AllenInstitute / AllenInstitute/ConnectsCommonConnectivity
Nested models (SpatialLocation) don't round-trip through the arrow layer
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Description
Problem: the write path is pydantic → dicts → arrow → parquet. flatten_refs collapses a nested model to its id string — fine for references, but SpatialLocation has no id, so it survives as a raw dict while build_arrow_schema maps embedded-model fields to string. A dict then hits a string column: pyarrow errors, or stringifies into an unqueryable text blob. Model → parquet → model loses structure.
Fix options: (a) struct columns in arrow_utils; (b) explicit JSON-column convention; (c) don't nest — #25 flattens spatial and bypasses this. Keep this issue as the general record for any future nested model.
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Read the arrow_utils entry points flatten_refs and build_arrow_schema, then trace the pydantic-to-dicts-to-arrow-to-parquet path described in the issue. Compare how nested models and reference models are represented at each step. Done means a SpatialLocation or other nested model can round-trip through parquet without becoming an invalid or unqueryable string.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-engineering, databases
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Active
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100