def apply_fix(self):
"""
Fix the affected file
This should replicate the Unix commands:
ncap2 -h -s 'tos=tos-273.15f' filename.nc filename.nc.temp
rm filename.nc
mv filename.nc.temp filename.nc
ncatted -h -a units,tos,m,c,'degC' filename.nc
"""
if not self._is_kelvin():
raise ExistingAttributeError(self.filename, 'units',
'Units are not K.')
self.command = (f"ncap2 -h -s '{self.variable_name}="
f"{self.variable_name}-273.15f'")
self._run_nco_command(Ncap2Error)
units_command = (
f"ncatted -h -a units,{self.variable_name},m,c,'degC' "
f"{os.path.join(self.directory, self.filename)}")
try:
run_command(units_command)
except Exception:
raise NcattedError(
type(self).__name__, self.filename, units_command,
traceback.format_exc())
def _calculate_new_value(self):
"""
Check the existing attribute is `AOGCM` and change it to `AGCM`.
"""
if self.existing_value != 'AOGCM':
raise ExistingAttributeError(self.filename, self.attribute_name,
'Existing value is not AOGCM.')
else:
self.new_value = 'AGCM'
def _calculate_new_value(self):
"""
Convert the tracking_id to the correct form.
"""
if self.existing_value.startswith('hdl:'):
raise ExistingAttributeError(self.filename, self.attribute_name,
'Existing tracking_id attribute '
'starts with hdl:')
self.new_value = 'hdl:21.14100/{}'.format(self.existing_value)
def _calculate_new_value(self):
"""
The new value is the existing string converted to a double.
"""
if not self.existing_value.startswith('http:'):
raise ExistingAttributeError(self.filename, self.attribute_name,
'Existing further_info_url attribute '
'does not start with http:')
self.new_value = self.existing_value.replace('http:', 'https:', 1)
def apply_fix(self):
"""
Run ncpdq and then swap the columns in lat_bnds.
"""
# check that the latitude is decreasing and that the fix is actually
# needed
if not self._is_lat_decreasing():
raise ExistingAttributeError(self.filename, 'latitude',
'Latitude is not decreasing.')
self.command = 'ncpdq -a -lat'
self._run_nco_command(NcpdqError)
original_nc = os.path.join(self.directory, self.filename)
bnds_file = original_nc + '.bnds'
corrected_bnds_file = bnds_file + '_corr'
# Remove any temporary files left over from a previous failed
# run as they can prevent ncks and ncpdq from running.
for filename in (bnds_file, corrected_bnds_file):
if os.path.exists(filename):
os.remove(filename)
commands = [
# Copy lat_bnds to a new file
f'ncks -v lat_bnds {original_nc} {bnds_file}',
# Swap the colums
f'ncpdq -a -bnds {bnds_file} {corrected_bnds_file}',
# Remove history from lat_bnds as this is pasted back into the file
f'ncatted -h -a history,global,d,, {corrected_bnds_file}',
# Paste the fixed bnds back into the original file
f'ncks -A -v lat_bnds {corrected_bnds_file} {original_nc}'
]
for cmd in commands:
try:
run_command(cmd)
except Exception:
exceptions = {
'ncks': NcksError,
'ncpdq': NcpdqError,
'ncatted': NcattedError
}
cmd_name = cmd.split()[0]
raise exceptions[cmd_name](type(self).__name__, self.filename,
cmd, traceback.format_exc())
os.remove(bnds_file)
os.remove(corrected_bnds_file)
def _calculate_new_value(self):
"""
The new value is the existing string converted to a double.
"""
if not self.existing_value.startswith(
'https://furtherinfo.es-doc.org/CMIP6'):
raise ExistingAttributeError(
self.filename,
self.attribute_name,
'Existing further_info_url attribute does not start with '
'https://furtherinfo.es-doc.org/CMIP6'
)
self.new_value = self.existing_value.replace(
'https://furtherinfo.es-doc.org/CMIP6',
'https://furtherinfo.es-doc.org/PRIMAVERA',
1
)