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[Bug][python] Corrupt example data used in Python notebooks #1777

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pablo-gar opened this issue Oct 10, 2023 · 0 comments
Closed

[Bug][python] Corrupt example data used in Python notebooks #1777

pablo-gar opened this issue Oct 10, 2023 · 0 comments
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@pablo-gar
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pablo-gar commented Oct 10, 2023

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

import tiledbsoma
experiment = 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
@pablo-gar pablo-gar added the bug Something isn't working label Oct 10, 2023
@johnkerl johnkerl self-assigned this Oct 10, 2023
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