def test_WHEN_get_user_model_runs_THEN_list_ordered_by_date_created_newest_first(self):
with session_scope(Session) as session:
# First add user
user1 = User()
user1.name = 'user1'
session.add(user1)
session.commit()
# Create three published models not in datetime order
model_run1 = ModelRun()
model_run1.user_id = user1.id
model_run1.name = "MR1"
model_run1.date_created = datetime(2013, 12, 7, 17, 15, 30)
session.add(model_run1)
session.commit()
model_run2 = ModelRun()
model_run2.user_id = user1.id
model_run2.name = "MR2"
model_run2.date_created = datetime(2014, 6, 9, 12, 30, 24)
session.add(model_run2)
session.commit()
model_run3 = ModelRun()
model_run3.user_id = user1.id
model_run3.name = "MR3"
model_run3.date_created = datetime(2014, 6, 9, 11, 39, 30)
session.add_all([model_run1, model_run2, model_run3])
model_runs = self.model_run_service.get_models_for_user(user1)
assert_that(model_runs[0].name, is_("MR2"))
assert_that(model_runs[1].name, is_("MR3"))
assert_that(model_runs[2].name, is_("MR1"))
def test_GIVEN_model_with_parameters_WHEN_get_parameter_value_THEN_parameter_value_returned(self):
with session_scope(Session) as session:
user = User()
user.name = 'user1'
session.add(user)
session.commit()
param = session.query(Parameter).first()
param_id = param.id
param_name = param.name
param_namelist = param.namelist.name
model_run = ModelRun()
model_run.name = "MR1"
model_run.user_id = user.id
model_run.status = self._status(constants.MODEL_RUN_STATUS_CREATED)
session.add(model_run)
session.commit()
parameter1 = ParameterValue()
parameter1.parameter_id = param_id
parameter1.set_value_from_python("param1 value")
parameter1.model_run_id = model_run.id
session.add(parameter1)
model_run_returned = self.model_run_service.get_model_being_created_with_non_default_parameter_values(user)
param_value_returned = model_run_returned.get_python_parameter_value([param_namelist, param_name])
assert_that(param_value_returned, is_("param1 value"))
def test_GIVEN_nonexistent_model_id_WHEN_make_public_model_THEN_ServiceException_raised(self):
# Add a user
with session_scope(Session) as session:
user = User()
user.name = 'user1'
session.add(user)
with self.assertRaises(ServiceException, msg="Should have raised a ServiceException"):
self.model_run_service.make_public_model(user, -100)
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_no_model_runs_WHEN_get_model_runs_for_user_THEN_empty_list(self):
# Add a user who doesn't have any model runs
with session_scope(Session) as session:
user = User()
user.name = 'Has No Model Runs'
session.add(user)
# Get the users model runs
model_runs = self.model_run_service.get_models_for_user(user)
assert_that(model_runs, is_([]))
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 test_GIVEN_model_doesnot_exist_WHEN_duplicate_THEN_not_found(self):
# Add a user who doesn't have any model runs
with session_scope(Session) as session:
user = User()
user.name = 'Has No Model Runs'
session.add(user)
# Get the users model runs
with self.assertRaises(NoResultFound, msg="Should have thrown a NoResultFound exception"):
model_runs = self.model_run_service.duplicate_run_model(10000, user)
def test_GIVEN_model_belongs_to_someone_else_WHEN_duplicate_THEN_not_found(self):
# Add a user who doesn't have any model runs
other_user = self.login("other_user")
model = self.create_run_model(10, "test", other_user)
with session_scope(Session) as session:
user = User()
user.name = 'Has No Model Runs'
session.add(user)
# Get the users model runs
with self.assertRaises(NoResultFound, msg="Should have thrown a NoResultFound exception"):
self.model_run_service.duplicate_run_model(model.id, user)
def test_create_user(self):
# Important - don't instantiate the mock class,
# as the session creation function in the service
# will do that for us
sample_user = User()
sample_user.username = '******'
sample_user.name = 'Test User'
sample_user.email = '*****@*****.**'
sample_user.access_level = 'External'
sample_user.first_name = "first_name"
sample_user.last_name = "last_name"
sample_user.storage_quota_in_gb = 89
self._mock_session.add = MagicMock()
self._mock_session.commit = MagicMock()
user_service = UserService(self._mock_session)
user_service.create(sample_user.username,
sample_user.first_name,
sample_user.last_name,
sample_user.email,
sample_user.access_level)
self._mock_session.add.assert_called_once_with(ANY)
self._mock_session.commit.assert_called_once_with()
def test_GIVEN_complete_model_WHEN_make_public_model_THEN_ServiceException_raised(self):
# Add a user and give them a model
with session_scope(Session) as session:
user = User()
user.name = 'user1'
session.add(user)
session.commit()
# Give them a model
model_run = ModelRun()
model_run.name = "MR1"
model_run.user_id = user.id
model_run.status = self._status(constants.MODEL_RUN_STATUS_COMPLETED)
session.add(model_run)
# Get the users model runs
with self.assertRaises(ServiceException, msg="Should have raised a ServiceException"):
self.model_run_service.make_public_model(user, model_run.id)
def test_GIVEN_user_has_model_run_WHEN_get_model_run_by_id_THEN_model_run_returned(self):
# Add a user and give them a model
with session_scope(Session) as session:
# First add user
user = User()
user.name = 'user1'
session.add(user)
session.commit()
# Give them a model
model_run = ModelRun()
model_run.name = "MR1"
model_run.user_id = user.id
model_run.status = self._status(constants.MODEL_RUN_STATUS_PUBLIC)
session.add(model_run)
# Get the users model runs
model_run_returned = self.model_run_service.get_model_by_id(user, model_run.id)
assert_that(model_run_returned.name, is_("MR1"))
def test_GIVEN_model_run_id_belongs_to_another_user_WHEN_get_model_run_by_id_THEN_NoResultFound_exception(self):
# Add two users and give one a model
with session_scope(Session) as session:
user = User()
user.name = 'user1'
user2 = User()
user2.name = 'user2'
session.add_all([user, user2])
session.commit()
# Give them a model
model_run = ModelRun()
model_run.name = "MR1"
model_run.user_id = user.id
model_run.status = self._status(constants.MODEL_RUN_STATUS_COMPLETED)
session.add(model_run)
# Get the users model runs
with self.assertRaises(NoResultFound, msg="Should have thrown a NoResultFound exception"):
self.model_run_service.get_model_by_id(user2, model_run.id)
def test_GIVEN_model_belongs_to_another_user_WHEN_make_public_model_THEN_ServiceException_raised(self):
# Add two users and give one a model
with session_scope(Session) as session:
user = User()
user.name = 'user1'
user2 = User()
user2.name = 'user2'
session.add_all([user, user2])
session.commit()
# Give them a model
model_run = ModelRun()
model_run.name = "MR1"
model_run.user_id = user.id
model_run.status = self._status(constants.MODEL_RUN_STATUS_PUBLISHED)
session.add(model_run)
# Get the users model runs
with self.assertRaises(ServiceException, msg="Should have raised a ServiceException"):
self.model_run_service.make_public_model(user2, model_run.id)
def test_GIVEN_user_has_completed_model_WHEN_publish_model_THEN_model_published(self):
# Add a user and give them a model
with session_scope(Session) as session:
user = User()
user.name = 'user1'
session.add(user)
session.commit()
# Give them a model
model_run = ModelRun()
model_run.name = "MR1"
model_run.user_id = user.id
model_run.status = self._status(constants.MODEL_RUN_STATUS_COMPLETED)
session.add(model_run)
# Get the users model runs
self.model_run_service.publish_model(user, model_run.id)
with session_scope(Session) as session:
updated_model_run = session.query(ModelRun).join(ModelRunStatus).filter(ModelRun.id == model_run.id).one()
assert_that(updated_model_run.status.name, is_(constants.MODEL_RUN_STATUS_PUBLISHED))
def test_GIVEN_user_has_public_model_run_WHEN_get_published_model_runs_THEN_only_public_model_run_returned(self):
# Add one user and give them a published and unpublished model run
with session_scope(Session) as session:
# First add user
user1 = User()
user1.name = 'user1'
session.add(user1)
session.commit()
# Give them each a model
model_run1 = ModelRun()
model_run1.name = "MR1"
model_run1.user_id = user1.id
model_run2 = ModelRun()
model_run2.name = "MR2"
model_run2.status = self._status(constants.MODEL_RUN_STATUS_PUBLIC)
model_run2.user_id = user1.id
session.add_all([model_run1, model_run2])
# Get the published model runs
model_runs = self.model_run_service.get_published_models()
assert_that(len(model_runs), is_(1))
assert_that(model_runs[0].name, is_("MR2"))
def test_GIVEN_user_has_published_model_run_WHEN_get_model_runs_for_user_THEN_published_model_is_returned(self):
# Add one user and give them a published and unpublished model run
with session_scope(Session) as session:
# First add user
user1 = User()
user1.name = 'user1'
session.add(user1)
session.commit()
# Give a model
model_run1 = ModelRun()
model_run1.name = "MR1"
model_run1.user_id = user1.id
model_run1.status = self._status(constants.MODEL_RUN_STATUS_CREATED)
model_run2 = ModelRun()
model_run2.name = "MR2"
model_run2.status = self._status(constants.MODEL_RUN_STATUS_PUBLISHED)
model_run2.user_id = user1.id
model_run2.status = self._status(constants.MODEL_RUN_STATUS_COMPLETED)
session.add_all([model_run1, model_run2])
# Get the users model runs
model_runs = self.model_run_service.get_models_for_user(user1)
assert_that(len(model_runs), is_(2))
def test_GIVEN_two_users_with_one_model_each_WHEN_get_model_runs_for_user_THEN_returns_correct_model(self):
# Add two users and give them each one model run
with session_scope(Session) as session:
# First add two users
user1 = User()
user1.name = 'user1'
user2 = User()
user2.name = 'user2'
session.add_all([user1, user2])
session.commit()
# Give them each a model
model_run1 = ModelRun()
model_run1.name = "MR1"
model_run1.user_id = user1.id
model_run2 = ModelRun()
model_run2.name = "MR2"
model_run2.user_id = user2.id
session.add_all([model_run1, model_run2])
# Get the users model runs
model_runs = self.model_run_service.get_models_for_user(user1)
assert_that(len(model_runs), is_(1))
assert_that(model_runs[0].name, is_("MR1"))
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'"))
def setup_app(command, conf, vars):
"""
Place any commands to setup joj here - currently creating db tables
:param command:
:param conf:
:param vars:
:return:
"""
# Don't reload the app if it was loaded under the testing environment
if not pylons.test.pylonsapp:
load_environment(conf.global_conf, conf.local_conf)
# Create the tables
Base.metadata.drop_all(bind=Session.bind)
Base.metadata.create_all(bind=Session.bind)
jules_config_parser = JulesNamelistParser()
with session_scope(Session) as session:
user = User()
user.name = 'John Holt'
user.first_name = 'John'
user.last_name = 'Holt'
user.username = '******'
user.email = '*****@*****.**'
user.access_level = "Admin"
user.storage_quota_in_gb = conf['storage_quota_admin_GB']
session.add(user)
user2 = User()
user2.name = 'Matt Kendall'
user2.first_name = 'Matt'
user2.last_name = 'Kendall'
user2.username = '******'
user2.email = '*****@*****.**'
user2.access_level = "Admin"
user2.storage_quota_in_gb = conf['storage_quota_admin_GB']
session.add(user2)
user3 = User()
user3.name = 'Matt Fry'
user3.first_name = 'Matt'
user3.last_name = 'Fry'
user3.username = '******'
user3.email = '*****@*****.**'
user3.access_level = "Admin"
user3.storage_quota_in_gb = conf['storage_quota_admin_GB']
session.add(user3)
user4 = User()
user4.name = 'Eleanor Blyth'
user4.first_name = 'Eleanor'
user4.last_name = 'Blyth'
user4.username = '******'
user4.email = '*****@*****.**'
user4.access_level = "Admin"
user4.storage_quota_in_gb = conf['storage_quota_admin_GB']
session.add(user4)
user5 = User()
user5.name = 'Sandeep Kaur'
user5.first_name = 'Sandeep'
user5.last_name = 'Kaur'
user5.username = '******'
user5.email = '*****@*****.**'
user5.access_level = "Admin"
user5.storage_quota_in_gb = conf['storage_quota_admin_GB']
session.add(user5)
core_user = User()
core_user.name = 'System'
core_user.first_name = 'The'
core_user.last_name = 'System'
core_user.username = constants.CORE_USERNAME
core_user.email = ''
core_user.storage_quota_in_gb = conf['storage_quota_total_GB'] # Total storage for the group workspace
session.add(core_user)
cover_dst = DatasetType(type=constants.DATASET_TYPE_COVERAGE)
session.add(cover_dst)
land_cover_frac_dst = DatasetType(type=constants.DATASET_TYPE_LAND_COVER_FRAC)
session.add(land_cover_frac_dst)
soil_prop_dst = DatasetType(type=constants.DATASET_TYPE_SOIL_PROP)
session.add(soil_prop_dst)
single_cell_dst = DatasetType(type=constants.DATASET_TYPE_SINGLE_CELL)
session.add(single_cell_dst)
transects_dst = DatasetType(type=constants.DATASET_TYPE_TRANSECT)
session.add(transects_dst)
level = UserLevel()
level.name = 'Beginner'
session.add(level)
stat_created = ModelRunStatus(constants.MODEL_RUN_STATUS_CREATED)
stat_submitted = ModelRunStatus(constants.MODEL_RUN_STATUS_SUBMITTED)
stat_pending = ModelRunStatus(constants.MODEL_RUN_STATUS_PENDING)
stat_running = ModelRunStatus(constants.MODEL_RUN_STATUS_RUNNING)
stat_completed = ModelRunStatus(constants.MODEL_RUN_STATUS_COMPLETED)
stat_published = ModelRunStatus(constants.MODEL_RUN_STATUS_PUBLISHED)
stat_public = ModelRunStatus(constants.MODEL_RUN_STATUS_PUBLIC)
stat_failed = ModelRunStatus(constants.MODEL_RUN_STATUS_FAILED)
stat_submit_failed = ModelRunStatus(constants.MODEL_RUN_STATUS_SUBMIT_FAILED)
stat_unknown = ModelRunStatus(constants.MODEL_RUN_STATUS_UNKNOWN)
map(session.add, [stat_created, stat_submitted, stat_pending, stat_running, stat_completed, stat_published,
stat_public, stat_failed, stat_submit_failed, stat_unknown])
session.add(SystemAlertEmail(
code=SystemAlertEmail.GROUP_SPACE_FULL_ALERT,
sent_frequency_in_s=conf['alert_email_frequency_in_s']))
default_code_version = CodeVersion()
default_code_version.name = conf.local_conf['default_code_version']
default_code_version.url_base = 'http://www.jchmr.org/jules/documentation/user_guide/vn3.4/'
default_code_version.is_default = True
session.add(default_code_version)
# Namelists from docs
jules_parameter_parser = JulesParameterParser()
namelist_files = jules_parameter_parser.parse_all("docs/Jules/user_guide/html/namelists/", default_code_version)
for namelist_file in namelist_files:
session.add(namelist_file)
# Output variable from docs
jules_output_variables_parser = JulesOutputVariableParser()
output_variables = jules_output_variables_parser.parse("docs/Jules/user_guide/html/output-variables.html")
session.add_all(output_variables)
# Add WATCH 100 Years run
watch_model_run = jules_config_parser.parse_namelist_files_to_create_a_model_run(
default_code_version,
"Watch data run over the length of the data",
"configuration/Jules/watch",
"Watch 100 Years Data",
namelist_files,
stat_published,
core_user,
None)
watch_model_run.date_created = datetime.datetime(2014, 8, 26, 16, 00, 00)
watch_model_run.date_submitted = datetime.datetime(2014, 8, 26, 16, 00, 00)
watch_model_run.date_started = datetime.datetime(2014, 8, 26, 16, 00, 00)
watch_model_run.last_status_change = datetime.datetime(2014, 8, 26, 16, 00, 00)
watch_model_run.storage_in_mb = 1000
land_cover_file = insert_before_file_extension(WATCH_FRAC_FILE, constants.MODIFIED_FOR_VISUALISATION_EXTENSION)
ancils = [
[WATCH_SOIL_PROPS_FILE, 'Soil Properties', 0, 10, soil_prop_dst],
[land_cover_file, 'Land Cover Fractions', 0, 10, land_cover_frac_dst]
]
for path, var, name, min, max in WATCH_DRIVING_DATA:
ds = Dataset()
ds.name = name
ds.wms_url = conf.local_conf['thredds.server_url'] \
+ "wms/model_runs/run1/data/WATCH_2D/driving/" + path + ".ncml"\
"?service=WMS&version=1.3.0&request=GetCapabilities"
ds.netcdf_url = conf.local_conf['thredds.server_url'] + "dodsC/model_runs/run1/data/WATCH_2D/driving/" + \
path + ".ncml"
ds.data_range_from = min
ds.data_range_to = max
ds.is_categorical = 0
ds.deleted = 0
ds.dataset_type = cover_dst
ds.is_input = True
ds.model_run = watch_model_run
for path, name, min, max, dataset_type in ancils:
ds = Dataset()
ds.name = name
ds.wms_url = conf.local_conf['thredds.server_url'] \
+ "wms/model_runs/run1/" + path + \
"?service=WMS&version=1.3.0&request=GetCapabilities"
ds.netcdf_url = conf.local_conf['thredds.server_url'] + "dodsC/model_runs/run1/" + path
ds.data_range_from = min
ds.data_range_to = max
ds.is_categorical = 0
ds.deleted = 0
ds.dataset_type = dataset_type
ds.is_input = True
ds.model_run = watch_model_run
profiles = ["Monthly"]
outputs = [
['gpp_gb_{}', 'Gridbox gross primary productivity ({})', 0, 1e-7],
['rad_net_{}', 'Surface net radiation of land points ({})', -50, 150],
['resp_p_gb_{}', 'Gridbox plant respiration ({})', 0, 4e-8],
['smc_tot_{}', 'Gridbox total soil moisture in column ({})', 0, 1500],
['sub_surf_roff_{}', 'Gridbox sub-surface runoff ({})', 0, 1e-6],
['surf_roff_{}', 'Gridbox surface runoff ({})', 0, 5e-5],
['swet_liq_tot_{}', 'Gridbox unfrozen soil moisture as fraction of saturation ({})', 0, 1]]
for profile in profiles:
for path_template, name_template, min, max in outputs:
path = path_template.format(profile.lower())
name = name_template.format(profile)
ds = Dataset()
ds.name = name
ds.wms_url = conf.local_conf['thredds.server_url'] \
+ "wms/model_runs/run1/output/majic." + path + ".ncml" + \
"?service=WMS&version=1.3.0&request=GetCapabilities"
ds.netcdf_url = conf.local_conf['thredds.server_url'] + "dodsC/model_runs/run1/output/majic." \
+ path + ".ncml"
ds.data_range_from = min
ds.data_range_to = max
ds.is_categorical = 0
ds.deleted = 0
ds.dataset_type = cover_dst
ds.is_input = False
ds.model_run = watch_model_run
session.add(watch_model_run)
jules_config_parser.parse_all(
"configuration/Jules/scientific_configurations/",
namelist_files,
core_user,
default_code_version,
stat_created)
with session_scope(Session) as session:
watch_driving_data_name = create_watch_driving_data(conf, cover_dst, land_cover_frac_dst, soil_prop_dst,
"configuration/Jules/country.csv")
chess_driving_data_name = create_chess_driving_data(conf, cover_dst, land_cover_frac_dst, soil_prop_dst)
with session_scope(Session) as session:
driving_ds_upload = DrivingDataset()
driving_ds_upload.name = constants.USER_UPLOAD_DRIVING_DATASET_NAME
driving_ds_upload.description = "Choose this option if you wish to use your own uploaded driving data for a " \
"single cell site"
driving_ds_upload.view_order_index = 1000
driving_ds_upload.is_restricted_to_admins = False
parameters_upload = [
[constants.JULES_PARAM_POST_PROCESSING_ID, "3"],
[constants.JULES_PARAM_INPUT_GRID_NX, "1"],
[constants.JULES_PARAM_INPUT_GRID_NY, "1"],
# Default soil properties, hopefully overridden in the background when the user sets the land cover.
[constants.JULES_PARAM_SOIL_PROPS_NVARS, "9"],
[constants.JULES_PARAM_SOIL_PROPS_VAR,
"'b' 'sathh' 'satcon' 'sm_sat' 'sm_crit' 'sm_wilt' 'hcap' 'hcon' 'albsoil'"],
[constants.JULES_PARAM_SOIL_PROPS_USE_FILE, ".false. .false. .false. .false. .false. .false. .false. "
".false. .false."],
[constants.JULES_PARAM_SOIL_PROPS_CONST_VAL,
"0.9 0.0 0.0 50.0 275.0 278.0 10.0 0.0"],
[constants.JULES_PARAM_INITIAL_NVARS, "10"],
[constants.JULES_PARAM_INITIAL_VAR,
"'sthuf' 'canopy' 'snow_tile' 'rgrain' 'tstar_tile' 't_soil' 'cs' 'gs' 'lai' 'canht'"],
[constants.JULES_PARAM_INITIAL_USE_FILE,
".false. .false. .false. .false. .false. .false. .false. .false. .false. .false."],
[constants.JULES_PARAM_INITIAL_CONST_VAL,
"0.9 0.0 0.0 50.0 275.0 278.0 10.0 0.0 1.0 2.0"]
]
model_run_service = ModelRunService()
for constant, value in parameters_upload:
ddpv = DrivingDatasetParameterValue(model_run_service, driving_ds_upload, constant, value)
driving_ds_upload.parameter_values.append(ddpv)
session.add(driving_ds_upload)
land_cover_types = {1: 'Broad-leaved Tree', 2: 'Needle-leaved Tree', 3: 'C3 Grass', 4: 'C4 Grass', 5: 'Shrub',
6: 'Urban', 7: 'Lake', 8: 'Soil', 9: constants.FRACTIONAL_ICE_NAME}
for index in land_cover_types:
land_cover_type = LandCoverValue()
land_cover_type.index = index
land_cover_type.name = land_cover_types[index]
session.add(land_cover_type)
with session_scope() as session:
watch_model = session.query(ModelRun).filter(ModelRun.name == watch_model_run.name).one()
science_config = session.query(ModelRun).filter(ModelRun.name == "Full carbon cycle").one()
driving_dataset = session.query(DrivingDataset).filter(DrivingDataset.name == watch_driving_data_name).one()
watch_model.science_configuration_id = science_config.id
watch_model.driving_dataset_id = driving_dataset.id
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_non_existent_user_WHEN_get_model_runs_for_user_THEN_returns_empty_list(self):
user = User()
user.id = -100
user.name = "Doesn't Exist"
model_runs = self.model_run_service.get_models_for_user(user)
assert_that(model_runs, is_([]))
def create_in_session(self,
session,
username,
first_name,
last_name,
email,
access_level,
institution="",
workbench_username=None):
"""
Creates a user within a session
:param session: session to use
:param username: The login name of the user
:param first_name: User's first name
:param last_name: User's last name
:param email: User's email address
:param access_level: Set to 'Admin' for administrative functions
:param institution: users institution may be blank
:param workbench_username: username within the workbench may be none
:return: nothing
"""
user = User()
user.username = username.strip()
user.name = " ".join([first_name, last_name])
user.email = email
user.access_level = access_level
user.first_name = first_name
user.last_name = last_name
user.institution = institution
user.workbench_username = workbench_username
if user.access_level == constants.USER_ACCESS_LEVEL_ADMIN:
user.storage_quota_in_gb = config['storage_quota_admin_GB']
else:
user.storage_quota_in_gb = config['storage_quota_user_GB']
session.add(user)
return user
