trouble in using Bokeh library for reading hdf file

Community Support
1

I’m working on project using BOKEH library, and when I’m
testing the notebook that you wrote using the data « water_data_all_years.hdf »( I joined the file to my post) I have an error message

water_data_all_years.hdf (33.2 KB)

···

HDF5ExtError Traceback (most
recent call last)

in ()

---->
1 wat_df = pd.read_hdf(‘water_data_all_years.hdf’, ‘df’)

2 san_df =
pd.read_hdf(‘san_data_all_years.hdf’)

\eden.ensae.fr\SourceLogicielsSeven\Python\Anaconda3\lib\site-packages\pandas\io\pytables.py
in read_hdf(path_or_buf, key, **kwargs)

308

can’t auto open/close if we are using an iterator

309

so delegate to the iterator

→
310 store = HDFStore(path_or_buf,
**kwargs)

311
auto_close = True

312

\eden.ensae.fr\SourceLogicielsSeven\Python\Anaconda3\lib\site-packages\pandas\io\pytables.py
in init(self, path, mode, complevel, complib, fletcher32, **kwargs)

402
self._fletcher32 = fletcher32

403
self._filters = None

→
404 self.open(mode=mode,
**kwargs)

405

406
@property

\eden.ensae.fr\SourceLogicielsSeven\Python\Anaconda3\lib\site-packages\pandas\io\pytables.py
in open(self, mode, **kwargs)

541

542
try:

→
543 self._handle =
tables.open_file(self._path, self._mode, **kwargs)

544
except (IOError) as e: # pragma:
no cover

545 if ‘can not be written’ in str(e):

\eden.ensae.fr\SourceLogicielsSeven\Python\Anaconda3\lib\site-packages\tables\file.py
in open_file(filename, mode, title, root_uep, filters, **kwargs)

316

317

Finally, create the File instance, and return it

→
318 return File(filename, mode,
title, root_uep, filters, **kwargs)

319

320 openFile = previous_api(open_file)

\eden.ensae.fr\SourceLogicielsSeven\Python\Anaconda3\lib\site-packages\tables\file.py
in init(self, filename, mode, title, root_uep, filters, **kwargs)

782

783

Now, it is time to initialize the File extension

→
784 self._g_new(filename, mode,
**params)

785

786

Check filters and set PyTables format version for new files.

tables\hdf5extension.pyx
in tables.hdf5extension.File._g_new (tables\hdf5extension.c:5584)()

HDF5ExtError:
HDF5 error back trace

File
“C:\aroot\work\hdf5-1.8.15-patch1\src\H5F.c”, line 604, in H5Fopen

unable to open file

File
“C:\aroot\work\hdf5-1.8.15-patch1\src\H5Fint.c”, line 1085, in
H5F_open

unable to read superblock

File
“C:\aroot\work\hdf5-1.8.15-patch1\src\H5Fsuper.c”, line 277, in
H5F_super_read

file signature not found

End
of HDF5 error back trace

Unable
to open/create file ‘water_data_all_years.hdf’

I’m
working on Jupyter and I don’t know why this occurs ?

Thanks
in advance for your help,

2

Hi,

This is a mailing list for questions regarding the usage of Bokeh. Your question seems to be solely related to the usage of HDF5, and has nothing to do with Bokeh in particular. I'd suggest that you should ask this question on an HDF5 mailing list, or perhaps StackOverflow (or perhaps a Pandas help forum, since the call generating the error is pd.read_hdf)

Thanks,

Bryan

···

On Oct 26, 2016, at 8:55 AM, [email protected] wrote:

I’m working on project using BOKEH library, and when I’m testing the notebook that you wrote using the data « water_data_all_years.hdf »( I joined the file to my post) I have an error message

                ---------------------------------------------------------------------------

                HDF5ExtError Traceback (most recent call last)

                <ipython-input-71-c977b136cd4c> in <module>()

                ----> 1 wat_df = pd.read_hdf('water_data_all_years.hdf', 'df')

                      2 san_df = pd.read_hdf('san_data_all_years.hdf')

                \\eden.ensae.fr\SourceLogicielsSeven\Python\Anaconda3\lib\site-packages\pandas\io\pytables.py in read_hdf(path_or_buf, key, **kwargs)

                    308 # can't auto open/close if we are using an iterator

                    309 # so delegate to the iterator

                --> 310 store = HDFStore(path_or_buf, **kwargs)

                    311 auto_close = True

                    312

                \\eden.ensae.fr\SourceLogicielsSeven\Python\Anaconda3\lib\site-packages\pandas\io\pytables.py in __init__(self, path, mode, complevel, complib, fletcher32, **kwargs)

                    402 self._fletcher32 = fletcher32

                    403 self._filters = None

                --> 404 self.open(mode=mode, **kwargs)

                    405

                    406 @property

                \\eden.ensae.fr\SourceLogicielsSeven\Python\Anaconda3\lib\site-packages\pandas\io\pytables.py in open(self, mode, **kwargs)

                    541

                    542 try:

                --> 543 self._handle = tables.open_file(self._path, self._mode, **kwargs)

                    544 except (IOError) as e: # pragma: no cover

                    545 if 'can not be written' in str(e):

                \\eden.ensae.fr\SourceLogicielsSeven\Python\Anaconda3\lib\site-packages\tables\file.py in open_file(filename, mode, title, root_uep, filters, **kwargs)

                    316

                    317 # Finally, create the File instance, and return it

                --> 318 return File(filename, mode, title, root_uep, filters, **kwargs)

                    319

                    320 openFile = previous_api(open_file)

                \\eden.ensae.fr\SourceLogicielsSeven\Python\Anaconda3\lib\site-packages\tables\file.py in __init__(self, filename, mode, title, root_uep, filters, **kwargs)

                    782

                    783 # Now, it is time to initialize the File extension

                --> 784 self._g_new(filename, mode, **params)

                    785

                    786 # Check filters and set PyTables format version for new files.

                tables\hdf5extension.pyx in tables.hdf5extension.File._g_new (tables\hdf5extension.c:5584)()

                HDF5ExtError: HDF5 error back trace

                  File "C:\aroot\work\hdf5-1.8.15-patch1\src\H5F.c", line 604, in H5Fopen

                    unable to open file

                  File "C:\aroot\work\hdf5-1.8.15-patch1\src\H5Fint.c", line 1085, in H5F_open

                    unable to read superblock

                  File "C:\aroot\work\hdf5-1.8.15-patch1\src\H5Fsuper.c", line 277, in H5F_super_read

                    file signature not found

                End of HDF5 error back trace

                Unable to open/create file 'water_data_all_years.hdf'

                I’m working on Jupyter and I don’t know why this occurs ?

                Thanks in advance for your help,

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<water_data_all_years.hdf>