PlantAI-dev/.planning/rnaseq_samples_authority/progress.md

Progress: RNA-seq samples.yaml authority

• 2026-07-15: Planning scope created; no business code modified.
• 2026-07-15: User-approved mapping direction recorded: fastq_1/fastq_2 at review boundary, r1/r2 downstream.
• 2026-07-15: Read PlanAI/CropAI/Karpathy/make-plan requirements and relevant CropAI layer/validation/contract references.
• 2026-07-15: Started three read-only evidence tracks for documentation/contracts, production backend paths, and test/validation patterns.
• 2026-07-15: CodeGraph located the production pipeline_backend.run_stage boundary; targeted extraction remains in progress.
• 2026-07-15: Confirmed two production filename gates (rnaseq_qc, legacy aggregate rnaseq) and the existing authoritative CLI YAML validator.
• 2026-07-15: Identified tests/unit/test_rnaseq_fastp_defaults.py as the minimal backend regression pattern.
• 2026-07-15: Expanded contract-closure scope to centralize sample-config selection across RNA-seq branches while leaving standardized downstream artifact discovery unchanged.
• 2026-07-15: Confirmed existing tests cover confirmation and backend command construction but not arbitrary filename execution authority.
• 2026-07-15: Consolidated documentation/contracts and tests/validation evidence; explicitly excluded adjacent semantics and provenance enhancements under Karpathy's surgical-change rule.
• 2026-07-15: Wrote the implementation-ready draft in PLAN.md; began the required read-only adversarial review.
• 2026-07-15: Resolved the active Codex CLI path to /home/xia-lab/.npm-global/bin/codex after the stale .nvm path failed.
• 2026-07-15: Adversarial review round 1 returned VERDICT: REVISE; recorded all nine findings and accepted a canonical-only trust boundary plus identity/status and negative-test closure.
• 2026-07-15: Revised PLAN.md: canonical-only explicit semantics, legacy aggregate reachability correction, frontend/diagnosis closure, config identity/status, direct and API decoy negatives, mandatory downstream smoke, /api/results, and contract/skill synchronization.