add_intracellular_recording should also accept a stimulus template

[lvsltz]

add_intracellular_recording should accept for the stimulus argument both a stimulus presentation and a stimulus template.

I think somebody else mentioned this, so I haven't tested it.

[oruebel]

If I remember our last discussion correctly, then @t-b requested that it should accept TimeSeries more broadly, rather than being restricted to PatchClampSeries. I believe that would also fix this issue.

[oruebel]

Closing in favor of #25 which should also cover this issue

[lvsltz]

Not sure if this is actually working. If I simply add the stimulus_template just before add_intracellular_recording:

nwbfile.add_stimulus_template(myPatchClampSeries)
row_id = nwbfile.add_intracellular_recording(electrode = electrode,
    stimulus = myPatchClampSeries,
    response = myotherPatchClampSeries)

I get a KeyError when I write.

I wonder if this line is complete without stimulus_template. Please let me know if I misunderstood how these checks work or how I should add the stimulus_template to nwbfile:

Error:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)

.../nwbwrite.py in saveNWB(self, nwbfile, nwb_filename)
    212         io = pynwb.NWBHDF5IO(nwb_path, 'w')
    213 
--> 214         io.write(nwbfile)

~/miniconda3/envs/nwb/lib/python3.7/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    451 
    452             if is_method:
--> 453                 return func(args[0], **parsed['args'])
    454             else:
    455                 return func(**parsed['args'])

~/miniconda3/envs/nwb/lib/python3.7/site-packages/hdmf/backends/hdf5/h5tools.py in write(self, **kwargs)
    267 
    268         cache_spec = popargs('cache_spec', kwargs)
--> 269         call_docval_func(super().write, kwargs)
    270         if cache_spec:
    271             ref = self.__file.attrs.get(SPEC_LOC_ATTR)

~/miniconda3/envs/nwb/lib/python3.7/site-packages/hdmf/utils.py in call_docval_func(func, kwargs)
    341 def call_docval_func(func, kwargs):
    342     fargs, fkwargs = fmt_docval_args(func, kwargs)
--> 343     return func(*fargs, **fkwargs)
    344 
    345 

~/miniconda3/envs/nwb/lib/python3.7/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    451 
    452             if is_method:
--> 453                 return func(args[0], **parsed['args'])
    454             else:
    455                 return func(**parsed['args'])

~/miniconda3/envs/nwb/lib/python3.7/site-packages/hdmf/backends/io.py in write(self, **kwargs)
     42         container = popargs('container', kwargs)
     43         f_builder = self.__manager.build(container, source=self.__source)
---> 44         self.write_builder(f_builder, **kwargs)
     45 
     46     @abstractmethod

~/miniconda3/envs/nwb/lib/python3.7/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    451 
    452             if is_method:
--> 453                 return func(args[0], **parsed['args'])
    454             else:
    455                 return func(**parsed['args'])

~/miniconda3/envs/nwb/lib/python3.7/site-packages/hdmf/backends/hdf5/h5tools.py in write_builder(self, **kwargs)
    534         f_builder, link_data, exhaust_dci = getargs('builder', 'link_data', 'exhaust_dci', kwargs)
    535         for name, gbldr in f_builder.groups.items():
--> 536             self.write_group(self.__file, gbldr, exhaust_dci=exhaust_dci)
    537         for name, dbldr in f_builder.datasets.items():
    538             self.write_dataset(self.__file, dbldr, link_data, exhaust_dci=exhaust_dci)

~/miniconda3/envs/nwb/lib/python3.7/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    451 
    452             if is_method:
--> 453                 return func(args[0], **parsed['args'])
    454             else:
    455                 return func(**parsed['args'])

~/miniconda3/envs/nwb/lib/python3.7/site-packages/hdmf/backends/hdf5/h5tools.py in write_group(self, **kwargs)
    694             for subgroup_name, sub_builder in subgroups.items():
    695                 # do not create an empty group without attributes or links
--> 696                 self.write_group(group, sub_builder, exhaust_dci=exhaust_dci)
    697         # write all datasets
    698         datasets = builder.datasets

~/miniconda3/envs/nwb/lib/python3.7/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    451 
    452             if is_method:
--> 453                 return func(args[0], **parsed['args'])
    454             else:
    455                 return func(**parsed['args'])

~/miniconda3/envs/nwb/lib/python3.7/site-packages/hdmf/backends/hdf5/h5tools.py in write_group(self, **kwargs)
    694             for subgroup_name, sub_builder in subgroups.items():
    695                 # do not create an empty group without attributes or links
--> 696                 self.write_group(group, sub_builder, exhaust_dci=exhaust_dci)
    697         # write all datasets
    698         datasets = builder.datasets

~/miniconda3/envs/nwb/lib/python3.7/site-packages/hdmf/utils.py in func_call(*args, **kwargs)
    451 
    452             if is_method:
--> 453                 return func(args[0], **parsed['args'])
    454             else:
    455                 return func(**parsed['args'])

~/miniconda3/envs/nwb/lib/python3.7/site-packages/hdmf/backends/hdf5/h5tools.py in write_group(self, **kwargs)
    686         parent, builder, exhaust_dci = getargs('parent', 'builder', 'exhaust_dci', kwargs)
    687         if builder.written:
--> 688             group = parent[builder.name]
    689         else:
    690             group = parent.create_group(builder.name)

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

~/miniconda3/envs/nwb/lib/python3.7/site-packages/h5py/_hl/group.py in __getitem__(self, name)
    262                 raise ValueError("Invalid HDF5 object reference")
    263         else:
--> 264             oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
    265 
    266         otype = h5i.get_type(oid)

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/_objects.pyx in h5py._objects.with_phil.wrapper()

h5py/h5o.pyx in h5py.h5o.open()

KeyError: "Unable to open object (object 'ccss_Test_eCode_0001' doesn't exist)"

[oruebel]

Thanks, I'll work on this early next week. Not sure yet why this would be broken. Since it happens on write, maybe somehow the object gets assigned a bad parent or something in my code (or it's a but outside of the extension). I'll check.

[oruebel]

@lvsltz #43 should fix this.