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Describe the bug
The data under ./apis/python/notebooks/data/sparse/pbmc3k is corrupt and cannot be read. Thus notebooks that utilize these data are not runnable
Example
importtiledbsomaexperiment=tiledbsoma.open("./apis/python/notebooks/data/dense/pbmc3k")
# ---------------------------------------------------------------------------# DoesNotExistError Traceback (most recent call last)# Cell In[21], line 1 # ----> 1 experiment = tiledbsoma.open("./apis/python/notebooks/data/dense/pbmc3k")# # File ~/opt/miniconda3/envs/test_tiledbsoma/lib/python3.11/site-packages/tiledbsoma/_factory.py:114, in open(uri, mode, soma_type, context, tiledb_timestamp) # 73 """Opens a TileDB SOMA object.# 74 # 75 Args:# (...) # 111 Experimental.# 112 """ # 113 context = _validate_soma_tiledb_context(context) # --> 114 obj = _open_internal(_tdb_handles.open, uri, mode, context, tiledb_timestamp)# 115 try: # 116 if soma_type:# # File ~/opt/miniconda3/envs/test_tiledbsoma/lib/python3.11/site-packages/tiledbsoma/_factory.py:143, in _open_internal(opener, uri, mode, context, timestamp) # 133 def _open_internal( # 134 opener: Callable[# 135 [str, options.OpenMode, SOMATileDBContext, Optional[OpenTimestamp]], _Wrapper# (...) # 140 timestamp: Optional[OpenTimestamp], # 141 ) -> "_tiledb_object.TileDBObject[_Wrapper]": # 142 """Lower-level open function for internal use only."""# --> 143 handle = opener(uri, mode, context, timestamp)# 144 try:# 145 return _reify_handle(handle) # # File ~/opt/miniconda3/envs/test_tiledbsoma/lib/python3.11/site-packages/tiledbsoma/_tdb_handles.py:50, in open(uri, mode, context, timestamp)# 48 obj_type = tiledb.object_type(uri, ctx=context.tiledb_ctx)# 49 if not obj_type: # ---> 50 raise DoesNotExistError(f"{uri!r} does not exist") # 51 if obj_type == "array":# 52 return ArrayWrapper.open(uri, mode, context, timestamp) # # DoesNotExistError: './apis/python/notebooks/data/dense/pbmc3k' does not exist
The text was updated successfully, but these errors were encountered:
Describe the bug
The data under
./apis/python/notebooks/data/sparse/pbmc3k
is corrupt and cannot be read. Thus notebooks that utilize these data are not runnableExample
The text was updated successfully, but these errors were encountered: