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Completing HRA branches #3735
Description
Progress report:
Status: HRA / bulk-NTR PRs from @zhengj2007 — layout compliance & blockers
Tracking issue for the batch of open HRA / bulk-NTR PRs from @zhengj2007 (plus the reference muscular PR). Assesses each against the agreed rules and captures blockers.
Agreed rules (from prior review)
- Large batches → ROBOT template registered as an ODK component (
components/*.owl+uberon-odk.yaml+ Makefile + catalog). Tooling/instructions on main (bulk_ntr_workflow/CLAUDE.mdStage 5,register_templates.py). - Small additions → added by hand (or via a local template) directly into
uberon-edit.obo; no ODK component. - Reports must NOT live under
src/templates/. Canonical location isbulk_ntr_workflow/outputs/<name>-reports/.
⚠️ Root-cause finding
The corrected "reports → bulk_ntr_workflow/outputs/<name>-reports/" instruction currently lives only on the muscular branch (add-hra-muscular-ntr, PR #3700), not on master. Master's bulk_ntr_workflow/CLAUDE.md/README.md still direct reports to src/templates/<name>-reports/. Every @zhengj2007 PR below branched off master, so they all followed the old layout. Merging the corrected docs to master (or cherry-picking them) is the key unblock.
Reference exemplar
- Add hra muscular ntr #3700 — muscular (@dosumis): the model layout. Reports under
bulk_ntr_workflow/outputs/hra-muscular-reports/; templates clean undersrc/templates/; fully ODK-registered. Also carries the corrected docs.
Status of @zhengj2007 PRs
On the right track (ODK-registered)
| PR | Terms | State | Notes |
|---|---|---|---|
| #3715 fallopian tube | 58 | CI green, blocked on review | Fully ODK-registered (best zhengj2007 example). Reports relocated to bulk_ntr_workflow/outputs/. |
| #3714 capillary | 31 | CI failing | Registration attempted (odk.yaml + import), but build breakage. Also 2 sparse defs + 1 generic parent flagged. |
Small addition, correctly hand-edited
| PR | Terms | State | Notes |
|---|---|---|---|
| #3713 eye | 2 | 1 CI failure | Converted to 2 stanzas in uberon-edit.obo per review. Remaining failure = leftover import: …/hra_eye.owl line. |
Not yet converted — old layout (unregistered templates; reports being relocated)
None of these touch uberon-odk.yaml/Makefile/catalog, so nothing actually enters the ontology; CI is "green" only because the build ignores them.
| PR | Terms | Suggested route |
|---|---|---|
| #3717 kidney | 2 | hand-edit into -edit.obo (kidney "papillary tip epithelium" still needs a real PMID) |
| #3716 intestine/liver/skin | 4 | hand-edit |
| #3719 palatine-tonsil | 7 | hand-edit (borderline) |
| #3712 brain | 12 | ODK-register — also: @RiveraAndrea83 asked to drop ifs1-4 and weak transition-zone terms |
| #3720 small-intestine | — | ODK-register |
| #3721 placenta | — | ODK-register |
| #3722 spleen | — | ODK-register |
| #3723 uterus | — | ODK-register |
| #3718 lymph | 41 | ODK-register (largest batch) |
Separate concern
| PR | Notes |
|---|---|
| #3704 added_by_HRA annotations (163 terms) | Direct -edit.obo edit; 3 CI failures — needs diagnosis, independent of the layout question. |
Blockers summary
- Corrected reports-location docs not on master (only on Add hra muscular ntr #3700) — merge/cherry-pick to unblock.
- 9 PRs still use the pre-instruction layout and need rework: small → hand-edit; large → ODK-register.
- CI red: Add HRA capillary NTR template (32 new capillary terms) #3714 (registration build), Add HRA eye NTR template: inner/outer cortex of lens #3713 (stray import), Added 'added_by_HRA' annotations to 163 terms #3704 (annotations).
- Curator judgment needed: add hra brain terms #3712 brain term pruning.
- All PRs are
MERGEABLEbutBLOCKEDon review approval; most past the 1-week-inactivity threshold for author self-merge.
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