AllenInstitute / AllenInstitute/ConnectsCommonConnectivity
Promote SpatialLocation to a first-class coordinates table
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- Dominant language
- Jupyter Notebook
- Stars
- 4
- Forks
- 1
- PR merge metrics
- No merged PRs in 30d
Description
Problem: per-cell coordinates are smuggled through generic CellFeatureSets (v1dd_soma_spatial: soma_voxel_x/y/z, …) — untyped floats, no reference-space semantics. SpatialLocation (x, y, z, reference_space) exists in core_schema.yaml but is unreachable on disk: its only attachment points were never written by any ETL, it has no id/WriteSpec (designed as an embedded struct), and the write path has no struct support (#27).
Fix: first-class table (dataitem_id, reference_space, x, y, z [, project_id]); reference_space distinguishes CCF-registered vs dataset-original vs dataset-corrected coordinates. Pilot: migrate v1dd_soma_spatial. Flattening to a table bypasses #27 (kept separate as the general bug).
Contributor guide
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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
Start with core_schema.yaml and trace how v1dd_soma_spatial is represented and written by the ETL. Review the existing attachment and write paths, keeping the missing general struct support in #27 separate. Done means the pilot coordinates are represented in a first-class table with dataitem_id, reference_space, x, y, z, and the stated coordinate reference semantics.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- data-engineering, databases
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Active
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100