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Description
combine_chunks fails on column of table, but does not error on table itself (but creates 3 chunks instead).
Is there a reason why they are not handled the same?
In [90]: pa.__version__
Out[90]: '4.0.0'
# Get shape
In [85]: pa_table.shape
Out[85]: (102753589, 1)In [86]: pa_col1_array = pa_table.column(0)
# Get number of chunks
In [87]: pa_col1_array.num_chunks
Out[87]: 4404
# Combining chunks on the pyarrow table with one column works.
In [88]: pa_table.combine_chunks()
Out[88]:
pyarrow.Table
# id=TEW__014e25__c14e1d__Multiome_RNA_brain_10x_no_perm: string
# Combining chunks on the column itself does not work.
In [89]: pa_col1_array.combine_chunks()
---------------------------------------------------------------------------
ArrowInvalid Traceback (most recent call last)
<ipython-input-89-fdd0d0056a8e> in <module>
----> 1 pa_col1_array.combine_chunks()
/software/miniconda3/envs/cisTopic/lib/python3.7/site-packages/pyarrow/table.pxi in pyarrow.lib.ChunkedArray.combine_chunks()
/software/miniconda3/envs/cisTopic/lib/python3.7/site-packages/pyarrow/array.pxi in pyarrow.lib.concat_arrays()
/software/miniconda3/envs/cisTopic/lib/python3.7/site-packages/pyarrow/error.pxi in pyarrow.lib.pyarrow_internal_check_status()
/software/miniconda3/envs/cisTopic/lib/python3.7/site-packages/pyarrow/error.pxi in pyarrow.lib.check_status()
ArrowInvalid: offset overflow while concatenating arrays
# Assign combine chunks table to new tabled.
In [91]: pa_table_combined = pa_table.combine_chunks()
# Get first column
In [92]: pa_col1_array_from_pa_table_combined = pa_table_combined.column(0)
# Get number of chunks
In [93]: pa_col1_array_from_pa_table_combined.num_chunks
Out[93]: 3
# Try to combine column 1 again.
In [94]: pa_col1_array_from_pa_table_combined.combine_chunks()
---------------------------------------------------------------------------
ArrowInvalid Traceback (most recent call last)
<ipython-input-94-e2e323e6519f> in <module>
----> 1 pa_col1_array_from_pa_table_combined.combine_chunks()
/software/miniconda3/envs/cisTopic/lib/python3.7/site-packages/pyarrow/table.pxi in pyarrow.lib.ChunkedArray.combine_chunks()
/software/miniconda3/envs/cisTopic/lib/python3.7/site-packages/pyarrow/array.pxi in pyarrow.lib.concat_arrays()
/software/miniconda3/envs/cisTopic/lib/python3.7/site-packages/pyarrow/error.pxi in pyarrow.lib.pyarrow_internal_check_status()
/software/miniconda3/envs/cisTopic/lib/python3.7/site-packages/pyarrow/error.pxi in pyarrow.lib.check_status()
ArrowInvalid: offset overflow while concatenating arrays
# Get sizes of each chunk.
In [106]: [chunk.nbytes for chunk in pa_col1_array_from_pa_table_combined.chunks]
Out[106]: [2341650593, 2342925682, 241257842]Reporter: Gert Hulselmans / @ghuls
Related issues:
- [C++] Allow automatic String -> LargeString promotions when concatenating tables (relates to)
- [C++][Python] Large strings cause ArrowInvalid: offset overflow while concatenating arrays (is related to)
Note: This issue was originally created as ARROW-13150. Please see the migration documentation for further details.