Repository navigation
Buggy del sdata.table #222
Description
After the planned io refactoring this problem will disappear. So not fixing this bug now, just tracking that we know it exists.
Currently if we try to delete a table we may get an error like this:
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
Cell In[73], line 1
----> 1 del sdata_patient1_visium.table
File ~/embl/projects/basel/spatialdata/src/spatialdata/_core/spatialdata.py:1090, in SpatialData.table(self)
1088 store = parse_url(self.path, mode="r+").store
1089 root = zarr.group(store=store)
-> 1090 del root["table/table"]
File ~/miniconda3/envs/ome/lib/python3.10/site-packages/zarr/hierarchy.py:464, in Group.__delitem__(self, item)
463 def __delitem__(self, item):
--> 464 return self._write_op(self._delitem_nosync, item)
File ~/miniconda3/envs/ome/lib/python3.10/site-packages/zarr/hierarchy.py:895, in Group._write_op(self, f, *args, **kwargs)
892 lock = self._synchronizer[group_meta_key]
894 with lock:
--> 895 return f(*args, **kwargs)
File ~/miniconda3/envs/ome/lib/python3.10/site-packages/zarr/hierarchy.py:472, in Group._delitem_nosync(self, item)
470 rmdir(self._store, path)
471 else:
--> 472 raise KeyError(item)
KeyError: 'table/table'
Activity
LucaMarconato commentedon Apr 11, 2023
This happens if
sdata.table = tablefails (for instance in this case #221) and then we calldel sdata.tableon it.LucaMarconato commentedon Feb 22, 2024
Closed by the multi-table PR #455 since it just deletes the table in-memory and not from disk.