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
for parameter in parameters:
if parameter_dict_name.lower() == parameter.name.lower():
pv = ParameterValue()
pv.parameter = parameter
pv.group_id = group_id
pv.value = parameter_dict_value
return pv
log.critical("Can not find matching parameter for %s" % parameter_dict_name)
exit()
if __name__ == "__main__":
logging.basicConfig(level=logging.DEBUG)
parser = JulesParameterParser()
base = '../docs/Jules/user_guide/html/namelists/'
default_namelist_files = parser.parse_all(base, None)
jules_namelist_parser = JulesNamelistParser()
jules_namelist_parser.parse_all('../configuration/Jules/scientific_configurations/',
default_namelist_files, None, None, None)
watch_model_run = jules_namelist_parser.parse_namelist_files_to_create_a_model_run(
None,
"Watch data run over the length of the data",
"../configuration/Jules/watch",
"Watch 100 Years Data",
default_namelist_files,
None,
None,