def multi_call_test():
cmor.setup(inpath='Tables',netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/common_user_input.json")
table='CMIP6_Amon.json'
cmor.load_table(table)
axes = [ {'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]},
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('ts', 'K', axis_ids)
cmor.write(varid, [275], time_vals = [15], time_bnds = [ [0,30] ])
print 'First write worked as expected'
try:
cmor.write(varid, [275], time_vals = [15], time_bnds = [ [0], [30] ])
raise Exception,"We shouldn't be getting in here"
except:
print 'Second write that should have failed did fail, good!'
pass
cmor.close(varid)
print 'Success'
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(
inpath='Tables',
netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_CMIP6_CV_badgridlabel.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso", axis_ids=[itime], units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
except:
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
testOK = self.getAssertTest()
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
# ------------------------------------------
# Check error after signal handler is back
# ------------------------------------------
self.assertIn("\"gs1n\"", testOK)
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath="Tables", netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_CMIP6_CV_badsourcetypeRequired.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(
table_entry="time",
units="months since 2010",
coord_vals=numpy.array([0, 1, 2, 3, 4.0]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.0]),
)
ivar = cmor.variable(table_entry="masso", axis_ids=[itime], units="kg")
data = numpy.random.random(5)
for i in range(0, 5):
a = cmor.write(ivar, data[i:i])
except:
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, "w", 0)
sys.stderr = os.fdopen(self.newstderr, "w", 0)
testOK = self.getAssertTest()
# ------------------------------------------
# Check error after signal handler is back
# ------------------------------------------
self.assertIn('"AOGCM ISM"', testOK)
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
global testOK
cmor.setup(inpath="Tables", netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_CMIP6_CV_furtherinfourl.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(
table_entry="time",
units="months since 2010",
coord_vals=numpy.array([0, 1, 2, 3, 4.0]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.0]),
)
ivar = cmor.variable(table_entry="masso", axis_ids=[itime], units="kg")
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
cmor.close()
except:
raise
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, "w", 0)
sys.stderr = os.fdopen(self.newstderr, "w", 0)
f = cdms2.open(cmor.get_final_filename(), "r")
a = f.getglobal("further_info_url")
self.assertEqual("http://furtherinfo.es-doc.org/CMIP6.NCC.MIROC-ESM.piControl-withism.none.r1i1p1f1", a)
def testCMIP6(self):
''' '''
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_CMIP6_CV_HISTORY.json")
cmor.load_table("CMIP6_Omon.json")
cmor.set_cur_dataset_attribute("history", "set for CMIP6 unittest")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso", axis_ids=[itime], units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
cmor.close()
f = cdms2.open(cmor.get_final_filename(), "r")
a = f.getglobal("history")
self.assertIn("set for CMIP6 unittest", a)
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
def testCMIP6(self):
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json("Test/common_user_input_hier.json")
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010', coord_vals=numpy.array(
[0, 1, 2, 3, 4.]), cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
# ,time_vals=numpy.array([i,]),time_bnds=numpy.array([i,i+1]))
cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
cmor.close()
f = cdms2.open(cmor.get_final_filename() , 'r')
self.assertEqual(f.coder, "Denis Nadeau")
self.assertEqual(f.hierarchical_attr_setting, "information")
self.assertEqual(f.creator, "PCMDI")
self.assertEqual(f.model, "Ocean Model")
self.assertEqual(f.country, "USA")
f.close()
def testCMIP6(self):
try:
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/CMOR_input_example.json")
cmor.set_cur_dataset_attribute("experiment_id", "piControlbad")
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010', coord_vals=numpy.array(
[0, 1, 2, 3, 4.]), cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
# ,time_vals=numpy.array([i,]),time_bnds=numpy.array([i,i+1]))
cmor.write(ivar, data[i:i])
cmor.close()
except BaseException:
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
testOK = self.getAssertTest()
self.assertIn('piControlbad', testOK)
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
global testOK
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json("Test/CMOR_input_example.json")
cmor.set_cur_dataset_attribute("source_id", "invalid")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
cmor.close()
except BaseException:
pass
self.assertCV("invalid")
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
global testOK
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/common_user_input.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time",
units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
filen = cmor.close()
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
f = cdms2.open(cmor.get_final_filename(), "r")
a = f.getglobal("tracking_id").split('/')[0]
self.assertNotIn("hdl:21.14100/", a)
except:
raise
def path_test():
cmor.setup(inpath='Test',netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_YYYMMDDHH_exp_fmt.json")
table='Tables/CMIP6_Amon.json'
cmor.load_table(table)
axes = [ {'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
'coord_vals': [15],
'cell_bounds': [0, 30]
},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]},
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('ts', 'K', axis_ids)
cmor.write(varid, [273])
path=cmor.close(varid, file_name=True)
print "Saved file: ",path
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
global testOK
cmor.setup(inpath='Tables',
netcdf_file_action=cmor.CMOR_REPLACE,
logfile=self.tmpfile)
cmor.dataset_json("Test/CMOR_input_example.json")
cmor.set_cur_dataset_attribute("source_id", "invalid")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time",
units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
cmor.close()
except BaseException:
pass
self.assertCV("invalid")
def testCMIP6_CDMS2(self):
import cdms2
cmor.setup(inpath='Tables',
netcdf_file_action=cmor.CMOR_REPLACE,
logfile=self.tmpfile)
cmor.dataset_json("Test/common_user_input_hier.json")
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time",
units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso", axis_ids=[itime], units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
# ,time_vals=numpy.array([i,]),time_bnds=numpy.array([i,i+1]))
cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
cmor.close()
f = cdms2.open(cmor.get_final_filename(), 'r')
self.assertEqual(f.coder, "Denis Nadeau")
self.assertEqual(f.hierarchical_attr_setting, "information")
self.assertEqual(f.creator, "PCMDI")
self.assertEqual(f.model, "Ocean Model")
self.assertEqual(f.country, "USA")
f.close()
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables',
netcdf_file_action=cmor.CMOR_REPLACE,
logfile=self.tmpfile)
cmor.dataset_json("Test/common_user_input_NOID.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time",
units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
cmor.close()
except BaseException:
pass
self.assertCV("Control Vocabulary file")
def testCMIP6(self):
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json("Test/CMOR_input_example.json")
cmor.set_cur_dataset_attribute("tracking_prefix", "hdl:21.14100")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2011',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
a = cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
cmor.close()
f = cdms2.open(cmor.get_final_filename(), "r")
a = f.getglobal("tracking_id").split('/')[0]
self.assertIn("hdl:21.14100", a)
def test():
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/common_user_input.json")
table = 'CMIP6_Amon.json'
cmor.load_table(table)
axes = [{'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]}
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('ts', 'K', axis_ids)
cmor.write(varid, [275], time_vals=[15], time_bnds=[[0, 30]])
cmor.close(varid)
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json("Test/CMOR_input_example.json")
cmor.set_cur_dataset_attribute("physics_index", "1A")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
cmor.close()
except BaseException:
pass
# ------------------------------------------
# Check error after signal handler is back
# ------------------------------------------
self.assertCV("\"1A\"")
def multi_call_test():
cmor.setup(inpath='Tables',netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_jamie_2.json")
table='CMIP6_Amon.json'
cmor.load_table(table)
axes = [ {'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]},
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('ts', 'K', axis_ids)
cmor.write(varid, [275], time_vals = [15], time_bnds = [ [0,30] ])
print 'First write worked as expected'
try:
cmor.write(varid, [275], time_vals = [15], time_bnds = [ [0], [30] ])
raise Exception,"We shouldn't be getting in here"
except:
print 'Second write that should have failed did fail, good!'
pass
cmor.close(varid)
print 'Success'
def testCMIP6_CDMS2(self):
import cdms2
cmor.setup(inpath='Tables',
netcdf_file_action=cmor.CMOR_REPLACE,
logfile=self.tmpfile)
cmor.dataset_json("Test/CMOR_input_example.json")
cmor.set_cur_dataset_attribute("tracking_prefix", "hdl:21.14100")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time",
units='months since 2011',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso", axis_ids=[itime], units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
a = cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
cmor.close()
f = cdms2.open(cmor.get_final_filename(), "r")
a = f.getglobal("tracking_id").split('/')[0]
self.assertIn("hdl:21.14100", a)
def testCMIP6(self):
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json("Test/CMOR_input_example.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2000',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
cmor.close()
f = cdms2.open(cmor.get_final_filename(), "r")
a = f.getglobal("further_info_url")
self.assertEqual(
"https://furtherinfo.es-doc.org/CMIP6.PCMDI.PCMDI-test-1-0.piControl-withism.none.r3i1p1f1",
a)
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json(
"Test/test_python_CMIP6_CV_badsourcetypeCHEMAER.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
cmor.close()
except BaseException:
pass
self.assertCV("invalid source")
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/common_user_input.json")
cmor.set_cur_dataset_attribute("nominal_resolution", "335 km")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time",
units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
cmor.close()
except:
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
testOK = self.getAssertTest()
self.assertIn("\"335 km\"", testOK)
def testCMIP6_CDMS2(self):
import cdms2
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables',
netcdf_file_action=cmor.CMOR_REPLACE,
logfile=self.tmpfile)
cmor.dataset_json("Test/CMOR_input_example.json")
cmor.load_table("CMIP6_Omon.json")
cmor.set_cur_dataset_attribute("history", "set for CMIP6 unittest")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time",
units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso", axis_ids=[itime], units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
f = cdms2.open(cmor.get_final_filename(), "r")
a = f.getglobal("history")
self.assertIn("set for CMIP6 unittest", a)
def testCMIP6(self):
''' '''
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/common_user_input.json")
cmor.load_table("CMIP6_Omon.json")
cmor.set_cur_dataset_attribute("history", "set for CMIP6 unittest")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time",
units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso", axis_ids=[itime], units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
cmor.close()
f = cdms2.open(cmor.get_final_filename(), "r")
a = f.getglobal("history")
self.assertIn("set for CMIP6 unittest", a)
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
def main():
missing = -99.
cmor.setup(inpath='Tables',
netcdf_file_action = cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_jamie_3.json")
table = 'CMIP6_Amon.json'
cmor.load_table(table)
axes = [ {'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]},
]
values = numpy.array([missing], numpy.float32)
myma = numpy.ma.masked_values(values, missing)
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('ts', 'K', axis_ids, missing_value = myma.fill_value)
cmor.write(varid, myma, time_vals = [15], time_bnds = [ [0,30] ])
cmor.close(varid)
def TestCase(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_CMIP6_CV_badsourcetypeCHEMAER.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso", axis_ids=[itime], units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
except:
raise
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
def testCMIP6(self):
''' '''
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json("Test/CMOR_input_example.json")
cmor.load_table("CMIP6_Omon.json")
cmor.set_cur_dataset_attribute("history", "set for CMIP6 unittest")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso", axis_ids=[itime], units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
f = cdms2.open(cmor.get_final_filename(), "r")
a = f.getglobal("history")
self.assertIn("set for CMIP6 unittest", a)
def testCMIP6(self):
try:
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/CMOR_input_example.json")
cmor.set_cur_dataset_attribute("activity_id", "CMIP5-PMIP")
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010', coord_vals=numpy.array(
[0, 1, 2, 3, 4.]), cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
# ,time_vals=numpy.array([i,]),time_bnds=numpy.array([i,i+1]))
cmor.write(ivar, data[i:i])
cmor.close()
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
testOK = self.getAssertTest()
self.assertIn('CMIP5-PMIP', testOK)
except BaseException:
raise
def setup_cmor(varname,
tables,
user_input_path,
component='ocean',
table=None):
'''Set up CMOR for MPAS-Ocean or MPAS-Seaice'''
logfile = os.path.join(os.getcwd(), 'cmor_logs')
if not os.path.exists(logfile):
os.makedirs(logfile)
logfile = os.path.join(logfile, varname + '.log')
cmor.setup(inpath=tables,
netcdf_file_action=cmor.CMOR_REPLACE,
logfile=logfile)
cmor.dataset_json(str(user_input_path))
if table is None:
if component == 'ocean':
table = 'CMIP6_Omon.json'
elif component == 'seaice':
table = 'CMIP6_SImon.json'
else:
raise ValueError('Unexpected component {}'.format(component))
try:
cmor.load_table(table)
except Exception:
raise ValueError('Unable to load table from {}'.format(varname))
def test():
cmor.setup(inpath='Tables',netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_obs4MIPs.json")
table='CMIP6_Amon.json'
cmor.load_table(table)
axes = [ {'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]},
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('ts', 'K', axis_ids)
cmor.write(varid, [275], time_vals = [15], time_bnds = [ [0,30] ])
cmor.close(varid)
def setUp(self):
cmor.setup(inpath='Test',
netcdf_file_action=cmor.CMOR_REPLACE_4)
cmor.dataset_json("Test/CMOR_input_example.json")
self.path = None
def testCMIP6(self):
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
try:
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json("Test/CMOR_input_example.json")
cmor.set_cur_dataset_attribute("grid_label", "gr-0")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(
table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
self.delete_files += [cmor.close(ivar, True)]
cmor.close()
except BaseException:
pass
# ------------------------------------------
# Check error after signal handler is back
# ------------------------------------------
self.assertCV("\"gr-0\"")
def initialize(metadata_path=conf_path_default, mode=cmor_mode_default, tabledir=table_dir_default,
tableprefix=prefix_default, outputdir=None, logfile=None, create_subdirs=True):
global prefix, table_dir, targets, metadata, cmor_mode
with open(metadata_path, 'r') as f:
metadata = json.load(f)
cmor_mode = mode
table_dir = tabledir
prefix = tableprefix
validate_setup_settings()
logname = logfile
if logfile is not None:
logname = '.'.join(logfile.split('.')[:-1] + ["cmor", "log"])
cmor.setup(table_dir, cmor_mode, logfile=logname, create_subdirectories=(1 if create_subdirs else 0))
if outputdir is not None:
metadata["outpath"] = outputdir
if "outpath" not in metadata:
metadata["outpath"] = os.path.join(os.getcwd(), "cmor")
hist = metadata.get("history", "")
newline = "processed by ece2cmor {version}, git rev. " \
"{sha}\n".format(version=__version__.version, sha=cmor_utils.get_git_hash())
metadata["history"] = newline + hist if len(hist) != 0 else newline
for key, val in metadata.items():
log.info("Metadata attribute %s: %s", key, val)
with tempfile.NamedTemporaryFile("r+w", suffix=".json", delete=False) as tmp_file:
json.dump(metadata, tmp_file)
cmor.dataset_json(tmp_file.name)
cmor.set_cur_dataset_attribute("calendar", "proleptic_gregorian")
targets = cmor_target.create_targets(table_dir, prefix)
tmp_file.close()
os.remove(tmp_file.name)
def setUp(self):
cmor.setup(inpath='Test',
netcdf_file_action=cmor.CMOR_REPLACE_4)
cmor.dataset_json("Test/CMOR_input_example.json")
self.path = None
def main():
missing = -99.
cmor.setup(inpath='Tables',
netcdf_file_action = cmor.CMOR_REPLACE)
cmor.dataset_json("Test/common_user_input.json")
table = 'CMIP6_Amon.json'
cmor.load_table(table)
axes = [ {'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]},
]
values = numpy.array([missing], numpy.float32)
myma = numpy.ma.masked_values(values, missing)
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('ts', 'K', axis_ids, missing_value = myma.fill_value)
cmor.write(varid, myma, time_vals = [15], time_bnds = [ [0,30] ])
cmor.close(varid)
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
global testOK
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/test_python_CMIP6_CV_trackingNoprefix.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso", axis_ids=[itime], units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
filen = cmor.close()
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
f = cdms2.open(cmor.get_final_filename(), "r")
a = f.getglobal("tracking_id").split('/')[0]
self.assertNotIn("hdl:21.14100/", a)
except:
raise
def testCMIP6(self):
try:
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/common_user_input.json")
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time",
units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(
ivar, data[i:i]
) # ,time_vals=numpy.array([i,]),time_bnds=numpy.array([i,i+1]))
cmor.close()
except:
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
self.assertIn('d', testOK)
def testCMIP6(self):
try:
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json(
"Test/test_python_CMIP6_CV_badsourcetypeCHEMAER.json")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time",
units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
cmor.close()
except BaseException:
pass
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
testOK = self.getAssertTest()
self.assertIn("invalid source", testOK)
def testParentExperimentID(self):
# ------------------------------------------------------
# Copy stdout and stderr file descriptor for cmor output
# ------------------------------------------------------
newstdout = os.dup(1)
newstderr = os.dup(2)
# --------------
# Create tmpfile
# --------------
tmpfile = tempfile.mkstemp()
os.dup2(tmpfile[0], 1)
os.dup2(tmpfile[0], 2)
os.close(tmpfile[0])
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
try:
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/common_user_input.json")
cmor.set_cur_dataset_attribute("parent_experiment_id",
"historical")
cmor.set_cur_dataset_attribute("parent_activity_id", "DCPP")
cmor.set_cur_dataset_attribute("experiment_id",
"dcppC-forecast-addAgung")
cmor.set_cur_dataset_attribute("activity_id", "DCPP")
cmor.set_cur_dataset_attribute("source_type", "AOGCM AER")
cmor.set_cur_dataset_attribute("sub_experiment_id", "s2014")
# ------------------------------------------
# load Omon table and create masso variable
# ------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time",
units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ivar = cmor.variable(table_entry="masso",
axis_ids=[itime],
units='kg')
data = numpy.random.random(5)
for i in range(0, 5):
cmor.write(ivar, data[i:i])
cmor.close()
except BaseException:
pass
os.dup2(newstdout, 1)
os.dup2(newstderr, 2)
sys.stdout = os.fdopen(newstdout, 'w', 0)
sys.stderr = os.fdopen(newstderr, 'w', 0)
f = open(tmpfile[1], 'r')
lines = f.readlines()
for line in lines:
if line.find('Error:') != -1:
self.assertIn('parent_experiment_id', line.strip())
break
f.close()
os.unlink(tmpfile[1])
def setup_cmor():
#-------------------------------------------------------------------------
# Initialise CMOR library
cmor.setup(inpath=MIP_TABLE_DIR, netcdf_file_action=cmor.CMOR_REPLACE_3,
set_verbosity=cmor.CMOR_NORMAL, create_subdirectories=0)
# Create CMOR dataset
cmor.dataset_json("Test/CMOR_input_example.json")
def setup_cmor() :
#---------------------------------------------------------------------------------------------------
# Initialise CMOR library
cmor.setup(inpath=MIP_TABLE_DIR, netcdf_file_action=cmor.CMOR_REPLACE_3,
set_verbosity=cmor.CMOR_NORMAL, create_subdirectories=0)
# Create CMOR dataset
cmor.dataset_json("Test/test_python_cfmip_site_axis_test.json")
def setup_cmor():
#-------------------------------------------------------------------------
# Initialise CMOR library
cmor.setup(inpath=MIP_TABLE_DIR, netcdf_file_action=cmor.CMOR_REPLACE_3,
set_verbosity=cmor.CMOR_NORMAL, create_subdirectories=0)
# Create CMOR dataset
cmor.dataset_json("Test/CMOR_input_example.json")
def test_init_nemo2cmor(self):
tab_dir = get_table_path()
conf_path = os.path.join(os.path.dirname(nemo2cmor.__file__), "resources", "metadata-template.json")
cmor.setup(tab_dir)
cmor.dataset_json(conf_path)
nemo2cmor.initialize(self.data_dir, "exp", os.path.join(tab_dir, "CMIP6"), datetime.datetime(1990, 3, 1),
datetime.timedelta(days=100))
nemo2cmor.finalize()
cmor.close()
def path_test():
cmor.setup(inpath='TestTables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/CMOR_input_example.json")
table = 'CMIP6_Amon.json'
cmor.load_table(table)
axes = [
{
'table_entry': 'time2',
'units': 'months since 2000-01-01 00:00:00',
# 'coord_vals': times,
# 'cell_bounds': times_bnds,
},
{
'table_entry':
'plev19',
'units':
'Pa',
'coord_vals': [
100000., 92500., 85000., 70000., 60000., 50000., 40000.,
30000., 25000., 20000., 15000., 10000., 7000., 5000., 3000.,
2000., 1000., 500, 100
]
},
{
'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]
},
{
'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]
},
]
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
varid = cmor.variable('co2Clim', '1.e-6', axis_ids)
import numpy
data = numpy.array([3, 4, 5])
data.resize((3, 19, 1, 1))
# cmor.write(varid, data)
# for i in range(len(data)):
# cmor.write(varid, data[i], time_vals=times[i], time_bnds=times_bnds[i])
cmor.write(varid,
data,
time_vals=[12, 15, 18],
time_bnds=[[10, 1234], [12, 1125], [15, 1128]])
path = cmor.close(varid, file_name=True)
print(path)
def prep_cmor():
cmor.setup(inpath="Tables",set_verbosity=cmor.CMOR_QUIET, netcdf_file_action = cmor.CMOR_REPLACE, exit_control = cmor.CMOR_EXIT_ON_MAJOR);
cmor.dataset_json("Test/test_python_user_interface_03.json")
tables=[]
a = cmor.load_table("CMIP6_Omon.json")
tables.append(a)
tables.append(cmor.load_table("CMIP6_Amon.json"))
return
def main():
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE_3)
cmor.dataset_json("Test/test_python_jamie_9.json")
table = 'CMIP6_Amon.json'
cmor.load_table(table)
axes = [
{
'table_entry': 'time',
'units': 'days since 2000-01-01 00:00:00',
},
{
'table_entry':
'plev19',
'units':
'Pa',
'coord_vals':
map(
float,
'100000. 92500. 85000. 70000. 60000. 50000. 40000. 30000. 25000. 20000. 15000. 10000. 7000. 5000. 3000. 2000. 1000. 500. 100.'
.split(' '))
},
{
'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]
},
{
'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]
},
]
axis_ids = list()
for axis in axes:
print 'doing:', axis
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
for var, units, value in (('ta', 'K', 274), ('ua', 'm s-1', 10)):
values = numpy.array([
value,
] * len(axes[1]['coord_vals']), numpy.float32)
varid = cmor.variable(var,
units,
axis_ids,
history='variable history',
missing_value=-99)
cmor.set_variable_attribute(varid, 'cell_measures', '')
cmor.write(varid, values, time_vals=[15], time_bnds=[[0, 30]])
cmor.close()
def setup_cmor():
#---------------------------------------------------------------------------------------------------
# Initialise CMOR library
cmor.setup(inpath=MIP_TABLE_DIR,
netcdf_file_action=cmor.CMOR_REPLACE_3,
set_verbosity=cmor.CMOR_NORMAL,
create_subdirectories=0)
# Create CMOR dataset
cmor.dataset_json("Test/test_python_cfmip_site_axis_test.json")
def test_Directory(self):
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
try:
cmor.dataset_json("Test/baddirectory.json")
except BaseException:
pass
self.assertCV("unable to create this directory")
def testLoadTables(self):
tables = glob.glob("Tables/CMIP6*json")
for table in tables:
if "formula_terms" in table:
continue
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/CMOR_input_example.json")
print("Loading table:", table)
ierr = cmor.load_table(table)
self.assertEqual(ierr, 0)
cmor.close()
def main():
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE_3)
cmor.dataset_json("Test/CMOR_input_example.json")
table = 'CMIP6_Oclim.json'
cmor.load_table(table)
axes = [
{
'table_entry': 'time2',
'units': 'days since 1850-01-01 00:00:00',
'coord_vals': [
15.5,
45,
],
'cell_bounds': [[0, 31], [31, 62]]
},
{
'table_entry': 'depth_coord',
'units': 'm',
'coord_vals': [5000., 3000., 2000., 1000.],
'cell_bounds': [5000., 3000., 2000., 1000., 0]
},
{
'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]
},
{
'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]
},
]
axis_ids = list()
for axis in axes:
print('doing:', axis)
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
for var, units, value in (('difvso', 'm2 s-1', 274.), ):
values = numpy.ones(map(lambda x: len(x["coord_vals"]), axes)) * value
values = values.astype("f")
varid = cmor.variable(var,
units,
axis_ids,
history='variable history',
missing_value=-99)
cmor.write(varid, values)
cmor.close()
def __init__(self, table_root_, config_file):
self.table_root = table_root_
self.current_table = None
self.tables = {}
self.grids = {}
self.time_axes = {}
self.depth_axes = {}
self.surface_pressure_id = None
self.surface_pressure_vals = None
cmor.setup(os.path.dirname(table_root_))
cmor.dataset_json(config_file)
def test_init_nemo2cmor(self):
tab_dir = get_table_path()
conf_path = ece2cmorlib.conf_path_default
cmor.setup(tab_dir)
cmor.dataset_json(conf_path)
cmor.set_cur_dataset_attribute("calendar", "proleptic_gregorian")
nemo2cmor.initialize(self.data_dir, "exp",
os.path.join(tab_dir, "CMIP6"),
datetime.datetime(1990, 3, 1))
nemo2cmor.finalize()
cmor.close()
def testLoadTables(self):
tables = glob.glob("Tables/CMIP6*json")
for table in tables:
if "formula_terms" in table:
continue
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/CMOR_input_example.json")
print("Loading table:", table)
ierr = cmor.load_table(table)
self.assertEqual(ierr, 0)
cmor.close()
def tstCMIP6(self):
nlat = 10
dlat = 180. / nlat
nlon = 20
dlon = 360. / nlon
nlev = 5
ntimes = 5
lats = numpy.arange(90 - dlat / 2., -90, -dlat)
blats = numpy.arange(90, -90 - dlat, -dlat)
lons = numpy.arange(0 + dlon / 2., 360., dlon)
blons = numpy.arange(0, 360. + dlon, dlon)
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json("Test/CMOR_input_example.json")
# --------------------------------------------
# load Omon table and create masscello variable
# --------------------------------------------
cmor.load_table("CMIP6_Omon.json")
itime = cmor.axis(table_entry="time", units='months since 2010',
coord_vals=numpy.array([0, 1, 2, 3, 4.]),
cell_bounds=numpy.array([0, 1, 2, 3, 4, 5.]))
ilat = cmor.axis(
table_entry='latitude',
coord_vals=lats,
cell_bounds=blats,
units='degrees_north')
ilon = cmor.axis(
table_entry='longitude',
coord_vals=lons,
cell_bounds=blons,
units='degrees_east')
ilev = cmor.axis(table_entry='depth_coord', length=5,
cell_bounds=numpy.arange(0, 12000, 2000), coord_vals=numpy.arange(0, 10000, 2000), units="m")
ivar = cmor.variable(
table_entry="masscello", axis_ids=[
itime, ilev, ilat, ilon, ], units='kg/m2')
data = numpy.random.random((ntimes, nlev, nlat, nlon)) * 100.
cmor.write(ivar, data)
self.delete_files += [cmor.close(ivar, True)]
cmor.close()
f = cdms2.open(cmor.get_final_filename(), "r")
a = f.getglobal("external_variables")
self.assertEqual("areacello volcello", a)
def testCMIP6(self):
# -------------------------------------------
# Run CMOR using unicode strings
# -------------------------------------------
try:
cmor.setup(inpath=u'Tables', netcdf_file_action=cmor.CMOR_REPLACE, logfile=self.tmpfile)
cmor.dataset_json(u"Test/CMOR_input_example.json")
cmor.load_table(u"CMIP6_CFsubhr.json")
axes = [{u'table_entry': u'time1',
u'units': u'days since 2000-01-01 00:00:00',
},
{u'table_entry': u'site',
u'units': u'',
u'coord_vals': [0]},
{u'table_entry': u'hybrid_height',
u'units': u'm',
u'coord_vals': numpy.array(range(2), dtype=numpy.float64),
u'cell_bounds': [[x, x + 1] for x in range(2)],
},
]
values = numpy.array([0.5, 0.5], numpy.float32)
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
igrid = cmor.grid([axis_ids[1]], [0.], [0.])
cmor.zfactor(axis_ids[2], u'b', axis_ids=[axis_ids[2]],
zfactor_values=numpy.array(range(2), dtype=numpy.float64),
zfactor_bounds=[[x, x + 1] for x in range(2)])
cmor.zfactor(axis_ids[2], u'orog', u'm', axis_ids=[igrid],
zfactor_values=[0.] )
ids_for_var = [axis_ids[0], igrid, axis_ids[2]]
varid = cmor.variable(u'tnhus',
u's-1',
ids_for_var,
history=u'variable history',
missing_value=-99,
)
for time in [x * 1800. / 86400 for x in range(48)]:
cmor.write(varid, values, time_vals=[time])
self.delete_files += [cmor.close(varid, True)]
cmor.close()
except BaseException:
raise
def main():
cmor.setup(inpath='Tables',
netcdf_file_action=cmor.CMOR_REPLACE)
cmor.dataset_json("Test/CMOR_input_example.json")
table = 'CMIP6_6hrLev.json'
cmor.load_table(table)
axes = [{'table_entry': 'time1',
'units': 'days since 2000-01-01 00:00:00'
},
{'table_entry': 'latitude',
'units': 'degrees_north',
'coord_vals': [0],
'cell_bounds': [-1, 1]},
{'table_entry': 'longitude',
'units': 'degrees_east',
'coord_vals': [90],
'cell_bounds': [89, 91]},
{'table_entry': 'hybrid_height',
'coord_vals': [0, 1],
'cell_bounds': [[0., 0.5], [0.5, 1.]],
'units': 'm',
},
]
values = numpy.array([1.2, 1.2], numpy.float32)
numpy.reshape(values, (2, 1, 1, 1))
axis_ids = list()
for axis in axes:
axis_id = cmor.axis(**axis)
axis_ids.append(axis_id)
print('cmor.axis calls complete')
cmor.zfactor(axis_ids[3], 'b', '', axis_ids[3:4],
'd', [0., 0.5], [[0., 0.25], [0.25, 1.]])
cmor.zfactor(axis_ids[3], 'orog', 'm', axis_ids[1:3], 'd', [[0.]])
print('cmor.zfactor calls complete')
varid = cmor.variable('ua',
'm s-1',
axis_ids,
missing_value=-99
)
print('cmor.variable call complete')
cmor.write(varid, values, time_vals=[6.0], time_bnds=[3., 12.])
print('cmor.write call complete')
cmor.close()
def prep_cmor():
cmor.setup(
inpath="Tables",
set_verbosity=cmor.CMOR_QUIET,
netcdf_file_action=cmor.CMOR_REPLACE,
exit_control=cmor.CMOR_EXIT_ON_MAJOR)
cmor.dataset_json("Test/CMOR_input_example.json")
tables = []
a = cmor.load_table("CMIP6_Omon.json")
tables.append(a)
tables.append(cmor.load_table("CMIP6_Amon.json"))
return
def setUp(self):
self.logfile = 'has_variable_attribute.log'
cmor.setup(inpath='Tables', logfile=self.logfile)
cmor.dataset_json('Test/test_python_CMIP6_experimentID.json')
cmor.load_table('CMIP6_Omon.json')
coord_vals = np.array([0., 1., 2., 3., 4.])
cell_bounds = np.array([0., 1., 2., 3., 4., 5.])
axis_id = cmor.axis(table_entry='time', units='months since 2010',
coord_vals=coord_vals, cell_bounds=cell_bounds)
self.variable_id = cmor.variable(table_entry='masso',
axis_ids=[axis_id], units='kg')
cmor.set_variable_attribute(self.variable_id, 'valid_attribute',
'valid_value')
def test_Directory(self):
# -------------------------------------------
# Try to call cmor with a bad institution_ID
# -------------------------------------------
cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
try:
cmor.dataset_json("Test/test_python_CMIP6_CV_baddirectory.json")
except:
testOK = self.getAssertTest()
os.dup2(self.newstdout, 1)
os.dup2(self.newstderr, 2)
sys.stdout = os.fdopen(self.newstdout, 'w', 0)
sys.stderr = os.fdopen(self.newstderr, 'w', 0)
self.assertIn("unable to create this directory", testOK)