It will have something to do with how IO is handled in Python 3. A
print statement before this error will show this. We may need to
detect the type that self.data is - in Python 2 and 3 it will probably
be a string and byte-array respectively - and then convert to the
correct type. It might be a relax problem. Though that depends on
what self.data is. If it was created by nmrglue, then the problem
might be with nmrglue. In any case, in data_store/nmrglue.py we can
test for the type and convert to the correct format for b64encode() to
work around the issue. An example already in relax is in the
version.py file:
# Decode Python 3 byte arrays.
if hasattr(line, 'decode'):
line = line.decode()
And in the ./pipe_control/dasha.py file:
# Encode to a Python 3 byte array.
if hasattr(line, 'encode'):
line = line.encode()
One of these conversions will be relevant here. See the files for more details.
Cheers,
Edward
On 15 January 2015 at 09:26, Troels Emtekær Linnet
<tlin...@nmr-relax.com> wrote:
> So this has nothing to do with nmrglue, I guess?
>
> But to the base64 module of python.
>
> Best
> Troels
>
> 2015-01-14 19:13 GMT+01:00 Edward d Auvergne
> <no-reply.invalid-addr...@gna.org>:
>>
>> Follow-up Comment #94, task #7873 (project relax):
>>
>> When I run the Nmrglue system tests in Python 2, they pass. However in
>> Python
>> 3 I see:
>>
>> $ python3 ./relax -s --time Nmrglue
>> Echoing of user function calls has been enabled.
>>
>>
>> =============================
>> = System / functional tests =
>> =============================
>>
>> . 0.00 s for Nmrglue.test_nmrglue_read
>> . 0.00 s for Nmrglue.test_nmrglue_read_several
>> . 0.16 s for Nmrglue.test_plot_contour
>> . 0.10 s for Nmrglue.test_plot_contour_cpmg
>> . 0.12 s for Nmrglue.test_plot_correlation
>> . 2.90 s for Nmrglue.test_plot_hist_cpmg
>> . 3.44 s for Nmrglue.test_plot_hist_cpmg_several
>> E 0.00 s for Nmrglue.test_save_state
>> . 0.00 s for Nmrglue.test_version
>>
>> ======================================================================
>> ERROR: test_save_state (test_suite.system_tests.nmrglue.Nmrglue)
>> Test saving a state with numpy arrays, reset relax, and read the state
>> again.
>> ----------------------------------------------------------------------
>>
>> relax> pipe.create(pipe_name='mf', pipe_type='mf', bundle=None)
>>
>> relax> spectrum.nmrglue_read(file='128_0_FT.ft2',
>>
>> dir='/data/relax/branches/nmrglue/test_suite/shared_data/dispersion/repeated_analysis/SOD1/cpmg_disp_sod1d90a_060518/cpmg_disp_sod1d90a_060518_normal.fid/ft2_data',
>> nmrglue_id='test')
>> Filesize of .ft2 file is: 527360
>> Type of encoding is: <class 'numpy.ndarray'>
>> Storing numpy array to: /tmp/tmpl4p2zk/data.npy
>> Filesize of .npy file is: 525392
>> Shape of data is 256x513
>> dtype of data is float32
>> Type of data[0][0]: <class 'numpy.float32'>
>>
>> relax> state.save(state='state', dir='/tmp/tmpl4p2zk', compress_type=1,
>> force=True)
>> Opening the file '/tmp/tmpl4p2zk/state.bz2' for writing.
>> Traceback (most recent call last):
>> File "/data/relax/branches/nmrglue/test_suite/system_tests/nmrglue.py",
>> line
>> 569, in test_save_state
>> self.interpreter.state.save('state', dir=dirpath, compress_type=1,
>> force=True)
>> File "/data/relax/branches/nmrglue/prompt/uf_objects.py", line 225, in
>> __call__
>> self._backend(*new_args, **uf_kargs)
>> File "/data/relax/branches/nmrglue/pipe_control/state.py", line 128, in
>> save_state
>> ds.to_xml(file)
>> File "/data/relax/branches/nmrglue/data_store/__init__.py", line 643, in
>> to_xml
>> self[pipe].to_xml(xmldoc, pipe_element,
>> pipe_type=self[pipe].pipe_type)
>> File "/data/relax/branches/nmrglue/data_store/pipe_container.py", line
>> 335,
>> in to_xml
>> self.nmrglue.to_xml(doc, element)
>> File "/data/relax/branches/nmrglue/data_store/data_classes.py", line
>> 244, in
>> to_xml
>> self[key].to_xml(doc, dict_item_element)
>> File "/data/relax/branches/nmrglue/data_store/nmrglue.py", line 138, in
>> to_xml
>> string = b64encode(self.data)
>> File "/usr/lib64/python3.3/base64.py", line 58, in b64encode
>> raise TypeError("expected bytes, not %s" % s.__class__.__name__)
>> TypeError: expected bytes, not ndarray
>>
>> ----------------------------------------------------------------------
>> Ran 9 tests in 6.725s
>>
>> FAILED (errors=1)
>>
>> _______________________________________________________
>>
>> Reply to this item at:
>>
>> <http://gna.org/task/?7873>
>>
>> _______________________________________________
>> Message sent via/by Gna!
>> http://gna.org/
>>
>
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