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"""Tests for earthdiagnostics.cmorizer module"""
from earthdiagnostics.cmorizer import Cmorizer
from earthdiagnostics.utils import TempFile, Utils
from earthdiagnostics.data_convention import DataConvention
from bscearth.utils import log
from unittest import TestCase
import os
import tempfile
import shutil
import iris
import iris.cube
from iris.coords import DimCoord
import tarfile
import numpy as np
import six
def _get_variable_and_alias(self, variable):
mock_alias = Mock()
mock_alias.basin = None
mock_alias.grid = None
mock_variable = self._get_variable(variable)
return mock_alias, mock_variable
def _get_variable(self, variable, silent=False):
mock_variable = Mock()
mock_variable.short_name = variable
mock_variable.domain = 'domain'
def _get_file_path(self, *args, **kwargs):
return os.path.join(self.tmp_dir, args[3], '{0[3]}.nc'.format(args))
def _get_file_path_grib(self, *args, **kwargs):
return os.path.join(self.tmp_dir, args[3], str(args[6]), '{0[3]}.nc'.format(args))
self.tmp_dir = tempfile.mkdtemp()
self.data_manager = Mock()
self.data_manager.is_cmorized.return_value = False
self.data_manager.config.data_dir = os.path.join(self.tmp_dir, 'data')
self.data_manager.config.scratch_dir = os.path.join(self.tmp_dir, 'scratch')
TempFile.scratch_folder = self.data_manager.config.scratch_dir
self.data_manager.config.data_convention = create_autospec(DataConvention)
self.data_manager.config.data_convention.name = 'data_convention'
self.data_manager.config.data_convention.lat_name = 'lat'
self.data_manager.config.data_convention.lon_name = 'lon'
self.data_manager.config.data_convention.get_file_path = self._get_file_path
self.data_manager.config.var_manager.get_variable_and_alias = self._get_variable_and_alias
self.data_manager.config.var_manager.get_variable = self._get_variable
self.data_manager.variable_list = self.data_manager.config.var_manager
self.data_manager.config.experiment.expid = 'expid'
self.data_manager.config.experiment.model = 'model'
self.data_manager.config.experiment.experiment_name = 'experiment_name'
self.data_manager.config.experiment.num_chunks = 1
self.data_manager.config.experiment.chunk_size = 1
self.data_manager.config.experiment.institute = 'institute'
self.data_manager.config.experiment.get_member_str.return_value = 'member'
self.data_manager.config.experiment.atmos_timestep = 6
self.data_manager.config.cmor.force = False
self.data_manager.config.cmor.ocean = True
self.data_manager.config.cmor.atmosphere = True
self.data_manager.config.cmor.use_grib = True
self.data_manager.config.cmor.filter_files = ''
self.data_manager.config.cmor.associated_experiment = 'associated_experiment'
self.data_manager.config.cmor.initialization_method = 'initialization_method'
self.data_manager.config.cmor.initialization_description = 'initialization_description'
self.data_manager.config.cmor.physics_version = 'physics_version'
self.data_manager.config.cmor.physics_description = 'physics_description'
self.data_manager.config.cmor.initialization_description = 'initialization_description'
self.data_manager.config.cmor.associated_model = 'initialization_description'
self.data_manager.config.cmor.source = 'source'
self.data_manager.config.cmor.get_requested_codes.return_value = {228, 142, 143, 201, 202, 129, 169, 180}
self.data_manager.config.cmor.get_variables.return_value = {228, 142, 143, 201, 202, 129, 169, 180}
self.data_manager.config.cmor.get_levels.return_value = None
os.makedirs(self.data_manager.config.data_dir)
os.makedirs(self.data_manager.config.scratch_dir)
def _create_ocean_files(self, filename, tar_name, gzip=False, backup=False):
folder_path = os.path.join(self.data_manager.config.data_dir, 'expid', 'original_files', '19900101', 'member',
'outputs')
file_path, filename = self._create_file(folder_path, filename, gzip)
if backup:
filename = os.path.join('backup', filename)
tar = tarfile.TarFile(os.path.join(folder_path, tar_name), mode='w')
tar.add(file_path, arcname=filename, recursive=False)
tar.close()
os.remove(file_path)
def _create_mma_files(self, filename, tar_name, gzip=False):
folder_path = os.path.join(self.data_manager.config.data_dir, 'expid', 'original_files', '19900101', 'member',
'outputs')
filepath_gg, filename_gg = self._create_file(folder_path, filename.replace('??', 'GG'), gzip)
filepath_sh, filename_sh = self._create_file(folder_path, filename.replace('??', 'SH'), gzip)
tar = tarfile.TarFile(os.path.join(folder_path, tar_name), mode='w')
tar.add(filepath_gg, arcname=filename_gg, recursive=False)
tar.add(filepath_sh, arcname=filename_sh, recursive=False)
tar.close()
os.remove(filepath_gg)
os.remove(filepath_sh)
def _create_file(self, folder_path, filename, gzip):
var1 = self._create_sample_cube('Variable 1', 'var1', threed=False, time_bounds=True)
var2 = self._create_sample_cube('Variable 2', 'var2', threed=True, time_bounds=True)
if not os.path.isdir(folder_path):
os.makedirs(folder_path)
file_path = os.path.join(folder_path, filename)
iris.save((var1, var2), file_path, zlib=True)
if gzip:
import subprocess
process = subprocess.Popen(('gzip', file_path), stdout=subprocess.PIPE)
comunicate = process.communicate()
file_path = "{0}.gz".format(file_path)
filename = "{0}.gz".format(filename)
if process.returncode != 0:
raise Exception('Can not compress: {0}'.format(comunicate))
def _create_sample_cube(self, long_name, var_name, threed, time_bounds):
coord_data = np.array([1, 2], np.float)
lat = DimCoord(coord_data, standard_name='latitude', long_name='latitude', var_name='lat',
units='degrees_north')
lon = DimCoord(coord_data, standard_name='longitude', long_name='longitude', var_name='lon',
units='degrees_east')
time = DimCoord(coord_data, standard_name='time', long_name='time', var_name='time',
units='days since 1950-01-01')
if time_bounds:
time.bounds = np.array([[0.5, 1.5], [1.5, 2.5]], np.float)
if threed:
data = np.random.rand(2, 2, 2, 2).astype(np.float)
depth = DimCoord(coord_data, standard_name='depth', long_name='Depth', var_name='lev', units='m')
else:
data = np.random.rand(2, 2, 2).astype(np.float)
cube = iris.cube.Cube(data, long_name=long_name, var_name=var_name)
cube.add_dim_coord(time, 0)
cube.add_dim_coord(lat, 1)
cube.add_dim_coord(lon, 2)
if threed:
cube.add_dim_coord(depth, 3)
return cube
def _test_ocean_cmor(self, success=True, error=False, critical=False, warnings=False, message='', check_vars=None):
self._test_cmorization(success=success, error=error, critical=critical, warnings=warnings, message=message,
def _test_atmos_cmor(self, success=True, error=False, critical=False, warnings=False, message='', check_vars=None):
self._test_cmorization(success=success, error=error, critical=critical, warnings=warnings, message=message,
ocean=False, check_vars=check_vars)
def _test_cmorization(self, success=True, error=False, critical=False, warnings=False, message='', ocean=True,
self._check_logs(critical, error, message, ocean, success, warnings)
if check_vars:
for variable, status in six.iteritems(check_vars):
if status:
self.assertTrue(os.path.isfile(os.path.join(self.tmp_dir, variable, '{}.nc'.format(variable))))
else:
self.assertFalse(os.path.isfile(os.path.join(self.tmp_dir, variable, '{}.nc'.format(variable))))
def _check_logs(self, critical, error, message, ocean, success, warnings):
if six.PY3:
with self.assertLogs(log.Log.log) as cmd:
cmorizer = Cmorizer(self.data_manager, '19900101', 0)
if ocean:
cmorizer.cmorize_ocean()
else:
cmorizer.cmorize_atmos()
if message:
self.assertTrue([record for record in cmd.records if record.message == message])
else:
for level, value in six.iteritems({log.Log.RESULT: success, log.Log.ERROR: error,
log.Log.CRITICAL: critical, log.Log.WARNING: warnings}):
if value:
self.assertTrue([record for record in cmd.records if record.levelno == level])
else:
self.assertFalse([record for record in cmd.records if record.levelno == level])
else:
cmorizer = Cmorizer(self.data_manager, '19900101', 0)
if ocean:
cmorizer.cmorize_ocean()
else:
cmorizer.cmorize_atmos()
def test_skip_ocean_cmorization(self):
"""Test ocean cmorization flag disabled option"""
self.data_manager.config.cmor.ocean = False
self._test_ocean_cmor(message='Skipping ocean cmorization due to configuration')
"""Test atmos cmorization flag disabled option"""
self.data_manager.config.cmor.atmosphere = False
if six.PY3:
with self.assertLogs(log.Log.log) as cmd:
cmorizer = Cmorizer(self.data_manager, '19900101', 0)
cmorizer.cmorize_atmos()
self.assertTrue([record for record in cmd.records if
record.message == 'Skipping atmosphere cmorization due to configuration'])
else:
cmorizer = Cmorizer(self.data_manager, '19900101', 0)
cmorizer.cmorize_ocean()
def test_skip_when_cmorized(self):
"""Test cmorization skipped if already done"""
self._create_ocean_files('expid_1d_19900101_19900131.nc', 'MMO_19900101-19900131.tar')
self.data_manager.is_cmorized.return_value = True
self._test_ocean_cmor(message='No need to unpack file 1/1')
def test_skip_when_not_requested(self):
"""Test cmorization skipped if chunk is not requested"""
self._create_ocean_files('expid_1d_19900101_19900131.nc', 'MMO_19900101-19900131.tar')
self.data_manager.config.cmor.chunk_cmorization_requested.return_value = False
self._test_ocean_cmor(message='No need to unpack file 1/1')
self._create_ocean_files('expid_1d_19900101_19900131.nc', 'MMO_19900101-19900131.tar')
self.data_manager.is_cmorized.return_value = True
self.data_manager.config.cmor.force = True
self._test_ocean_cmor()
"""Test ocean cmorization report error if no input data"""
self._test_ocean_cmor(success=False, error=True)
def test_ocean_cmorization_not_vars_requested(self):
"""Test ocean cmorization report success if no vars qhere requested"""
self._create_ocean_files('expid_1d_19900101_19900131.nc', 'MMO_19900101-19900131.tar')
self.data_manager.config.cmor.any_required.return_value = False
self._test_ocean_cmor(check_vars={'var1': False, 'var2': False})
def test_ocean_cmorization_no_vars_recognized(self):
"""Test ocean cmorization report success if no vars where recognized"""
self._create_ocean_files('expid_1d_19900101_19900131.nc', 'MMO_19900101-19900131.tar')
def not_recognized(*args):
return None, None
self.data_manager.config.var_manager.get_variable_and_alias = not_recognized
self._test_ocean_cmor(check_vars={'var1': False, 'var2': False})
def test_ocean_cmorization_var2_not_requested(self):
"""Test ocean cmorization with var2 not recognized"""
self._create_ocean_files('expid_1d_19900101_19900131.nc', 'MMO_19900101-19900131.tar')
def _reject_var2(cmor_var):
return cmor_var.short_name != 'var2'
self.data_manager.config.cmor.cmorize = _reject_var2
self._test_ocean_cmor(check_vars={'var1': True, 'var2': False})
"""Test basic ocean cmorization"""
self._create_ocean_files('expid_1d_19900101_19900131.nc', 'MMO_19900101-19900131.tar')
self._test_ocean_cmor(check_vars={'var1': True, 'var2': True})
def test_ocean_cmorization_with_filter(self):
"""Test ocean cmorization filtering files"""
self._create_ocean_files('expid_1d_19900101_19900131.nc', 'MMO_19900101-19900131.tar')
self.data_manager.config.cmor.filter_files = 'expid'
self._test_ocean_cmor(check_vars={'var1': True, 'var2': True})
def test_ocean_cmorization_with_bad_filter(self):
"""Test ocean cmorization fails if a bad filter is added"""
self._create_ocean_files('expid_1d_19900101_19900131.nc', 'MMO_19900101-19900131.tar')
self.data_manager.config.cmor.filter_files = 'badfilter'
self._test_ocean_cmor(warnings=True, check_vars={'var1': False, 'var2': False})
"""Test ocean cmorization if tars are also zipped"""
self._create_ocean_files('expid_1d_19900101_19900131.nc', 'MMO_19900101-19900131.tar', gzip=True)
self._test_ocean_cmor(check_vars={'var1': True, 'var2': True})
def test_ocean_cmorization_backup(self):
"""Test ocean cmorization when files are in backup path"""
self._create_ocean_files('expid_1d_19900101_19900131.nc', 'MMO_19900101-19900131.tar', backup=True)
self._test_ocean_cmor(check_vars={'var1': True, 'var2': True})
"""Test ocean cmorization when files are PPO"""
self._create_ocean_files('expid_1d_19900101_19900131.nc', 'PPO_expid_1D_xx_19900101_19900131.tar')
self._test_ocean_cmor(check_vars={'var1': True, 'var2': True})
"""Test ocean cmorization when files are diags"""
self._create_ocean_files('expid_1d_19900101_19900131.nc', 'diags_expid_1D_xx_19900101_19900131.tar')
self._test_ocean_cmor(check_vars={'var1': True, 'var2': True})
def test_atmos_cmorization(self):
"""Test basic atmos cmorization from nc"""
self._create_mma_files('MMA_1d_??_19900101_19900131.nc', 'MMA_expid_19901101_fc0_19900101-19900131.tar')
self._test_atmos_cmor(check_vars={'var1': True, 'var2': True})
def test_skip_when_not_requested_mma(self):
"""Test atmos cmorization is skipped if chunk is not requested"""
self._create_mma_files('MMA_1d_??_19900101_19900131.nc', 'MMA_expid_19901101_fc0_19900101-19900131.tar')
self.data_manager.config.cmor.chunk_cmorization_requested.return_value = False
self._test_atmos_cmor(message='No need to unpack file 1/1')
def test_force_mma(self):
"""Test force atmos cmorization"""
self._create_mma_files('MMA_1d_??_19900101_19900131.nc', 'MMA_expid_19901101_fc0_19900101-19900131.tar')
self.data_manager.is_cmorized.return_value = True
self.data_manager.config.cmor.force = True
self._test_atmos_cmor()
def test_atmos_cmorization_no_mma_files(self):
"""Test atmos cmorization report error if there are no files"""
self._test_atmos_cmor(success=False, error=True)
def _create_grib_files(self, filename, month):
coord_data = np.array([0, 1], np.float)
folder_path = os.path.join(self.data_manager.config.data_dir, 'expid', 'original_files', '19900101', 'member',
'outputs')
self._create_file_for_grib(coord_data, folder_path, filename.replace('??', 'GG'), [142, 143, 129, 169, 180],
month)
self._create_file_for_grib(coord_data, folder_path, filename.replace('??', 'SH'), [201, 202],
month)
def _create_file_for_grib(self, coord_data, folder_path, filename, codes, month):
lat = DimCoord(coord_data, standard_name='latitude', long_name='latitude', var_name='lat',
units='degrees_north')
lon = DimCoord(coord_data, standard_name='longitude', long_name='longitude', var_name='lon',
units='degrees_east')
month_days = calendar.monthrange(1990, month)[1]
month -= 1
time_data = np.arange(0.25, month_days + 0.25, 0.25, np.float) + month * 31
time = DimCoord(time_data, standard_name='time', long_name='time', var_name='time',
units='days since 1990-01-01 00:00:00')
var = iris.cube.Cube(np.ones((month_days * 4, 2, 2), np.float) * code,
long_name='Variable {}'.format(code),
var_name='var{}'.format(code))
for x, data in enumerate(time_data):
var.data[x, ...] += data
var.add_dim_coord(time, 0)
var.add_dim_coord(lat, 1)
var.add_dim_coord(lon, 2)
var.attributes['table'] = np.int32(128)
var.attributes['code'] = np.int32(code)
if not os.path.isdir(folder_path):
os.makedirs(folder_path)
file_path = os.path.join(folder_path, filename)
iris.save(variables, file_path, zlib=True, local_keys=('table', 'code'))
Utils.cdo.settaxis('1990-0{}-01,06:00,6hour'.format(month + 1),
input=file_path,
output=file_path.replace('.nc', '.grb'),
options='-f grb2')
os.remove(file_path)
def test_grib_cmorization(self):
self.data_manager.config.data_convention.get_file_path = self._get_file_path_grib
self.data_manager.config.experiment.chunk_size = 2
self.data_manager.get_file_path = self._get_file_path_grib
self._create_grib_files('ICM??expid+19900{}.nc', 1)
self._create_grib_files('ICM??expid+19900{}.nc', 2)
variables = {
'CP': 143,
'EWSS': 180,
'MN2T': 202,
'MX2T': 201,
'SSRD': 169,
'Z': 129
}
for var, code in six.iteritems(variables):
self.assertTrue(os.path.isdir(os.path.join(self.tmp_dir, var)))
base_data = np.ones((2, 2), np.float) * code
if var in ('EWSS', 'TP', 'MN2T', 'MX2T', 'SSRD', 'TP'):
if var == 'MX2T':
month_offsets = np.array((16, 45.5))
daily_offsets = np.arange(1.0, 60.0)
elif var == 'MN2T':
month_offsets = np.array((15.25, 44.75))
daily_offsets = np.arange(0.25, 59.25)
else:
month_offsets = np.array((15.625, 45.125))
daily_offsets = np.arange(0.625, 59.625)
hourly_offsets = np.arange(0.25, 59.25, 0.25)
else:
month_offsets = np.array((15.5, 44.875))
daily_offsets = np.arange(0.375, 59.375)
daily_offsets[0] = 0.5
hourly_offsets = np.arange(0.25, 59, 0.25)
if code == 129:
factor = 9.81
elif code in (180, 169):
base_data = np.ones((2, 2, 2), np.float) * (142 + 143)
month_offsets *= 2
daily_offsets *= 2
hourly_offsets *= 2
base_data /= factor
month_offsets /= factor
daily_offsets /= factor
hourly_offsets /= factor
monthly = iris.load_cube(os.path.join(self.tmp_dir, var, 'mon', '{}.nc'.format(var)))
self._test_data(monthly, base_data, month_offsets, var, 'Month')
daily = iris.load_cube(os.path.join(self.tmp_dir, var, 'day', '{}.nc'.format(var)))
self._test_data(daily, base_data, daily_offsets, var, 'Day')
hourly = iris.load_cube(os.path.join(self.tmp_dir, var, '6hr', '{}.nc'.format(var)))
self._test_data(hourly, base_data, hourly_offsets, var, 'Hour')
def _test_data(self, data, base_data, offsets, var, freq):
self.assertEqual(data.coord('time').shape, (len(offsets),))
for x, offset in enumerate(offsets):
self.assertTrue(np.allclose(data.data[x, ...], base_data + offset),
'{} {} data wrong for {}: {}'.format(freq, x, var, data.data[x, ...] - base_data))