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"'TableIterator' object is not an iterator" when calling df.read_hdf() #16739

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xkortex opened this issue Jun 20, 2017 · 1 comment
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API Design Duplicate Report Duplicate issue or pull request IO HDF5 read_hdf, HDFStore

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@xkortex
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xkortex commented Jun 20, 2017

Code Sample, a copy-pastable example if possible

reader = pd.read_hdf(filename, 'foo', chunksize=1000)
next(reader)
TypeError: 'TableIterator' object is not an iterator

Problem description

Unless I'm missing something, I would expect something called TableIterator to be (itself) an iterator. Since this is an analog of df.read_csv(), I would expect it to behave along the same lines (which is TextFileReader and works with next()).

reader.__iter__() is defined, so for chunk in reader works. It's just slightly surprising that TextFileReader defines __next__(), but TableIterator does not.

Expected Output

next(reader) should give the dataframe corresponding to that chunk.

(yes I know Iterators and Iterables are slightly different, but in this case I would expect both to be supported)

Output of pd.show_versions()

INSTALLED VERSIONS

commit: None
python: 3.5.2.final.0
python-bits: 64
OS: Linux
OS-release: 4.4.0-79-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: en_US.UTF-8

pandas: 0.19.2
nose: None
pip: 9.0.1
setuptools: 36.0.1
Cython: None
numpy: 1.12.1
scipy: 0.19.0
statsmodels: None
xarray: None
IPython: 6.1.0
sphinx: None
patsy: None
dateutil: 2.6.0
pytz: 2016.10
blosc: None
bottleneck: None
tables: 3.4.2
numexpr: 2.6.2
matplotlib: 2.0.0
openpyxl: None
xlrd: None
xlwt: None
xlsxwriter: None
lxml: None
bs4: 4.5.3
html5lib: 0.999999999
httplib2: None
apiclient: None
sqlalchemy: None
pymysql: None
psycopg2: None
jinja2: 2.9.6
boto: None
pandas_datareader: None

@jreback jreback added API Design Duplicate Report Duplicate issue or pull request IO HDF5 read_hdf, HDFStore labels Jun 21, 2017
@jreback jreback added this to the No action milestone Jun 21, 2017
@jreback
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jreback commented Jun 21, 2017

this is not implemented (well it IS but it doesn't inherit from the proper machinery), see the issue here: #9496. Its a pretty easy PR actually if you'd like to do this.

Here's a full repro

In [1]: tm.makeMixedDataFrame().to_hdf('foo.h5', 'df', mode='w', format='table')

In [2]: pd.read_hdf('foo.h5')
Out[2]: 
     A    B     C          D
0  0.0  0.0  foo1 2009-01-01
1  1.0  1.0  foo2 2009-01-02
2  2.0  0.0  foo3 2009-01-05
3  3.0  1.0  foo4 2009-01-06
4  4.0  0.0  foo5 2009-01-07

In [3]: it = pd.read_hdf('foo.h5', chunksize=1)

In [4]: next(it)
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-4-2cdb14c0d4d6> in <module>()
----> 1 next(it)

TypeError: 'TableIterator' object is not an iterator

@jreback jreback closed this as completed Jun 21, 2017
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