cfdm.write fails for a vertical CRS with no coordinates

[davidhassell]

We get an untrapped TypeError: 'NoneType object is not subscriptable error when writing some fields that have vertical coordinate reference systems:

>>> f.dump()
-------------------------------------------------------------------------
Field: eastward_wind (ncvar%UM_m01s00i002_vn1107_true_latitude_longitude)
-------------------------------------------------------------------------
Conventions = 'CF-1.9'
_FillValue = -1073741824.0
history = 'Converted from UM/PP by cf-python v3.11.0'
lbproc = '0'
lbtim = '12'
long_name = 'U COMPNT OF WIND AFTER TIMESTEP'
runid = 'aaaaa'
source = 'UM vn1107'
standard_name = 'eastward_wind'
stash_code = '2'
submodel = '1'
um_stash_source = 'm01s00i002'
units = 'm s-1'

Data(time(3), atmosphere_hybrid_height_coordinate(85), latitude(144), longitude(192)) = [[[[-1.71728515625, ..., 3.736572265625]]]] m s-1

Cell Method: time(3): point

Domain Axis: atmosphere_hybrid_height_coordinate(85)
Domain Axis: latitude(144)
Domain Axis: longitude(192)
Domain Axis: time(3)

Dimension coordinate: time
    axis = 'T'
    calendar = '360_day'
    standard_name = 'time'
    units = 'days since 1988-1-1'
    Data(time(3)) = [1988-09-01 00:20:00, 1988-09-01 00:40:00, 1988-09-01 01:00:00] 360_day

Dimension coordinate: atmosphere_hybrid_height_coordinate
    axis = 'Z'
    positive = 'up'
    standard_name = 'atmosphere_hybrid_height_coordinate'
    units = ''
    Data(atmosphere_hybrid_height_coordinate(85)) = [0.00011764710370232077, ..., 0.9652942095588235]
    Bounds:units = ''
    Bounds:Data(atmosphere_hybrid_height_coordinate(85), 2) = [[0.0, ..., 85000.0]]

Dimension coordinate: latitude
    axis = 'Y'
    standard_name = 'latitude'
    units = 'degrees_north'
    Data(latitude(144)) = [-89.375, ..., 89.375] degrees_north
    Bounds:units = 'degrees_north'
    Bounds:Data(latitude(144), 2) = [[-90.0, ..., 90.0]] degrees_north

Dimension coordinate: longitude
    axis = 'X'
    standard_name = 'longitude'
    units = 'degrees_east'
    Data(longitude(192)) = [0.0, ..., 358.125] degrees_east
    Bounds:units = 'degrees_east'
    Bounds:Data(longitude(192), 2) = [[-0.9375, ..., 359.0625]] degrees_east

Auxiliary coordinate: model_level_number
    standard_name = 'model_level_number'
    units = '1'
    Data(atmosphere_hybrid_height_coordinate(85)) = [1, ..., 85] 1

Domain ancillary: id%UM_atmosphere_hybrid_height_coordinate_a
    long_name = 'height based hybrid coeffient a'
    units = 'm'
    Data(atmosphere_hybrid_height_coordinate(85)) = [10.000003814697266, ..., 82050.0078125] m
    Bounds:units = 'm'
    Bounds:Data(atmosphere_hybrid_height_coordinate(85), 2) = [[0.0, ..., 85000.0]] m

Domain ancillary: id%UM_atmosphere_hybrid_height_coordinate_b
    long_name = 'height based hybrid coeffient b'
    units = '1'
    Data(atmosphere_hybrid_height_coordinate(85)) = [0.998870313167572, ..., 0.0] 1
    Bounds:units = '1'
    Bounds:Data(atmosphere_hybrid_height_coordinate(85), 2) = [[1.0, ..., 0.0]] 1

Coordinate reference: standard_name:atmosphere_hybrid_height_coordinate
    Coordinate conversion:standard_name = atmosphere_hybrid_height_coordinate
    Coordinate conversion:a = Domain Ancillary: id%UM_atmosphere_hybrid_height_coordinate_a
    Coordinate conversion:b = Domain Ancillary: id%UM_atmosphere_hybrid_height_coordinate_b
    Coordinate conversion:orog = 

>>> cfdm.write(f, 'delme.nc')
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-2-512c49024828> in <module>
----> 1 cf.write(f[0], 'delme.nc')

~/cf/lib/python3.8/site-packages/cfdm/decorators.py in verbose_override_wrapper(*args, **kwargs)
    169         # enabling
    170         try:
--> 171             return method_with_verbose_kwarg(*args, **kwargs)
    172         except Exception:
    173             raise

~/cf/lib/python3.8/site-packages/cf/read_write/write.py in write(fields, filename, fmt, mode, overwrite, global_attributes, file_descriptors, external, Conventions, datatype, least_significant_digit, endian, compress, fletcher32, shuffle, reference_datetime, verbose, cfa_options, single, double, variable_attributes, string, warn_valid, group, coordinates, HDF_chunksizes, no_shuffle, unlimited)
    716         # --- End: if
    717 
--> 718         netcdf.write(
    719             fields,
    720             filename,

~/cf/lib/python3.8/site-packages/cfdm/decorators.py in verbose_override_wrapper(*args, **kwargs)
    169         # enabling
    170         try:
--> 171             return method_with_verbose_kwarg(*args, **kwargs)
    172         except Exception:
    173             raise

~/cf/lib/python3.8/site-packages/cfdm/read_write/netcdf/netcdfwrite.py in write(self, fields, filename, fmt, mode, overwrite, global_attributes, variable_attributes, file_descriptors, external, Conventions, datatype, least_significant_digit, endian, compress, fletcher32, shuffle, scalar, string, extra_write_vars, verbose, warn_valid, group, coordinates)
   4810                 )
   4811 
-> 4812         self._file_io_iteration(
   4813             mode=effective_mode,
   4814             overwrite=overwrite,

~/cf/lib/python3.8/site-packages/cfdm/read_write/netcdf/netcdfwrite.py in _file_io_iteration(self, mode, overwrite, fields, filename, fmt, global_attributes, variable_attributes, file_descriptors, external, Conventions, datatype, least_significant_digit, endian, compress, fletcher32, shuffle, scalar, string, extra_write_vars, warn_valid, group)
   5090         # ------------------------------------------------------------
   5091         for f in fields:
-> 5092             self._write_field_or_domain(f)
   5093 
   5094         # ------------------------------------------------------------

~/cf/lib/python3.8/site-packages/cfdm/read_write/netcdf/netcdfwrite.py in _write_field_or_domain(self, f, add_to_seen, allow_data_insert_dimension)
   3726                 f, owning_coord_key
   3727                 )) # DCH
-> 3728                 z_axis = self.implementation.get_construct_data_axes(
   3729                     f, owning_coord_key
   3730                 )[0]

TypeError: 'NoneType' object is not subscriptable
>>>

>>> cfdm.environment(paths=False)
Platform: Linux-4.12.14-197.56_9.1.45-cray_shasta_c-x86_64-with-glibc2.10
HDF5 library: 1.10.6
netcdf library: 4.8.0
Python: 3.8.5
netCDF4: 1.5.6
numpy: 1.20.3
cfdm.core: 1.9.0.1
cftime: 1.5.0
netcdf_flattener: 1.2.0
cfdm: 1.9.0.1

[sadielbartholomew]

FYI (not sure by the written context here if you were aware @davidhassell), this bug was probably the underlying cause of NCAS-CMS/cf-python#272 as well (I have asked to get confirmation about that, and if it is I can close that issue too now that this one has since been resolved).