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 _run_ncatted(self, nco_mode):
"""
Run the command
:param str nco_mode: The mode to run nco in.
"""
for attr_name in [
'attribute_name', 'attribute_visibility', 'new_value'
]:
attr_value = getattr(self, attr_name, None)
if attr_value is None:
raise InstanceVariableNotDefinedError(
type(self).__name__, attr_name)
# Aiming for:
# ncatted -h -a branch_time_in_parent,global,o,d,10800.0
quote_mark = "'" if isinstance(self.new_value, str) else ""
cmd = 'ncatted -h -a {},{},{},{},{}{}{} {}'.format(
self.attribute_name, self.attribute_visibility, nco_mode,
self.attribute_type, quote_mark, self.new_value, quote_mark,
os.path.join(self.directory, self.filename))
try:
run_command(cmd)
except Exception:
raise NcattedError(
type(self).__name__, self.filename, cmd,
traceback.format_exc())
def _set_attribute(filepath, attr_name, attr_value):
"""
Overwrite the specified global attribute value on the specified netCDF
file.
:param str filepath: The name of the netCDF file to update
:param str attr_name: The name of the attribute to set
:param str attr_value: The new value of the specified attribute
:raises RunTimeError: if ncatted doesn't complete successfully
"""
cmd = "ncatted -h -a {},global,o,c,'{}' {}".format(attr_name, attr_value,
filepath)
run_command(cmd)
def apply_fix(self):
"""
Use cdo to set the reference time.
"""
self.command = f"ncks -h -A -v height {self.reference_file}"
self._run_ncks_command()
units_command = (f"ncatted -h -a coordinates,{self.variable_name},o,c,"
f"'height' "
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 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 _run_command(self, cmd, cmd_error):
"""
Run `cmd` and raise `cmd_error` if it fails when the specified
temporary files are deleted.
:param str cmd: The command to run
:param PreProcError cmd_error: The exception to raise if the command
fails
"""
try:
run_command(cmd)
except Exception:
for fn in self.intermediate_files:
if os.path.exists(fn):
os.remove(fn)
raise cmd_error(
type(self).__name__, self.filename, cmd,
traceback.format_exc())
def _run_nco_command(self, command_error):
"""
Run the nco command
"""
output_file = os.path.join(self.directory, self.filename)
temp_file = output_file + '.temp'
# Remove any temporary file left over from a previous failed
# run as it could prevent some nco commands from running.
if os.path.exists(temp_file):
os.remove(temp_file)
cmd = f'{self.command} {output_file} {temp_file}'
try:
run_command(cmd)
except Exception:
if os.path.exists(temp_file):
os.remove(temp_file)
raise command_error(
type(self).__name__, self.filename, cmd,
traceback.format_exc())
os.remove(output_file)
os.rename(temp_file, output_file)
