Starlitnightly
commented
1 year ago Hi,
This error is usually due to the fact that a column in the DataFrame of obs or var is not of the same category, such as False mixed with NaN. We can find out through your error message that it is the adata.obs['name'] or adata.var['name'] that has different attribute information in it.
Solution: You can either delete the column or replace all NaNs with .fillna(0) or specify the column's attributes with .asype(str).
amaukisumi
I'm get an error when saving h5ad file, do you have any suggestion or solution for this?
Traceback
```python --------------------------------------------------------------------------- TypeError Traceback (most recent call last) File ~/.local/lib/python3.8/site-packages/anndata/_io/utils.py:214, in report_write_key_on_error..func_wrapper(elem, key, val, *args, **kwargs)
213 try:
--> 214 return func(elem, key, val, *args, **kwargs)
215 except Exception as e:
File ~/.local/lib/python3.8/site-packages/anndata/_io/specs/registry.py:175, in write_elem(f, k, elem, modifiers, *args, **kwargs)
174 else:
--> 175 _REGISTRY.get_writer(dest_type, t, modifiers)(f, k, elem, *args, **kwargs)
File ~/.local/lib/python3.8/site-packages/anndata/_io/specs/registry.py:24, in write_spec..decorator..wrapper(g, k, *args, **kwargs)
22 @wraps(func)
23 def wrapper(g, k, *args, **kwargs):
---> 24 result = func(g, k, *args, **kwargs)
25 g[k].attrs.setdefault("encoding-type", spec.encoding_type)
File ~/.local/lib/python3.8/site-packages/anndata/_io/specs/methods.py:400, in write_recarray(f, k, elem, dataset_kwargs)
397 @_REGISTRY.register_write(H5Group, (np.ndarray, "V"), IOSpec("rec-array", "0.2.0"))
398 @_REGISTRY.register_write(H5Group, np.recarray, IOSpec("rec-array", "0.2.0"))
399 def write_recarray(f, k, elem, dataset_kwargs=MappingProxyType({})):
--> 400 f.create_dataset(k, data=_to_hdf5_vlen_strings(elem), **dataset_kwargs)
File ~/.local/lib/python3.8/site-packages/h5py/_hl/group.py:183, in Group.create_dataset(self, name, shape, dtype, data, **kwds)
181 group = self.require_group(parent_path)
--> 183 dsid = dataset.make_new_dset(group, shape, dtype, data, name, **kwds)
184 dset = dataset.Dataset(dsid)
File ~/.local/lib/python3.8/site-packages/h5py/_hl/dataset.py:168, in make_new_dset(parent, shape, dtype, data, name, chunks, compression, shuffle, fletcher32, maxshape, compression_opts, fillvalue, scaleoffset, track_times, external, track_order, dcpl, dapl, efile_prefix, virtual_prefix, allow_unknown_filter, rdcc_nslots, rdcc_nbytes, rdcc_w0)
167 if (data is not None) and (not isinstance(data, Empty)):
--> 168 dset_id.write(h5s.ALL, h5s.ALL, data)
170 return dset_id
File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper()
File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper()
File h5py/h5d.pyx:280, in h5py.h5d.DatasetID.write()
File h5py/_proxy.pyx:145, in h5py._proxy.dset_rw()
File h5py/_conv.pyx:444, in h5py._conv.str2vlen()
File h5py/_conv.pyx:110, in h5py._conv.generic_converter()
File h5py/_conv.pyx:249, in h5py._conv.conv_str2vlen()
TypeError: Can't implicitly convert non-string objects to strings
The above exception was the direct cause of the following exception:
TypeError Traceback (most recent call last)
Cell In[86], line 1
----> 1 adata.write("20230721.h5ad")
File ~/.local/lib/python3.8/site-packages/anndata/_core/anndata.py:1918, in AnnData.write_h5ad(self, filename, compression, compression_opts, force_dense, as_dense)
1915 if filename is None:
1916 filename = self.filename
-> 1918 _write_h5ad(
1919 Path(filename),
1920 self,
1921 compression=compression,
1922 compression_opts=compression_opts,
1923 force_dense=force_dense,
1924 as_dense=as_dense,
1925 )
1927 if self.isbacked:
1928 self.file.filename = filename
File ~/.local/lib/python3.8/site-packages/anndata/_io/h5ad.py:105, in write_h5ad(filepath, adata, force_dense, as_dense, dataset_kwargs, **kwargs)
103 write_elem(f, "varp", dict(adata.varp), dataset_kwargs=dataset_kwargs)
104 write_elem(f, "layers", dict(adata.layers), dataset_kwargs=dataset_kwargs)
--> 105 write_elem(f, "uns", dict(adata.uns), dataset_kwargs=dataset_kwargs)
File ~/.local/lib/python3.8/site-packages/anndata/_io/utils.py:214, in report_write_key_on_error..func_wrapper(elem, key, val, *args, **kwargs)
211 @wraps(func)
212 def func_wrapper(elem, key, val, *args, **kwargs):
213 try:
--> 214 return func(elem, key, val, *args, **kwargs)
215 except Exception as e:
216 if "Above error raised while writing key" in format(e):
File ~/.local/lib/python3.8/site-packages/anndata/_io/specs/registry.py:175, in write_elem(f, k, elem, modifiers, *args, **kwargs)
171 _REGISTRY.get_writer(dest_type, (t, elem.dtype.kind), modifiers)(
172 f, k, elem, *args, **kwargs
173 )
174 else:
--> 175 _REGISTRY.get_writer(dest_type, t, modifiers)(f, k, elem, *args, **kwargs)
File ~/.local/lib/python3.8/site-packages/anndata/_io/specs/registry.py:24, in write_spec..decorator..wrapper(g, k, *args, **kwargs)
22 @wraps(func)
23 def wrapper(g, k, *args, **kwargs):
---> 24 result = func(g, k, *args, **kwargs)
25 g[k].attrs.setdefault("encoding-type", spec.encoding_type)
26 g[k].attrs.setdefault("encoding-version", spec.encoding_version)
File ~/.local/lib/python3.8/site-packages/anndata/_io/specs/methods.py:281, in write_mapping(f, k, v, dataset_kwargs)
279 g = f.create_group(k)
280 for sub_k, sub_v in v.items():
--> 281 write_elem(g, sub_k, sub_v, dataset_kwargs=dataset_kwargs)
File ~/.local/lib/python3.8/site-packages/anndata/_io/utils.py:214, in report_write_key_on_error..func_wrapper(elem, key, val, *args, **kwargs)
211 @wraps(func)
212 def func_wrapper(elem, key, val, *args, **kwargs):
213 try:
--> 214 return func(elem, key, val, *args, **kwargs)
215 except Exception as e:
216 if "Above error raised while writing key" in format(e):
File ~/.local/lib/python3.8/site-packages/anndata/_io/specs/registry.py:175, in write_elem(f, k, elem, modifiers, *args, **kwargs)
171 _REGISTRY.get_writer(dest_type, (t, elem.dtype.kind), modifiers)(
172 f, k, elem, *args, **kwargs
173 )
174 else:
--> 175 _REGISTRY.get_writer(dest_type, t, modifiers)(f, k, elem, *args, **kwargs)
File ~/.local/lib/python3.8/site-packages/anndata/_io/specs/registry.py:24, in write_spec..decorator..wrapper(g, k, *args, **kwargs)
22 @wraps(func)
23 def wrapper(g, k, *args, **kwargs):
---> 24 result = func(g, k, *args, **kwargs)
25 g[k].attrs.setdefault("encoding-type", spec.encoding_type)
26 g[k].attrs.setdefault("encoding-version", spec.encoding_version)
File ~/.local/lib/python3.8/site-packages/anndata/_io/specs/methods.py:281, in write_mapping(f, k, v, dataset_kwargs)
279 g = f.create_group(k)
280 for sub_k, sub_v in v.items():
--> 281 write_elem(g, sub_k, sub_v, dataset_kwargs=dataset_kwargs)
File ~/.local/lib/python3.8/site-packages/anndata/_io/utils.py:220, in report_write_key_on_error..func_wrapper(elem, key, val, *args, **kwargs)
218 else:
219 parent = _get_parent(elem)
--> 220 raise type(e)(
221 f"{e}\n\n"
222 f"Above error raised while writing key {key!r} of {type(elem)} "
223 f"to {parent}"
224 ) from e
TypeError: Can't implicitly convert non-string objects to strings
Above error raised while writing key 'names' of to /
```