lfrank
commented
2 years ago The best solution here is to fix the mount point to always be /stelmo
Can you do that?
On May 24, 2022, at 5:13 PM, Shijie Gu @.***> wrote:
Describe the bug The nwb file path is not made from SPYGLASS_BASE_DIR. To Reproduce Steps to reproduce the behavior: Make an nwb file with /opt/stelmo Do IntervalPositionInfo.populate() on a machine that mounts stelmo at / directly. ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization.
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Describe the bug The nwb file path is not made from SPYGLASS_BASE_DIR.
To Reproduce Steps to reproduce the behavior:
- Make an nwb file with /opt/stelmo
- Do IntervalPositionInfo.populate() on a machine that mounts stelmo at / directly.
Expected behavior If on a different machine, the SPYGLASS_BASE_DIR on /stelmo, the code should run. SpikeSortingRecording.populate() uses SPYGLASS_BASE_DIR
Screenshots
Computing position for: {'position_info_param_name': 'default_decoding', 'nwb_filename': 'fern20211007.nwb', 'interval_list_name': 'pos 0 valid times'} Writing new NWB file fern20211007_1KSTEBUVJM.nwb
FileNotFoundError Traceback (most recent call last) Input In [4], in <cell line: 27>() 15 IntervalPositionInfoSelection.insert1( 16 {'nwb_file_name': nwb_copy_file_name, 17 'interval_list_name': pos_intvl, 18 'position_info_param_name': 'default' #default parameters are in the database already 19 }, skip_duplicates=True) 21 IntervalPositionInfoSelection.insert1( 22 {'nwb_file_name': nwb_copy_file_name, 23 'interval_list_name': pos_intvl, 24 'position_info_param_name': 'default_decoding' #upsampled for decoding, default parameters are in the database already 25 }, skip_duplicates=True) ---> 27 IntervalPositionInfo.populate()
File ~/anaconda3/envs/spyglass/lib/python3.8/site-packages/datajoint/autopopulate.py:229, in AutoPopulate.populate(self, suppress_errors, return_exception_objects, reserve_jobs, order, limit, max_calls, display_progress, processes, make_kwargs, *restrictions) 225 if processes == 1: 226 for key in ( 227 tqdm(keys, desc=self.class.name) if display_progress else keys 228 ): --> 229 error = self._populate1(key, jobs, **populate_kwargs) 230 if error is not None: 231 error_list.append(error)
File ~/anaconda3/envs/spyglass/lib/python3.8/site-packages/datajoint/autopopulate.py:281, in AutoPopulate._populate1(self, key, jobs, suppress_errors, return_exception_objects, make_kwargs) 279 self.class._allow_insert = True 280 try: --> 281 make(dict(key), **(make_kwargs or {})) 282 except (KeyboardInterrupt, SystemExit, Exception) as error: 283 try:
File ~/Documents/spyglass/src/spyglass/common/common_position.py:81, in IntervalPositionInfo.make(self, key) 78 print(f'Computing position for: {key}') 79 key['analysis_file_name'] = AnalysisNwbfile().create( 80 key['nwb_file_name']) ---> 81 raw_position = (RawPosition() & 82 {'nwb_file_name': key['nwb_file_name'], 83 'interval_list_name': key['interval_list_name'] 84 }).fetch_nwb()[0] 85 position_info_parameters = ( 86 PositionInfoParameters() & 87 {'position_info_param_name': key['position_info_param_name'] 88 }).fetch1() 90 head_position = pynwb.behavior.Position()
File ~/Documents/spyglass/src/spyglass/common/common_behav.py:89, in RawPosition.fetch_nwb(self, *attrs, kwargs) 88 def fetch_nwb(self, *attrs, *kwargs): ---> 89 return fetch_nwb(self, (Nwbfile, 'nwb_file_abs_path'), attrs, kwargs)
File ~/Documents/spyglass/src/spyglass/common/dj_helper_fn.py:74, in fetch_nwb(query_expression, nwb_master, *attrs, kwargs) 71 if not attrs: 72 attrs = query_expression.heading.names ---> 74 rec_dicts = (query_expression tbl.proj(nwb2load_filepath=attr_name) 75 ).fetch(attrs, 'nwb2load_filepath', kwargs) 77 if not rec_dicts or not np.any(['object_id' in key for key in rec_dicts[0]]): 78 return rec_dicts
File ~/anaconda3/envs/spyglass/lib/python3.8/site-packages/datajoint/fetch.py:228, in Fetch.call(self, offset, limit, order_by, format, as_dict, squeeze, download_path, attrs) 226 attributes = [a for a in attrs if not is_key(a)] 227 ret = self._expression.proj(attributes) --> 228 ret = ret.fetch( 229 offset=offset, 230 limit=limit, 231 order_by=order_by, 232 as_dict=False, 233 squeeze=squeeze, 234 download_path=download_path, 235 format="array", 236 ) 237 if attrs_as_dict: 238 ret = [ 239 {k: v for k, v in zip(ret.dtype.names, x) if k in attrs} 240 for x in ret 241 ]
File ~/anaconda3/envs/spyglass/lib/python3.8/site-packages/datajoint/fetch.py:288, in Fetch.call(self, offset, limit, order_by, format, as_dict, squeeze, download_path, *attrs) 285 raise e 286 for name in heading: 287 # unpack blobs and externals --> 288 ret[name] = list(map(partial(get, heading[name]), ret[name])) 289 if format == "frame": 290 ret = pandas.DataFrame(ret).set_index(heading.primary_key)
File ~/anaconda3/envs/spyglass/lib/python3.8/site-packages/datajoint/fetch.py:50, in _get(connection, attr, data, squeeze, download_path) 46 if data is None: 47 return 49 extern = ( ---> 50 connection.schemas[attr.database].external[attr.store] 51 if attr.is_external 52 else None 53 ) 55 # apply attribute adapter if present 56 adapt = attr.adapter.get if attr.adapter else lambda x: x
File ~/anaconda3/envs/spyglass/lib/python3.8/site-packages/datajoint/external.py:477, in ExternalMapping.getitem(self, store) 470 """ 471 Triggers the creation of an external table. 472 Should only be used when ready to save or read from external storage. 473 :param store: the name of the store 474 :return: the ExternalTable object for the store 475 """ 476 if store not in self._tables: --> 477 self._tables[store] = ExternalTable( 478 connection=self.schema.connection, 479 store=store, 480 database=self.schema.database, 481 ) 482 return self._tables[store]
File ~/anaconda3/envs/spyglass/lib/python3.8/site-packages/datajoint/external.py:56, in ExternalTable.init(self, connection, store, database) 54 self._s3 = None 55 if self.spec["protocol"] == "file" and not Path(self.spec["location"]).is_dir(): ---> 56 raise FileNotFoundError( 57 "Inaccessible local directory %s" % self.spec["location"] 58 ) from None
FileNotFoundError: Inaccessible local directory /opt/stelmo/nwb/raw
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shijiegu
Describe the bug The nwb file path is not made from
SPYGLASS_BASE_DIR.To Reproduce Steps to reproduce the behavior:
IntervalPositionInfo.populate()on a machine that mounts stelmo at / directly.Expected behavior If on a different machine, the SPYGLASS_BASE_DIR on /stelmo, the code should run.
SpikeSortingRecording.populate()uses SPYGLASS_BASE_DIRScreenshots