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um_stash_source attribute improved handling (#4035)
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* Modified pyke rule

* Tests added

* Black and whatsnew

* Include PR number

* Remove latest.rst

* Add what's new
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@jonseddon
jonseddon authored Mar 2, 2021
1 parent 2557426 commit 4885e12
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3 changes: 2 additions & 1 deletion docs/iris/src/whatsnew/3.0.2.rst
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Expand Up @@ -18,7 +18,8 @@ This document explains the changes made to Iris for this release

🐛 **Bugs Fixed**

#.
#. `@jonseddon`_ handled a malformed ``um_stash_source`` CF variable attribute in
a netCDF file rather than raising a ``ValueError``. (:pull:`4035`)

📚 **Documentation**

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35 changes: 33 additions & 2 deletions lib/iris/fileformats/_pyke_rules/fc_rules_cf.krb
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Expand Up @@ -1022,8 +1022,7 @@ fc_attribute_ukmo__um_stash_source
foreach
check hasattr(engine.cf_var, 'ukmo__um_stash_source') or hasattr(engine.cf_var, 'um_stash_source')
assert
python attr_value = getattr(engine.cf_var, 'um_stash_source', None) or getattr(engine.cf_var, 'ukmo__um_stash_source')
python engine.cube.attributes['STASH'] = pp.STASH.from_msi(attr_value)
python get_um_stash_source(engine)
python engine.rule_triggered.add(rule.name)

#
Expand Down Expand Up @@ -1775,6 +1774,38 @@ fc_extras
return cf_bounds_var, climatological


################################################################################
def get_um_stash_source(engine):
"""
If the CF variable has the um_stash_source or ukmo__um_stash_source
attributes and they are valid MSI STASH codes then the cube STASH
attribute is set with their value. If the attributes are not valid MSI
stash codes then the corresponding cube attribute is set with the value
from the variable and a warning is displayed. ukmo__um_stash_source
takes precedence over um_stash_source if both attributes exist.

"""
attr = None
value = None

for attr_name in ['ukmo__um_stash_source', 'um_stash_source']:
if hasattr(engine.cf_var, attr_name):
attr = attr_name
value = getattr(engine.cf_var, attr_name)
break

if attr:
try:
stash_code = pp.STASH.from_msi(value)
except (TypeError, ValueError) as exc:
engine.cube.attributes[attr] = value
msg = (f'Unable to set attribute STASH as not a valid MSI '
f'string "mXXsXXiXXX", got {value}')
warnings.warn(msg)
else:
engine.cube.attributes['STASH'] = stash_code


################################################################################
def reorder_bounds_data(bounds_data, cf_bounds_var, cf_coord_var):
"""
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141 changes: 141 additions & 0 deletions lib/iris/tests/test_netcdf.py
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Expand Up @@ -499,6 +499,147 @@ def test_default_units(self):
cubes[0].cell_measure("areas").units, as_unit("unknown")
)

def test_um_stash_source(self):
"""Test that um_stash_source is converted into a STASH code"""
# Note: using a CDL string as a test data reference, rather than a binary file.
ref_cdl = """
netcdf cm_attr {
dimensions:
axv = 3 ;
ayv = 2 ;
variables:
int64 qqv(ayv, axv) ;
qqv:long_name = "qq" ;
qqv:ancillary_variables = "my_av" ;
qqv:cell_measures = "area: my_areas" ;
qqv:um_stash_source = "m01s02i003" ;
int64 ayv(ayv) ;
ayv:long_name = "y" ;
int64 axv(axv) ;
axv:units = "1" ;
axv:long_name = "x" ;
double my_av(axv) ;
my_av:long_name = "refs" ;
double my_areas(ayv, axv) ;
my_areas:long_name = "areas" ;
data:
axv = 11, 12, 13;
ayv = 21, 22;
my_areas = 110., 120., 130., 221., 231., 241.;
}
"""
self.tmpdir = tempfile.mkdtemp()
cdl_path = os.path.join(self.tmpdir, "tst.cdl")
nc_path = os.path.join(self.tmpdir, "tst.nc")
# Write CDL string into a temporary CDL file.
with open(cdl_path, "w") as f_out:
f_out.write(ref_cdl)
# Use ncgen to convert this into an actual (temporary) netCDF file.
command = "ncgen -o {} {}".format(nc_path, cdl_path)
check_call(command, shell=True)
# Load with iris.fileformats.netcdf.load_cubes, and check expected content.
cubes = list(nc_load_cubes(nc_path))
self.assertEqual(len(cubes), 1)
self.assertEqual(
cubes[0].attributes["STASH"], iris.fileformats.pp.STASH(1, 2, 3)
)

def test_ukmo__um_stash_source_priority(self):
"""
Test that ukmo__um_stash_source is converted into a STASH code with a
higher priority than um_stash_source.
"""
# Note: using a CDL string as a test data reference, rather than a binary file.
ref_cdl = """
netcdf cm_attr {
dimensions:
axv = 3 ;
ayv = 2 ;
variables:
int64 qqv(ayv, axv) ;
qqv:long_name = "qq" ;
qqv:ancillary_variables = "my_av" ;
qqv:cell_measures = "area: my_areas" ;
qqv:um_stash_source = "m01s02i003" ;
qqv:ukmo__um_stash_source = "m09s08i007" ;
int64 ayv(ayv) ;
ayv:long_name = "y" ;
int64 axv(axv) ;
axv:units = "1" ;
axv:long_name = "x" ;
double my_av(axv) ;
my_av:long_name = "refs" ;
double my_areas(ayv, axv) ;
my_areas:long_name = "areas" ;
data:
axv = 11, 12, 13;
ayv = 21, 22;
my_areas = 110., 120., 130., 221., 231., 241.;
}
"""
self.tmpdir = tempfile.mkdtemp()
cdl_path = os.path.join(self.tmpdir, "tst.cdl")
nc_path = os.path.join(self.tmpdir, "tst.nc")
# Write CDL string into a temporary CDL file.
with open(cdl_path, "w") as f_out:
f_out.write(ref_cdl)
# Use ncgen to convert this into an actual (temporary) netCDF file.
command = "ncgen -o {} {}".format(nc_path, cdl_path)
check_call(command, shell=True)
# Load with iris.fileformats.netcdf.load_cubes, and check expected content.
cubes = list(nc_load_cubes(nc_path))
self.assertEqual(len(cubes), 1)
self.assertEqual(
cubes[0].attributes["STASH"], iris.fileformats.pp.STASH(9, 8, 7)
)

def test_bad_um_stash_source(self):
"""Test that um_stash_source not in strict MSI form is kept"""
# Note: using a CDL string as a test data reference, rather than a binary file.
ref_cdl = """
netcdf cm_attr {
dimensions:
axv = 3 ;
ayv = 2 ;
variables:
int64 qqv(ayv, axv) ;
qqv:long_name = "qq" ;
qqv:ancillary_variables = "my_av" ;
qqv:cell_measures = "area: my_areas" ;
qqv:um_stash_source = "10*m01s02i003" ;
int64 ayv(ayv) ;
ayv:long_name = "y" ;
int64 axv(axv) ;
axv:units = "1" ;
axv:long_name = "x" ;
double my_av(axv) ;
my_av:long_name = "refs" ;
double my_areas(ayv, axv) ;
my_areas:long_name = "areas" ;
data:
axv = 11, 12, 13;
ayv = 21, 22;
my_areas = 110., 120., 130., 221., 231., 241.;
}
"""
self.tmpdir = tempfile.mkdtemp()
cdl_path = os.path.join(self.tmpdir, "tst.cdl")
nc_path = os.path.join(self.tmpdir, "tst.nc")
# Write CDL string into a temporary CDL file.
with open(cdl_path, "w") as f_out:
f_out.write(ref_cdl)
# Use ncgen to convert this into an actual (temporary) netCDF file.
command = "ncgen -o {} {}".format(nc_path, cdl_path)
check_call(command, shell=True)
# Load with iris.fileformats.netcdf.load_cubes, and check expected content.
with self.assertWarns(UserWarning):
cubes = list(nc_load_cubes(nc_path))
self.assertEqual(len(cubes), 1)
self.assertFalse(hasattr(cubes[0].attributes, "STASH"))
self.assertEqual(
cubes[0].attributes["um_stash_source"], "10*m01s02i003"
)

def test_units(self):
# Test exercising graceful cube and coordinate units loading.
cube0, cube1 = sorted(
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