[ARROW-13150] [Python] combine_chunks fails on column of table, but does not error on table itself

• Type: Bug
• Status: Open
• Priority: Minor
• Resolution: Unresolved
• Component/s: Python
• External issue URL: https://github.com/apache/arrow/issues/28850
• Assignee: Unassigned
• Reporter: Gert Hulselmans
• Created: 23/Jun/21 16:21
• Updated: 11/Jan/23 08:31

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]

Issue Links

• is related to: ARROW-17828 [C++][Python] Large strings cause ArrowInvalid: offset overflow while concatenating arrays
• relates to: ARROW-7245 [C++] Allow automatic String -> LargeString promotions when concatenating tables