[c++] Fix ManagedQuery usage in SOMAArray write path

[nguyenv]

Issue and/or context:

#2928

Changes:

Commits should be viewed individually. Although much of this code already existed prior to this PR, there were enough modifications that the changes were too noisy to read clearly.

1. First commit labels all the old code as legacy
2. ManagedQuery::setup_write_column takes in a column name, number of elements, and pointers to buffers that contain the passed in data. This use to be three separate calls to ManagedQuery::setup_column_data, ColumnBuffer::set_data, and ManagedQuery::set_column_data but now simplified
3. The old SOMAArray::set_array_data made a copy of the passed in ArrowTable and then passed the casted buffers to ColumnBuffer::set_data. We now iterate through each column calling SOMAArray::_cast_column, which casts the values into temporary vectors and the passes the std::vector::data() pointer into ManagedQuery::setup_write_column
4. SOMAArray::_cast_column handles all permutations of attributes with or without enumerations and columns with or without dictionaries.
   1. In the case where the attribute has a enumeration but the passed in column does not have a dictionary, error out.
   2. In the case where the attribute is not enumerated but the passed column does have a dictionary, call SOMAArray::_promote_indexes_to_values which maps the dictionary's indexes to the associated dictionary values and passes that dictionary value mapping vector into ManagedQuery::setup_write_column
   3. In all other cases, call SOMAArray::_cast_column_aux for further processing
5. SOMAArray::_promote_indexes_to_values calls SOMAArray::_cast_dictionary_values. It retrieves the dictionary's indexes via SOMAArray::_get_index_vector and then iterates through the index vector and maps and casts to the correct dictionary value
6. SOMAArray::_cast_column_aux calls SOMAArray::_set_column.
   1. If the attribute is enumerated and the column has a dictionary, we need to write out the dictionary indexes and potentially extend the enumeration if there are any new values
   2. In all other cases, place the values into a a temporary vector, iterate and cast these values to the type on disk, and pass the casted vector into ManagedQuery::setup_write_buffer
7. SOMAArray::_extend_enumeration calls SOMAArray::_extend_and_evolve_schema which check if any new enumerations have been introduced
   1. If so, then we need to call SOMAArray::_remap_indexes which calls SOMAArray::_remap_indexes_aux to iterate through the original indexes and shift them to match the new extended enumeration on-disk. SOMAArray::_cast_shifted_indexes casts the shifted index values to the type on disk and passes this into ManagedQuery::setup_write_buffer
   2. If not, then pass the dictionary's index as-is into ManagedQuery::setup_write_column
8. Return a vector<uint8_t> of Boolean mappings instead of casting inplace
9. Correct unit test to pass in offset buffer for variable length string columns
10. Last commit removes all dead code

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 89.79%. Comparing base (d9bd18d) to head (37dadf5).
Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2989      +/-   ##
==========================================
+ Coverage   89.64%   89.79%   +0.14%     
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  Files          39       39              
  Lines        4096     4096              
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+ Hits         3672     3678       +6     
+ Misses        424      418       -6     

Flag	Coverage Δ
python	89.79% <ø> (+0.14%)	⬆️

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Components	Coverage Δ
python_api	89.79% <ø> (+0.14%)	⬆️
libtiledbsoma	∅ <ø> (∅)

[johnkerl]

This is a well-organized PR, easy to review and easy for everyone to understand later. Thank you!!

There are a couple items here, both of which can be follow-on PRs if you like.

[nguyenv]

I will move the bit to uin8_t conversion method and do the extend enumeration fix in two separate follow up PRs.