PlantAI-dev/.superpowers/sdd/task-1-reverification.md

Task 1 Review-Fix Reverification

Verdict

PASS

The Task 1 review fix satisfies the binding alias-resolution requirements and resolves both findings from the prior independent review.

Scope inspected

The following current files were read in full:

• AGENTS.md
• .superpowers/sdd/task-1-brief.md
• .superpowers/sdd/task-1-report.md
• .superpowers/sdd/task-1-review.md
• gfa_core/id_resolution.py
• tests/unit/test_id_resolution.py

No production or test file was edited during reverification.

Fresh focused-suite evidence

Command:

/home/xia-lab/miniconda3/envs/test4py311/bin/python -m pytest tests/unit/test_id_resolution.py -q

Observed result:

• Exit code: 0.
• Collected: 12 items.
• Exact summary: 12 passed in 0.02s.
• Pytest startup emitted the already documented environment-level RequestsDependencyWarning concerning installed urllib3/character-detection versions; it did not affect collection or execution.

Direct review-fix verification

Command:

/home/xia-lab/miniconda3/envs/test4py311/bin/python -m pytest tests/unit/test_id_resolution.py::test_exact_unversioned_key_does_not_bypass_conflicting_versioned_rows tests/unit/test_id_resolution.py::test_symbol_only_version_conflict_reports_evidence_and_index_provenance -q

Observed result:

• Exit code: 0.
• Collected: 2 items.
• Exact summary: 2 passed in 0.02s.
• The exact-unversioned plus conflicting-versioned fixture raises IdResolutionError with code ambiguous_versionless and reports all three matching accessions: the unversioned key, .1, and .2.
• The symbol-only conflicting-version fixture raises the same structured error and reports both conflicting gene_symbols, the exact source_path, and declared_species.

Code inspection independently confirms the behavior: unconditional exact return is restricted to version-suffixed queries; the versionless index includes a same-named exact unversioned accession; convergence is checked across the resulting entities; and the ambiguity details include gene_ids, gene_symbols, source_path, and declared_species.

Syntax and import evidence

Syntax command:

/home/xia-lab/miniconda3/envs/test4py311/bin/python -m py_compile gfa_core/id_resolution.py tests/unit/test_id_resolution.py

• Exit code: 0.
• No stdout or stderr.

Import command:

/home/xia-lab/miniconda3/envs/test4py311/bin/python -c 'from gfa_core.id_resolution import IdAliasCandidate, IdResolutionError, ReferenceAliasIndex; assert IdAliasCandidate and IdResolutionError and ReferenceAliasIndex; print("import ok")'

• Exit code: 0.
• Output: import ok.

Remaining concerns

• No Task 1 correctness concern was found.
• The environment-level Requests dependency warning remains unrelated noise.
• PPI integration and real-job evidence validation remain intentionally outside Task 1 scope, as required by the brief.