Code Sample, a copy-pastable example if possible
# Your code here
data.to_hdf('data.h5',mode='w',format='f')
data = pd.read_hdf('data.h5')
####Traceback
AttributeError Traceback (most recent call last)
<ipython-input-5-13fe6d5eccfa> in <module>()
----> 1 ndata = pd.read_hdf('cleaned_data_v1.h5')
/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in read_hdf(path_or_buf, key, mode, **kwargs)
368 'contains multiple datasets.')
369 key = candidate_only_group._v_pathname
--> 370 return store.select(key, auto_close=auto_close, **kwargs)
371 except:
372 # if there is an error, close the store
/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in select(self, key, where, start, stop, columns, iterator, chunksize, auto_close, **kwargs)
715 chunksize=chunksize, auto_close=auto_close)
716
--> 717 return it.get_result()
718
719 def select_as_coordinates(
/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in get_result(self, coordinates)
1455
1456 # directly return the result
-> 1457 results = self.func(self.start, self.stop, where)
1458 self.close()
1459 return results
/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in func(_start, _stop, _where)
708 return s.read(start=_start, stop=_stop,
709 where=_where,
--> 710 columns=columns, **kwargs)
711
712 # create the iterator
/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in read(self, start, stop, **kwargs)
2893 for i in range(self.nblocks):
2894
-> 2895 blk_items = self.read_index('block%d_items' % i)
2896 values = self.read_array('block%d_values' % i,
2897 start=_start, stop=_stop)
/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in read_index(self, key, **kwargs)
2475
2476 def read_index(self, key, **kwargs):
-> 2477 variety = _ensure_decoded(getattr(self.attrs, '%s_variety' % key))
2478
2479 if variety == u('multi'):
/opt/conda/lib/python3.6/site-packages/tables/attributeset.py in __getattr__(self, name)
290 if not name in self._v_attrnames:
291 raise AttributeError("Attribute '%s' does not exist in node: "
--> 292 "'%s'" % (name, self._v__nodepath))
293
294 # Read the attribute from disk. This is an optimization to read
AttributeError: Attribute 'block2_items_variety' does not exist in node: '/cleaned_data'
#### Problem description
We are working remotely on a Jupyter notebook on a server doing some
data preprocessing, having loaded an unprocessed .h5 file that was created
using the pd.to_hdf() command we then did a number of preprocessing operations
and added some new columns to dataframe.
Next we saved the data using data.to_hdf command and generated the file data.h5. after
that we used the command read_hdf to read the file but we get the error:
"Attribute 'block2_items_variety' does not exist in node: /cleaned_data".
#### Expected Output
reading the file successfully.
#### Output of ``pd.show_versions()``
[paste the output of ``pd.show_versions()`` here below this line]
INSTALLED VERSIONS
------------------
commit: None
python: 3.6.3.final.0
python-bits: 64
OS: Linux
OS-release: 4.5.7-docker-4
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: en_US.UTF-8
LANG: en_US.UTF-8
LOCALE: en_US.UTF-8
pandas: 0.21.0
pytest: 3.3.1
pip: 9.0.1
setuptools: 36.6.0
Cython: 0.25.2
numpy: 1.12.1
scipy: 0.19.1
pyarrow: None
xarray: None
IPython: 6.2.1
sphinx: None
patsy: 0.4.1
dateutil: 2.6.1
pytz: 2017.3
blosc: None
bottleneck: None
tables: 3.4.2
numexpr: 2.6.2
feather: None
matplotlib: 2.0.2
openpyxl: None
xlrd: 1.0.0
xlwt: None
xlsxwriter: None
lxml: None
bs4: 4.5.3
html5lib: 0.999999999
sqlalchemy: 1.1.13
pymysql: None
psycopg2: None
jinja2: 2.9.6
s3fs: None
fastparquet: None
pandas_gbq: None
pandas_datareader: None
**Comment From: TomAugspurger**
Could you edit your original post to include
1. code that creates a sample DataFrame that generates the exception when written and read
2. The traceback when reading
**Comment From: seanysull**
I have added the full traceback, I am in the process of trying to recreate an example I can share here, however, I am working with data I can not easily share so it will take a while if I am even able to do it.
**Comment From: jreback**
you would have to show a reproducible example
**Comment From: JanKalin**
I get a similar error. I have an application that reads DEWESoft files, converts them to pandas DataFrame and writes them to HDF5 file(s). The complete code used for conversion is downloadable from https://github.com/JanKalin/python_dewesoft. The data file in question can be copied from ftp://zaguser:zagpublic@ftp.zag.si/publicftp/JanK/Pandas/Ravbarkomanda_2018_04_04_132938.dxd
Call `dws2hdf5 Ravbarkomanda_2018_04_04_132938.dxd --fields 1 --rename :5:T_P13N4SN` to start conversion, which fails:
2018-07-03 12:52:58.939000 1/1 Ravbarkomanda_2018_04_04_132938.dxd,
Traceback (most recent call last):
File "J:\python\dws2hdf5.py", line 111, in
The HDF5 file available at ftp://zaguser:zagpublic@ftp.zag.si/publicftp/JanK/Pandas/2018_04_04_13_29_40_110000.hdf5 is left in a mangled state,:
quark % python Python 2.7.15 (v2.7.15:ca079a3ea3, Apr 30 2018, 16:22:17) [MSC v.1500 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information.
import pandas as pd pd.read_hdf("2018_04_04_13_29_40_110000.hdf5") Traceback (most recent call last): File "
", line 1, in File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 370, in read_hdf return store.select(key, auto_close=auto_close, kwargs) File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 717, in select return it.get_result() File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 1457, in get_result results = self.func(self.start, self.stop, where) File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 710, in func columns=columns, kwargs) File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 2902, in read blk_items = self.read_index('block%d_items' % i) File "C:\Python27\lib\site-packages\pandas\io\pytables.py", line 2484, in read_index variety = _ensure_decoded(getattr(self.attrs, '%s_variety' % key)) File "C:\Python27\lib\site-packages\tables\attributeset.py", line 305, in getattr "'%s'" % (name, self._v__nodepath)) AttributeError: Attribute 'block0_items_variety' does not exist in node: '/a_2018_04_04_13_29_40_110000' pd.show_versions()
INSTALLED VERSIONS
commit: None python: 2.7.15.final.0 python-bits: 32 OS: Windows OS-release: 7 machine: AMD64 processor: Intel64 Family 6 Model 26 Stepping 5, GenuineIntel byteorder: little LC_ALL: None LANG: None LOCALE: None.None
pandas: 0.22.0 pytest: None pip: 10.0.1 setuptools: 39.0.1 Cython: None numpy: 1.14.3 scipy: 1.0.1 pyarrow: None xarray: None IPython: 5.6.0 sphinx: 1.7.4 patsy: None dateutil: 2.7.2 pytz: 2018.4 blosc: None bottleneck: None tables: 3.4.3 numexpr: 2.6.5 feather: None matplotlib: 2.2.2 openpyxl: 2.5.4 xlrd: 1.1.0 xlwt: 1.3.0 xlsxwriter: None lxml: 4.2.1 bs4: None html5lib: 1.0.1 sqlalchemy: None pymysql: None psycopg2: None jinja2: 2.10 s3fs: None fastparquet: None pandas_gbq: None pandas_datareader: None
**Comment From: JanKalin**
The problem apparently only occurs on 32-bit Python. With 64-bit running inside a 64-bit virtual machine the conversion goes well:
Y:>c:\Users\jank\test\dws2hdf5.py Ravbarkomanda_2018_04_04_132938.dxd --fields 1 @rename.opt 2018-07-04 09:53:22.973000 1/1 Ravbarkomanda_2018_04_04_132938.dxd, a_2018_04_04 _13_29_40_110000, T_2018_04_04_13_29_40_110000, done
Y:>python Python 2.7.15 (v2.7.15:ca079a3ea3, Apr 30 2018, 16:30:26) [MSC v.1500 64 bit (AM D64)] on win32 Type "help", "copyright", "credits" or "license" for more information.
import pandas as pd pd.show_versions()
INSTALLED VERSIONS
commit: None python: 2.7.15.final.0 python-bits: 64 OS: Windows OS-release: 7 machine: AMD64 processor: Intel64 Family 6 Model 26 Stepping 5, GenuineIntel byteorder: little LC_ALL: None LANG: None LOCALE: None.None
pandas: 0.23.1 pytest: None pip: 10.0.1 setuptools: 39.0.1 Cython: None numpy: 1.14.5 scipy: None pyarrow: None xarray: None IPython: 5.7.0 sphinx: 1.7.5 patsy: None dateutil: 2.7.3 pytz: 2018.5 blosc: None bottleneck: None tables: None numexpr: 2.6.5 feather: None matplotlib: None openpyxl: None xlrd: None xlwt: None xlsxwriter: None lxml: None bs4: None html5lib: 1.0.1 sqlalchemy: None pymysql: None psycopg2: None jinja2: 2.10 s3fs: None fastparquet: None pandas_gbq: None pandas_datareader: None
**Comment From: JanKalin**
And the problem disappears with the latest version of Pandas, 0.23.2
**Comment From: AiAlex**
Got this error
`AttributeError: Attribute 'block1_items_variety' does not exist in node: '/dataset'`
on
Pandas 0.25.3
Python 3.6.3 :: Anaconda, Inc.
**Comment From: alice17**
I experienced the same error:
`AttributeError: Attribute 'block0_items_variety' does not exist in node: '/train'` when calling the function `pd.read_hdf(fileInPath, key="train")`.
pandas 0.24.2
tables 3.5.2
python 3.6
**Comment From: gerritholl**
I experience this error with the attached file.
[72047299999.h5.gz](https://github.com/pandas-dev/pandas/files/4096382/72047299999.h5.gz)
MWE is rather simple:
```python
import pandas
pandas.read_hdf("/data/gholl/cache/fogtools/2019/72047299999.h5", "root")
The resulting traceback:
Traceback (most recent call last):
File "mwe15.py", line 2, in <module>
pandas.read_hdf("/data/gholl/cache/fogtools/2019/72047299999.h5", "root")
File "/media/nas/x21324/miniconda3/envs/py37e/lib/python3.7/site-packages/pandas/io/pytables.py", line 428, in read_hdf
auto_close=auto_close,
File "/media/nas/x21324/miniconda3/envs/py37e/lib/python3.7/site-packages/pandas/io/pytables.py", line 814, in select
return it.get_result()
File "/media/nas/x21324/miniconda3/envs/py37e/lib/python3.7/site-packages/pandas/io/pytables.py", line 1829, in get_result
results = self.func(self.start, self.stop, where)
File "/media/nas/x21324/miniconda3/envs/py37e/lib/python3.7/site-packages/pandas/io/pytables.py", line 798, in func
return s.read(start=_start, stop=_stop, where=_where, columns=columns)
File "/media/nas/x21324/miniconda3/envs/py37e/lib/python3.7/site-packages/pandas/io/pytables.py", line 3068, in read
blk_items = self.read_index(f"block{i}_items")
File "/media/nas/x21324/miniconda3/envs/py37e/lib/python3.7/site-packages/pandas/io/pytables.py", line 2752, in read_index
variety = _ensure_decoded(getattr(self.attrs, f"{key}_variety"))
File "/media/nas/x21324/miniconda3/envs/py37e/lib/python3.7/site-packages/tables/attributeset.py", line 301, in __getattr__
"'%s'" % (name, self._v__nodepath))
AttributeError: Attribute 'block0_items_variety' does not exist in node: '/root'
Closing remaining open files:/data/gholl/cache/fogtools/2019/72047299999.h5...done
Software versions:
Pandas 1.0.0rc0, pytables 3.6.1, Python 3.7.3. See below for a full output of conda list:
# packages in environment at /media/nas/x21324/miniconda3/envs/py37e:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main conda-forge
affine 2.3.0 py_0 conda-forge
aggdraw 1.3.11 py37hc56bac0_0 conda-forge
alabaster 0.7.12 py_0 conda-forge
appdirs 1.4.3 pypi_0 pypi
asciitree 0.3.3 py_2 conda-forge
attrs 19.3.0 py_0 conda-forge
awscli 1.16.287 py37_0 conda-forge
babel 2.7.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
beautifulsoup4 4.8.1 py37_0 conda-forge
behave 1.2.6 py37_1000 conda-forge
bitstring 3.1.6 pypi_0 pypi
bleach 3.1.0 py_0 conda-forge
blosc 1.17.0 he1b5a44_1 conda-forge
bokeh 1.4.0 py37_0 conda-forge
boost-cpp 1.70.0 h8e57a91_2 conda-forge
boto3 1.10.23 py_0 conda-forge
botocore 1.13.23 py_0 conda-forge
bzip2 1.0.8 h516909a_1 conda-forge
ca-certificates 2019.11.28 hecc5488_0 conda-forge
cairo 1.16.0 hfb77d84_1002 conda-forge
cartopy 0.17.0 py37hc5b2455_1008 conda-forge
certifi 2019.11.28 py37_0 conda-forge
cffi 1.13.2 py37h8022711_0 conda-forge
cfgrib 0.9.7.3 py_0 conda-forge
cfitsio 3.470 hb60a0a2_2 conda-forge
cftime 1.0.4.2 py37hc1659b7_0 conda-forge
chardet 3.0.4 py37_1003 conda-forge
click 7.0 py_0 conda-forge
click-plugins 1.1.1 py_0 conda-forge
cligj 0.5.0 py_0 conda-forge
cloudpickle 1.2.2 py_1 conda-forge
codecov 2.0.15 py_1 conda-forge
colorama 0.4.1 py_0 conda-forge
colorcet 2.0.1 py_0 conda-forge
configobj 5.0.6 py_0 conda-forge
coverage 4.5.4 py37h516909a_0 conda-forge
coveralls 1.9.2 py_0 conda-forge
cryptography 2.8 py37h72c5cf5_0 conda-forge
curl 7.65.3 hf8cf82a_0 conda-forge
cycler 0.10.0 py_2 conda-forge
cython 0.29.14 py37he1b5a44_0 conda-forge
cytoolz 0.10.1 py37h516909a_0 conda-forge
dask 2.8.0 py_1 conda-forge
dask-core 2.8.0 py_0 conda-forge
datashader 0.8.0 py_0 conda-forge
datashape 0.5.4 py_1 conda-forge
dbus 1.13.6 he372182_0 conda-forge
decorator 4.4.1 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
distributed 2.8.0 py_1 conda-forge
docopt 0.6.2 py_1 conda-forge
docutils 0.15.2 py37_0 conda-forge
eccodes 2.14.1 hc4140ea_3 conda-forge
entrypoints 0.3 py37_1000 conda-forge
expat 2.2.5 he1b5a44_1004 conda-forge
fasteners 0.14.1 py_3 conda-forge
fcitools 0.1.0.post0.dev5+ga19d0d1 pypi_0 pypi
fiona 1.8.11 py37h900e953_0 conda-forge
flake8 3.7.9 py37_0 conda-forge
fogpy 1.2.0+dev21.g2b0d49d.get.validation.output.for.fog.mask pypi_0 pypi
fogtools 0.0.post0.dev8+g85b3564.dirty dev_0 <develop>
fontconfig 2.13.1 h86ecdb6_1001 conda-forge
freetype 2.10.0 he983fc9_1 conda-forge
freetype-py 2.1.0.post1 py_0 conda-forge
freexl 1.0.5 h14c3975_1002 conda-forge
fsspec 0.6.0 py_0 conda-forge
g2clib 1.6.0 hf3f1b0b_9 conda-forge
gdal 3.0.2 py37hbb6b9fb_3 conda-forge
geopandas 0.6.2 py_0 conda-forge
geos 3.7.2 he1b5a44_2 conda-forge
geotiff 1.5.1 hbd99317_7 conda-forge
geoviews 1.6.5 py_0 conda-forge
geoviews-core 1.6.5 py_0 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
giflib 5.1.7 h516909a_1 conda-forge
glib 2.58.3 py37h6f030ca_1002 conda-forge
goesr 0.5.2 pypi_0 pypi
gst-plugins-base 1.14.5 h0935bb2_0 conda-forge
gstreamer 1.14.5 h36ae1b5_0 conda-forge
h5netcdf 0.7.4 py_0 conda-forge
h5py 2.10.0 nompi_py37h513d04c_100 conda-forge
hdf4 4.2.13 hf30be14_1003 conda-forge
hdf5 1.10.5 nompi_h3c11f04_1104 conda-forge
hdfeos2 2.20 h64bfcee_1000 conda-forge
hdfeos5 5.1.16 h8b6279f_5 conda-forge
heapdict 1.0.1 py_0 conda-forge
holoviews 1.12.6 py_0 conda-forge
icu 64.2 he1b5a44_1 conda-forge
idna 2.8 py37_1000 conda-forge
imageio 2.6.1 py37_0 conda-forge
imagesize 1.1.0 py_0 conda-forge
importlib_metadata 0.23 py37_0 conda-forge
ipdb 0.12.2 py_0 conda-forge
ipykernel 5.1.3 py37h5ca1d4c_0 conda-forge
ipython 7.9.0 py37h5ca1d4c_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.5.1 py_0 conda-forge
jasper 1.900.1 h07fcdf6_1006 conda-forge
jedi 0.15.1 py37_0 conda-forge
jinja2 2.10.3 py_0 conda-forge
jmespath 0.9.4 py_0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
json-c 0.13.1 h14c3975_1001 conda-forge
jsonschema 3.2.0 py37_0 conda-forge
jupyter 1.0.0 py_2 conda-forge
jupyter_client 5.3.3 py37_1 conda-forge
jupyter_console 6.0.0 py_0 conda-forge
jupyter_core 4.6.1 py37_0 conda-forge
kealib 1.4.10 h58c409b_1005 conda-forge
kiwisolver 1.1.0 py37hc9558a2_0 conda-forge
krb5 1.16.3 h05b26f9_1001 conda-forge
libaec 1.0.4 hf484d3e_0 conda-forge
libblas 3.8.0 14_openblas conda-forge
libcblas 3.8.0 14_openblas conda-forge
libclang 9.0.0 default_hde54327_4 conda-forge
libcurl 7.65.3 hda55be3_0 conda-forge
libdap4 3.20.4 hd3bb157_0 conda-forge
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.2.0 hdf63c60_0 conda-forge
libgdal 3.0.2 h5534617_3 conda-forge
libgfortran-ng 7.3.0 hdf63c60_2 conda-forge
libiconv 1.15 h516909a_1005 conda-forge
libkml 1.3.0 h4fcabce_1010 conda-forge
liblapack 3.8.0 14_openblas conda-forge
libllvm8 8.0.1 hc9558a2_0 conda-forge
libllvm9 9.0.0 hc9558a2_3 conda-forge
libnetcdf 4.7.1 nompi_h94020b1_101 conda-forge
libopenblas 0.3.7 h6e990d7_3 conda-forge
libpng 1.6.37 hed695b0_0 conda-forge
libpq 11.5 hd9ab2ff_2 conda-forge
libsodium 1.0.17 h516909a_0 conda-forge
libspatialindex 1.9.3 he1b5a44_1 conda-forge
libspatialite 4.3.0a h4f6d029_1032 conda-forge
libssh2 1.8.2 h22169c7_2 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_0 conda-forge
libtiff 0.4.2 pypi_0 pypi
libuuid 2.32.1 h14c3975_1000 conda-forge
libwebp 1.0.2 hf4e8a37_4 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxkbcommon 0.9.1 hebb1f50_0 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
libxslt 1.1.33 h31b3aaa_0 conda-forge
line_profiler 2.1.2 py37h516909a_1003 conda-forge
llvmlite 0.30.0 py37h8b12597_1 conda-forge
locket 0.2.0 py_2 conda-forge
lxml 4.4.1 py37h7ec2d77_0 conda-forge
lz4-c 1.8.3 he1b5a44_1001 conda-forge
lzo 2.10 h14c3975_1000 conda-forge
markupsafe 1.1.1 py37h516909a_0 conda-forge
matplotlib 3.1.2 py37_1 conda-forge
matplotlib-base 3.1.2 py37h250f245_1 conda-forge
mccabe 0.6.1 py_1 conda-forge
mechanicalsoup 0.12.0 py_0 conda-forge
mistune 0.8.4 py37h516909a_1000 conda-forge
mock 3.0.5 py37_0 conda-forge
monotonic 1.5 py_0 conda-forge
more-itertools 7.2.0 py_0 conda-forge
msgpack-python 0.6.2 py37hc9558a2_0 conda-forge
multipledispatch 0.6.0 py_0 conda-forge
munch 2.5.0 py_0 conda-forge
nbconvert 5.6.1 py37_0 conda-forge
nbformat 4.4.0 py_1 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
netcdf4 1.5.3 py37hf3213d6_0 conda-forge
networkx 2.4 py_0 conda-forge
notebook 6.0.1 py37_0 conda-forge
nspr 4.23 he1b5a44_0 conda-forge
nss 3.47 he751ad9_0 conda-forge
numba 0.46.0 py37hb3f55d8_1 conda-forge
numcodecs 0.6.4 py37he1b5a44_0 conda-forge
numexpr 2.7.1 py37hb3f55d8_0 conda-forge
numpy 1.17.3 py37h95a1406_0 conda-forge
olefile 0.46 py_0 conda-forge
opencv-python 4.1.0.25 pypi_0 pypi
openjpeg 2.3.1 h21c5421_1 conda-forge
openssl 1.1.1d h516909a_0 conda-forge
owslib 0.19.0 py_0 conda-forge
packaging 19.2 py_0 conda-forge
pandas 1.0.0rc0 pypi_0 pypi
pandoc 2.7.3 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
param 1.9.2 py_0 conda-forge
parse 1.12.1 py_0 conda-forge
parse_type 0.5.2 py37_0 conda-forge
parso 0.5.1 py_0 conda-forge
partd 1.0.0 py_0 conda-forge
pcre 8.43 he1b5a44_0 conda-forge
pexpect 4.7.0 py37_0 conda-forge
pickleshare 0.7.5 py37_1000 conda-forge
pillow 6.2.1 py37hd70f55b_1 conda-forge
pip 19.3.1 py37_0 conda-forge
pixman 0.38.0 h516909a_1003 conda-forge
pluggy 0.13.0 py37_0 conda-forge
poppler 0.67.0 h14e79db_8 conda-forge
poppler-data 0.4.9 1 conda-forge
postgresql 11.5 hc63931a_2 conda-forge
progressbar2 3.47.0 py_0 conda-forge
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Comment From: gerritholl
@jreback I have attached a file with a reproduceable example. Are you able to reproduce this? Could this be reopened please?
Comment From: jreback
@gerritholl
you would need to show writing and reading read_hdf is only capable of reading its own format
pls open a new issue if you have a repro example
Comment From: gerritholl
@jreback See #31199