per run:
parameter.parameter_values = [ParameterValue(value=expected_parameter_value)]
namelist = Namelist(name=constants.JULES_PARAM_POINTS_FILE[0])
namelist_file = NamelistFile(filename='filename')
namelist.parameters = [parameter]
namelist.namelist_file = namelist_file
namelist.index_in_file = expected_index
model_run = ModelRun()
model_run.id = 101
model_run.land_cover_frac = "1 2 3 4 5 6 7 8 9"
code_version = CodeVersion(name='Jules v3.4.1')
model_run.code_version = code_version
code_version.parameters = [parameter]
user = User()
user.id = 1
user.email = "email"
user.username = "******"
model_run.user = user
result = job_runner_client.convert_model_to_dictionary(model_run, code_version.parameters, [])
assert_that(result[constants.JSON_MODEL_RUN_ID], is_(model_run.id), "value is correct")
assert_that(result[constants.JSON_MODEL_CODE_VERSION], is_(model_run.code_version.name), "value is correct")
assert_that(result[constants.JSON_USER_ID], is_(user.id), "user id")
assert_that(result[constants.JSON_USER_NAME], is_(user.username), "user name")
assert_that(result[constants.JSON_USER_EMAIL], is_(user.email), "user email")
namelist_file_result = result[constants.JSON_MODEL_NAMELIST_FILES][0]
assert_that(namelist_file_result[constants.JSON_MODEL_NAMELIST_FILE_FILENAME],
is_(namelist_file.filename), "value is correct")
assert_that(namelist_file_result[constants.JSON_MODEL_NAMELISTS][0][constants.JSON_MODEL_NAMELIST_NAME],
is_(namelist.name), "namelist name")
assert_that(namelist_file_result[constants.JSON_MODEL_NAMELISTS][0][constants.JSON_MODEL_NAMELIST_INDEX],
is_(namelist.index_in_file), "namelist index")
parameters_result = namelist_file_result[constants.JSON_MODEL_NAMELISTS][0][constants.JSON_MODEL_PARAMETERS]
assert_that(parameters_result, is_({parameter.name: expected_parameter_value}), "value is correct")
def _create_new_model_run(self, session, user):
"""
Create a brand new model run for user
:param session: session to use
:param user: Currently logged in user
:return: New model run
"""
model_run = ModelRun()
model_run.change_status(session, constants.MODEL_RUN_STATUS_CREATED)
model_run.user = user
parameters = [
[constants.JULES_PARAM_TIMESTEP_LEN, constants.TIMESTEP_LEN, None],
[constants.JULES_PARAM_OUTPUT_RUN_ID, constants.RUN_ID, None],
[constants.JULES_PARAM_OUTPUT_OUTPUT_DIR, "./" + constants.OUTPUT_DIR, None],
]
# Add CHESS defaults:
chess_defaults = ['surf_roff', 'sub_surf_roff', 'fqw_gb', 'rad_net', 'ftl_gb', 'gpp_gb', 'resp_p_gb',
'tstar_gb', 'snow_mass_gb', 't_soil', 'smc_tot', 'smcl', 'swet_liq_tot']
chess_periods = [(constants.JULES_MONTHLY_PERIOD, "_monthly")]
group_id = 0
for output_variable in chess_defaults:
for period, period_profile_name in chess_periods:
parameters.append([constants.JULES_PARAM_OUTPUT_VAR, output_variable, group_id])
parameters.append([constants.JULES_PARAM_OUTPUT_PERIOD, period, group_id])
parameters.append([constants.JULES_PARAM_OUTPUT_PROFILE_NAME,
output_variable + period_profile_name, group_id])
parameters.append([constants.JULES_PARAM_OUTPUT_NVARS, 1, group_id])
parameters.append([constants.JULES_PARAM_OUTPUT_MAIN_RUN, True, group_id])
parameters.append([constants.JULES_PARAM_OUTPUT_TYPE, 'M', group_id])
group_id += 1
parameters.append([constants.JULES_PARAM_OUTPUT_NPROFILES, group_id, None])
for constant, value, group_id in parameters:
param = self.parameter_service.get_parameter_by_constant(constant, session)
param_value = ParameterValue()
param_value.parameter = param
param_value.model_run = model_run
param_value.group_id = group_id
param_value.set_value_from_python(value)
return model_run
def setUp(self):
self.clean_database()
self.user = self.login()
self.create_two_driving_datasets()
dds = DatasetService().get_driving_datasets(self.user)[0]
with session_scope() as session:
model_run = ModelRun()
model_run.name = "model run"
model_run.change_status(session, MODEL_RUN_STATUS_CREATED)
model_run.user = self.user
model_run.driving_dataset_id = dds.id
session.add(model_run)
session.commit()
self.model_run_service = ModelRunService()
model_run = self.model_run_service._get_model_run_being_created(session, self.user)
parameter_val = ParameterValue()
parameter_val.parameter = self.model_run_service.get_parameter_by_constant(JULES_PARAM_LATLON_REGION)
parameter_val.set_value_from_python(True)
parameter_val.model_run_id = model_run.id
session.add(parameter_val)
self.add_land_cover_region(model_run)
def test_GIVEN_model_contains_repeated_namelists_WHEN_convert_to_dictionary_THEN_namelists_grouped_correctly(self):
job_runner_client = JobRunnerClient(config)
def _alter_yearly_monthly_output_profiles(params):
return params
def _alter_driving_data_start(params):
return params
job_runner_client.alter_yearly_monthly_output_profiles = _alter_yearly_monthly_output_profiles
job_runner_client.alter_driving_data_start = _alter_driving_data_start
# Set the namelists here:
nml_output = Namelist(name=constants.JULES_NML_OUTPUT)
nml_output_profile = Namelist(name=constants.JULES_NML_OUTPUT_PROFILE)
nml_output.namelist_file = nml_output_profile.namelist_file = NamelistFile(filename="output.nml")
nml_model_grid = Namelist(name=constants.JULES_PARAM_LATLON_REGION[0])
nml_model_grid.namelist_file = NamelistFile(filename="model_grid.nml")
# Set the parameters here:
param_nprofiles = Parameter(name=constants.JULES_PARAM_OUTPUT_NPROFILES[1])
param_profile_name = Parameter(name=constants.JULES_PARAM_OUTPUT_PROFILE_NAME[1])
param_var = Parameter(name=constants.JULES_PARAM_OUTPUT_VAR[1])
param_latlon_region = Parameter(name=constants.JULES_PARAM_LATLON_REGION[1])
# Set the parameter values
param_nprofiles.parameter_values = [ParameterValue(value=2)]
param_profile_name.parameter_values = [ParameterValue(value="monthly", group_id=0),
ParameterValue(value="yearly", group_id=1)]
param_var.parameter_values = [ParameterValue(value='"emis_gb", "ftl_gb"', group_id=0),
ParameterValue(value='"snow_mass_gb", "tstar_gb"', group_id=1)]
param_latlon_region.parameter_values = [ParameterValue(value=".true.")]
# Assign the parameters to namelists
nml_output.parameters = [param_nprofiles]
nml_output_profile.parameters = [param_profile_name, param_var]
nml_model_grid.parameters = [param_latlon_region]
model_run = ModelRun()
model_run.id = 101
code_version = CodeVersion(name='Jules v3.4.1')
user = User()
user.id = 1
user.email = "email"
user.username = "******"
model_run.user = user
model_run.code_version = code_version
code_version.parameters = [param_profile_name, param_var, param_nprofiles, param_latlon_region]
result = job_runner_client.convert_model_to_dictionary(model_run, code_version.parameters, [])
# Check the result dictionary has the correct run ID and code version
assert_that(result[constants.JSON_MODEL_RUN_ID], is_(model_run.id), "value is correct")
assert_that(result[constants.JSON_MODEL_CODE_VERSION], is_(model_run.code_version.name), "value is correct")
# Check that the namelist_files has the correct namelist file
namelist_file_result = result[constants.JSON_MODEL_NAMELIST_FILES][0]
assert_that(namelist_file_result[constants.JSON_MODEL_NAMELIST_FILE_FILENAME],
is_("output.nml"), "value is correct")
# Check that the namelist file contains the three namelists
namelists = namelist_file_result[constants.JSON_MODEL_NAMELISTS]
assert_that(len(namelists), is_(3))
# Check the dictionaries are as expected
profiles_dict1 = {constants.JSON_MODEL_NAMELIST_GROUP_ID: 0,
constants.JSON_MODEL_NAMELIST_INDEX: None,
constants.JSON_MODEL_NAMELIST_NAME: constants.JULES_NML_OUTPUT_PROFILE,
constants.JSON_MODEL_PARAMETERS: {
constants.JULES_PARAM_OUTPUT_VAR[1]: '"emis_gb", "ftl_gb"',
constants.JULES_PARAM_OUTPUT_PROFILE_NAME[1]: "monthly"
}}
profiles_dict2 = {constants.JSON_MODEL_NAMELIST_GROUP_ID: 1,
constants.JSON_MODEL_NAMELIST_INDEX: None,
constants.JSON_MODEL_NAMELIST_NAME: constants.JULES_NML_OUTPUT_PROFILE,
constants.JSON_MODEL_PARAMETERS: {
constants.JULES_PARAM_OUTPUT_VAR[1]: '"snow_mass_gb", "tstar_gb"',
constants.JULES_PARAM_OUTPUT_PROFILE_NAME[1]: "yearly"
}}
output_dict = {constants.JSON_MODEL_NAMELIST_GROUP_ID: None,
constants.JSON_MODEL_NAMELIST_INDEX: None,
constants.JSON_MODEL_NAMELIST_NAME: constants.JULES_NML_OUTPUT,
constants.JSON_MODEL_PARAMETERS: {
constants.JULES_PARAM_OUTPUT_NPROFILES[1]: 2
}}
assert_that(namelists, contains_inanyorder(profiles_dict1, profiles_dict2, output_dict))
def test_GIVEN_model_with_land_cover_actions_WHEN_convert_to_dictionary_THEN_land_cover_actions_present(self):
job_runner_client = JobRunnerClient(config)
def _alter_yearly_monthly_output_profiles(params):
return params
def _alter_driving_data_start(params):
return params
job_runner_client.alter_yearly_monthly_output_profiles = _alter_yearly_monthly_output_profiles
job_runner_client.alter_driving_data_start = _alter_driving_data_start
parameter = Parameter(name='file')
expected_parameter_value = "'base_frac_file.nc'"
parameter.parameter_values = [ParameterValue(value=expected_parameter_value)]
parameter2 = Parameter(name='frac_name')
expected_parameter_value2 = "'frac'"
parameter2.parameter_values = [ParameterValue(value=expected_parameter_value2)]
parameter3 = Parameter(name='latlon_region')
expected_parameter_value3 = ".true."
parameter3.parameter_values = [ParameterValue(value=expected_parameter_value3)]
namelist = Namelist(name='JULES_FRAC')
namelist_file = NamelistFile(filename='filename')
expected_index = 3
namelist.parameters = [parameter, parameter2]
namelist.namelist_file = namelist_file
namelist.index_in_file = expected_index
namelist2 = Namelist(name='JULES_MODEL_GRID')
namelist_file = NamelistFile(filename='filename')
expected_index = 3
namelist2.parameters = [parameter3]
namelist2.namelist_file = namelist_file
namelist2.index_in_file = expected_index
model_run = ModelRun()
model_run.id = 101
code_version = CodeVersion(name='Jules v3.4.1')
model_run.code_version = code_version
code_version.parameters = [parameter, parameter2, parameter3]
user = User()
user.id = 1
user.email = "email"
user.username = "******"
model_run.user = user
lcr1 = LandCoverRegion()
lcr1.mask_file = "region1.nc"
lca1 = LandCoverAction()
lca1.value_id = 9
lca1.order = 1
lca1.region = lcr1
lcr2 = LandCoverRegion()
lcr2.mask_file = "region2.nc"
lca2 = LandCoverAction()
lca2.value_id = 5
lca2.order = 2
lca2.region = lcr2
land_cover_actions = [lca1, lca2]
result = job_runner_client.convert_model_to_dictionary(model_run, code_version.parameters, land_cover_actions)
result_lc = result[constants.JSON_LAND_COVER]
assert_that(result_lc[constants.JSON_LAND_COVER_BASE_FILE], is_("base_frac_file.nc"))
assert_that(result_lc[constants.JSON_LAND_COVER_BASE_KEY], is_("frac"))
assert_that(result_lc[constants.JSON_LAND_COVER_ICE_INDEX], is_(9))
result_lc_actions = result_lc[constants.JSON_LAND_COVER_ACTIONS]
assert_that(len(result_lc_actions), is_(2))
action1 = result_lc_actions[0]
assert_that(action1[constants.JSON_LAND_COVER_MASK_FILE], is_("region1.nc"))
assert_that(action1[constants.JSON_LAND_COVER_ORDER], is_(1))
assert_that(action1[constants.JSON_LAND_COVER_VALUE], is_(9))
action2 = result_lc_actions[1]
assert_that(action2[constants.JSON_LAND_COVER_MASK_FILE], is_("region2.nc"))
assert_that(action2[constants.JSON_LAND_COVER_ORDER], is_(2))
assert_that(action2[constants.JSON_LAND_COVER_VALUE], is_(5))
namelist_file_result = result[constants.JSON_MODEL_NAMELIST_FILES][0]
parameters_result = namelist_file_result[constants.JSON_MODEL_NAMELISTS][0][constants.JSON_MODEL_PARAMETERS]
assert_that(parameters_result['file'], is_("'" + constants.USER_EDITED_FRACTIONAL_FILENAME + "'"))
assert_that(parameters_result['frac_name'], is_("'frac'"))