AllenInstitute / AllenInstitute/ConnectsCommonConnectivity
CellCellConnectivityLong: add connectome_id
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- Dominant language
- Jupyter Notebook
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- 4
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Description
Problem: no measurement-context discriminator — rows from two measurement contexts are indistinguishable and their overwrite predicates clobber each other. Hence today's one-subdirectory-per-connectome workaround (cellcellconnectivitylong_*).
Semantics: connectome_id identifies the measurement context (segmentation version + proofreading state + measurement semantics), not the cohort. Cohorts are read-side filters: write the superset connectome once; pull subsets by joining dataitem_dataset_association or cluster membership. Minnie's two folders (proofread_pre_to_csm_post, proofread_to_proofread) are two measurement contexts → two connectome_ids in one table.
Fix: add connectome_id; register a WriteSpec (overwrite_scoped on (project_id, connectome_id)); rerun affected ETLs with the new io + schema (no folder migration); add a subset-read helper (ties to #23). Needs its own planning session before implementation.
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 by locating the CellCellConnectivityLong schema, its io and WriteSpec registration, and the affected ETLs. Review the planned relationship to issue #23 and use the planning session to settle the subset-read helper. Done means the new connectome_id supports scoped overwrites, affected ETLs use the updated schema and io, and no folder migration is required.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- data-engineering, databases
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Active
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100