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Try to improve error messages when creating Variables #1268

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merged 3 commits into from
Aug 31, 2023
Merged

Try to improve error messages when creating Variables #1268

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7c4e800
Flip guard-clause conditional in `_ensure_nc_success`
ZedThree Aug 2, 2023
2a97db9
Include variable and group names in error messages in `Variable`
ZedThree Aug 2, 2023
04f29b8
Add changelog entry for error message reporting
ZedThree Aug 29, 2023
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1 change: 1 addition & 0 deletions Changelog
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
version 1.6.5 (not yet released)
===============================
* fix for issue #1271 (mask ignored if bool MA assinged to uint8 var)
* include information on specific object when reporting errors from netcdf-c

version 1.6.4 (tag v1.6.4rel)
===============================
Expand Down
77 changes: 46 additions & 31 deletions src/netCDF4/_netCDF4.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -2016,16 +2016,22 @@ cdef _get_vars(group):
free(varids) # free pointer holding variable ids.
return variables

cdef _ensure_nc_success(ierr, err_cls=RuntimeError, filename=None):
def _ensure_nc_success(ierr, err_cls=RuntimeError, filename=None, extra_msg=None):
# print netcdf error message, raise error.
if ierr != NC_NOERR:
err_str = (<char *>nc_strerror(ierr)).decode('ascii')
if issubclass(err_cls, OSError):
if isinstance(filename, bytes):
filename = filename.decode()
raise err_cls(ierr, err_str, filename)
else:
raise err_cls(err_str)
if ierr == NC_NOERR:
return

err_str = (<char *>nc_strerror(ierr)).decode('ascii')
if issubclass(err_cls, OSError):
if isinstance(filename, bytes):
filename = filename.decode()
raise err_cls(ierr, err_str, filename)

if extra_msg:
if isinstance(extra_msg, bytes):
extra_msg = extra_msg.decode()
err_str = f"{err_str}: {extra_msg}"
raise err_cls(err_str)

# these are class attributes that
# only exist at the python level (not in the netCDF file).
Expand Down Expand Up @@ -4016,6 +4022,10 @@ behavior is similar to Fortran or Matlab, but different than numpy.
cdef size_t sizep, nelemsp
cdef size_t *chunksizesp
cdef float preemptionp

# Extra information for more helpful error messages
error_info = f"(variable '{name}', group '{grp.name}')"

# flag to indicate that orthogonal indexing is supported
self.__orthogonal_indexing__ = True
# For backwards compatibility, deprecated zlib kwarg takes
Expand Down Expand Up @@ -4059,7 +4069,7 @@ behavior is similar to Fortran or Matlab, but different than numpy.
compression = None # if compression evaluates to False, set to None.
pass
else:
raise ValueError("Unsupported value for compression kwarg")
raise ValueError(f"Unsupported value for compression kwarg {error_info}")
self._grpid = grp._grpid
# make a weakref to group to avoid circular ref (issue 218)
# keep strong reference the default behaviour (issue 251)
Expand Down Expand Up @@ -4117,14 +4127,15 @@ behavior is similar to Fortran or Matlab, but different than numpy.
'Variable length strings are only supported for the '
'NETCDF4 format. For other formats, consider using '
'netCDF4.stringtochar to convert string arrays into '
'character arrays with an additional dimension.')
'character arrays with an additional dimension.'
f' {error_info}')
datatype = VLType(self._grp, str, None)
self._vltype = datatype
xtype = datatype._nc_type
# make sure this a valid user defined datatype defined in this Group
with nogil:
ierr = nc_inq_type(self._grpid, xtype, namstring, NULL)
_ensure_nc_success(ierr)
_ensure_nc_success(ierr, extra_msg=error_info)
# dtype variable attribute is a numpy datatype object.
self.dtype = datatype.dtype
elif datatype.str[1:] in _supportedtypes:
Expand All @@ -4135,7 +4146,7 @@ behavior is similar to Fortran or Matlab, but different than numpy.
# dtype variable attribute is a numpy datatype object.
self.dtype = datatype
else:
raise TypeError('illegal primitive data type, must be one of %s, got %s' % (_supportedtypes,datatype))
raise TypeError(f'Illegal primitive data type, must be one of {_supportedtypes}, got {datatype} {error_info}')
if 'id' in kwargs:
self._varid = kwargs['id']
else:
Expand All @@ -4161,6 +4172,12 @@ behavior is similar to Fortran or Matlab, but different than numpy.
with nogil:
ierr = nc_def_var(self._grpid, varname, xtype, ndims,
NULL, &self._varid)

if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4':
grp._enddef()
_ensure_nc_success(ierr, extra_msg=error_info)

# set chunk cache size if desired
# default is 1mb per var, can cause problems when many (1000's)
# of vars are created. This change only lasts as long as file is
Expand All @@ -4169,16 +4186,14 @@ behavior is similar to Fortran or Matlab, but different than numpy.
with nogil:
ierr = nc_get_var_chunk_cache(self._grpid, self._varid, &sizep,
&nelemsp, &preemptionp)
_ensure_nc_success(ierr)
_ensure_nc_success(ierr, extra_msg=error_info)
# reset chunk cache size, leave other parameters unchanged.
sizep = chunk_cache
with nogil:
ierr = nc_set_var_chunk_cache(self._grpid, self._varid, sizep,
nelemsp, preemptionp)
_ensure_nc_success(ierr)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
_ensure_nc_success(ierr)
_ensure_nc_success(ierr, extra_msg=error_info)

# set compression, shuffle, chunking, fletcher32 and endian
# variable settings.
# don't bother for NETCDF3* formats.
Expand All @@ -4198,7 +4213,7 @@ behavior is similar to Fortran or Matlab, but different than numpy.
ierr = nc_def_var_deflate(self._grpid, self._varid, 0, 1, icomplevel)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
_ensure_nc_success(ierr)
_ensure_nc_success(ierr, extra_msg=error_info)
if szip:
IF HAS_SZIP_SUPPORT:
try:
Expand All @@ -4211,7 +4226,7 @@ behavior is similar to Fortran or Matlab, but different than numpy.
ierr = nc_def_var_szip(self._grpid, self._varid, iszip_coding, iszip_pixels_per_block)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
_ensure_nc_success(ierr)
_ensure_nc_success(ierr, extra_msg=error_info)
ELSE:
msg = """
compression='szip' only works if linked version of hdf5 has szip functionality enabled"""
Expand All @@ -4223,7 +4238,7 @@ compression='szip' only works if linked version of hdf5 has szip functionality e
ierr = nc_def_var_zstandard(self._grpid, self._varid, icomplevel)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
_ensure_nc_success(ierr)
_ensure_nc_success(ierr, extra_msg=error_info)
ELSE:
msg = """
compression='zstd' only works with netcdf-c >= 4.9.0. To enable, install Cython, make sure you have
Expand All @@ -4236,7 +4251,7 @@ version 4.9.0 or higher netcdf-c with zstandard support, and rebuild netcdf4-pyt
ierr = nc_def_var_bzip2(self._grpid, self._varid, icomplevel)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
_ensure_nc_success(ierr)
_ensure_nc_success(ierr, extra_msg=error_info)
ELSE:
msg = """
compression='bzip2' only works with netcdf-c >= 4.9.0. To enable, install Cython, make sure you have
Expand All @@ -4255,7 +4270,7 @@ version 4.9.0 or higher netcdf-c with bzip2 support, and rebuild netcdf4-python.
iblosc_shuffle)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
_ensure_nc_success(ierr)
_ensure_nc_success(ierr, extra_msg=error_info)
ELSE:
msg = """
compression='blosc_*' only works with netcdf-c >= 4.9.0. To enable, install Cython, make sure you have
Expand All @@ -4267,7 +4282,7 @@ version 4.9.0 or higher netcdf-c with blosc support, and rebuild netcdf4-python.
ierr = nc_def_var_fletcher32(self._grpid, self._varid, 1)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
_ensure_nc_success(ierr)
_ensure_nc_success(ierr, extra_msg=error_info)
# set chunking stuff.
if ndims: # don't bother for scalar variable.
if contiguous:
Expand Down Expand Up @@ -4295,7 +4310,7 @@ version 4.9.0 or higher netcdf-c with blosc support, and rebuild netcdf4-python.
free(chunksizesp)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
_ensure_nc_success(ierr)
_ensure_nc_success(ierr, extra_msg=error_info)
# set endian-ness of variable
if endian == 'little':
with nogil:
Expand Down Expand Up @@ -4327,17 +4342,17 @@ version 4.9.0 or higher netcdf-c with blosc support, and rebuild netcdf4-python.

ELSE:
if significant_digits is not None:
msg = """
msg = f"""
significant_digits kwarg only works with netcdf-c >= 4.9.0. To enable, install Cython, make sure you have
version 4.9.0 or higher netcdf-c, and rebuild netcdf4-python. Otherwise, use least_significant_digit
kwarg for quantization."""
kwarg for quantization. {error_info}"""
raise ValueError(msg)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
_ensure_nc_success(ierr)
_ensure_nc_success(ierr, extra_msg=error_info)
else:
if endian != 'native':
msg="only endian='native' allowed for NETCDF3 files"
msg=f"only endian='native' allowed for NETCDF3 files {error_info}"
raise RuntimeError(msg)
# set a fill value for this variable if fill_value keyword
# given. This avoids the HDF5 overhead of deleting and
Expand All @@ -4354,7 +4369,7 @@ kwarg for quantization."""
ierr = nc_def_var_fill(self._grpid, self._varid, 1, NULL)
if ierr != NC_NOERR:
if grp.data_model != 'NETCDF4': grp._enddef()
_ensure_nc_success(ierr)
_ensure_nc_success(ierr, extra_msg=error_info)
else:
if self._isprimitive or self._isenum or \
(self._isvlen and self.dtype == str):
Expand All @@ -4379,7 +4394,7 @@ kwarg for quantization."""
# set ndim attribute (number of dimensions).
with nogil:
ierr = nc_inq_varndims(self._grpid, self._varid, &numdims)
_ensure_nc_success(ierr)
_ensure_nc_success(ierr, extra_msg=error_info)
self.ndim = numdims
self._name = name
# default for automatically applying scale_factor and
Expand Down