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Description
Bug Report
Description
The repo's Instructions say: "We recommend you start by navigating to the notebooks directory on the left panel and go through the demo_prepare.ipynb".
When executing code cell 5 in that notebook
populate_settings = {"display_progress": True}
ephys.EphysRecording.populate(**populate_settings)
a FileNotFoundError occurs.
Reproducibility
Repository environment created with Dev Containers extension.
Navigate to demo_prepare.ipynb notebook, select kernel and execute code.
Error stack:
Output exceeds the [size limit](command:workbench.action.openSettings?[). Open the full output data [in a text editor](command:workbench.action.openLargeOutput?5cae5363-0515-4d6b-9fe4-f0979c9a6448)
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
Cell In[5], line 3
1 populate_settings = {"display_progress": True}
----> 3 ephys.EphysRecording.populate(**populate_settings)
File /usr/local/lib/python3.9/site-packages/datajoint/autopopulate.py:241, in AutoPopulate.populate(self, suppress_errors, return_exception_objects, reserve_jobs, order, limit, max_calls, display_progress, processes, make_kwargs, *restrictions)
237 if processes == 1:
238 for key in (
239 tqdm(keys, desc=self.__class__.__name__) if display_progress else keys
240 ):
--> 241 error = self._populate1(key, jobs, **populate_kwargs)
242 if error is not None:
243 error_list.append(error)
File /usr/local/lib/python3.9/site-packages/datajoint/autopopulate.py:292, in AutoPopulate._populate1(self, key, jobs, suppress_errors, return_exception_objects, make_kwargs)
290 self.__class__._allow_insert = True
291 try:
--> 292 make(dict(key), **(make_kwargs or {}))
293 except (KeyboardInterrupt, SystemExit, Exception) as error:
294 try:
File /usr/local/lib/python3.9/site-packages/element_array_ephys/ephys_acute.py:291, in EphysRecording.make(self, key)
289 def make(self, key):
290 """Populates table with electrophysiology recording information."""
...
43 "No valid full-path found (from {})"
44 " for {}".format(root_directories, relative_path)
45 )
FileNotFoundError: No valid full-path found (from [PosixPath('/workspaces/workflow-array-ephys/example_data/raw'), PosixPath('/workspaces/workflow-array-ephys/example_data/processed')]) for subject5/session1
Expected Behavior
The data should be downloaded first then used to populate the database.