Preserve shared labels and preflight variable lineage dependencies

[TonisOrmisson]

Phase 2 — in-place metadata integrity

Keeps existing canonical-plan and SPSS entry points, dataset/table identity, and ordered execution. No dependencies, new configuration, workflow installation, or persistent rollback/copy layer.

Changes

• Detach a variable from its old value-label set before pruning it; preserve labels while another variable still references that set.
• Reject deletion of original variable IDs referenced by published derived lineage with variable_has_dependents, before any plan mutation. Same-name recreation cannot bypass this guard; plan-local create/delete sequences remain supported.
• Enable and verify native SQLite foreign-key enforcement on apply-owned connections before the existing transaction begins.
• Changes are confined to one production file and one existing test file.

Validation

• RED commit 0927d6a: 7 reproduced failures and 1 already-working sequential control.
• GREEN commit 395cbc0: all 8 scenarios pass; related frontend/workflow/CLI/apply suites: 158 passed.
• Full local non-service suite: 381 passed, 8 skipped, 49 service cases deselected.
• git diff --check passes; independent full-diff local subagent review: No findings.
• Both push and PR CI passed all 14 jobs: Python 3.11–3.14, package build/install, PostgreSQL 17.10/18.4, MySQL 8.4.11/9.7.2, MariaDB 11.4.12/11.8.8/12.3.2, and Dolt 2.2.2/2.2.3 default-write integration. Local evidence uses temporary SQLite databases; live coverage is not inferred from mocks.

Scope and next phase

Phase 1 PHP import-integrity PR OpenStatSpec/php#12 is merged. Phase 2 is ready for handoff at 395cbc0: independent local full-diff review found no issues; latest-head @codex review completed without findings and confirmed 👍; CodeRabbit also reported no actionable comments. All GitHub checks pass. Its optional docstring-percentage suggestion does not justify unrelated boilerplate.

Next: phase 3 — Python export reads values and metadata from one consistent database snapshot without database writes, in a separate PR.

Do not merge automatically. Worktree is clean and both logical commits are pushed. The overall phase plan is not yet complete.

[TonisOrmisson]

@codex review

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-08T06:14:01.229587Z	395cbc0	Manual request

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[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Advanced

Run ID: 00e6dfad-426c-4b5e-a11a-03cd3fbc58bc

📥 Commits

Reviewing files that changed from the base of the PR and between 214e4a1 and 395cbc0.

📒 Files selected for processing (2)

• src/openstatspec/sql/inplace_transform.py
• tests/test_inplace_transform.py

Included review availability: Your plan provides up to 1 included review per hour; 0 remain after this review.

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📝 Walkthrough

Walkthrough

Changes

The in-place transformation workflow now preserves shared value-label records, blocks deletion of variables with published lineage, enables SQLite foreign-key enforcement, and validates rollback behavior.

In-place transformation integrity

Layer / File(s)	Summary
Shared value-label ownership src/openstatspec/sql/inplace_transform.py, tests/test_inplace_transform.py	Value-label replacement keeps records used by sibling variables and removes them after the final owner is replaced.
Lineage-aware variable lifecycle src/openstatspec/sql/inplace_transform.py, tests/test_inplace_transform.py	Variable deletion checks published lineage before mutation. Tests cover local deletion and recreation of unreferenced variables.
Connection integrity and rollback src/openstatspec/sql/inplace_transform.py, tests/test_inplace_transform.py	SQLite connections enable foreign-key enforcement. Tests verify rollback after trigger-driven constraint failures.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Merge Risk: ⚪ Minimal · up to 395cb

In-place transformations now preserve shared labels, prevent deletion of published lineage sources, and enforce SQLite foreign keys. The covered behavior is ready to merge with no identified outstanding production risk.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 9.09% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 11 functions across 2 files.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly summarizes the two main changes: preserving shared value labels and preflighting variable lineage dependencies before deletion.

• Fix all pre-merge checks with AI

✨ Finishing Touches 💡 1

📝 Generate docstrings 💡

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix/inplace-metadata-integrity

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[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. Hooray!

Reviewed commit: 395cbc09f2

ℹ️ About Codex in GitHub

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