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

Task 1 Independent Verification

Verdict

PASS

No blocking defect was found. The implementation satisfies the binding Task 1 interfaces, validation rules, deterministic alias ordering/deduplication, species scoping, ambiguity handling, and offline/standard-library-only constraints.

Files reviewed completely

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

Production and test code were not edited during this verification.

Fresh commands and outputs

Focused tests

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

• Exit code: 0
• Collected: 10 items
• Result: 10 passed in 0.02s
• Warning: pytest startup emitted one environment-level RequestsDependencyWarning from requests/__init__.py because the installed urllib3 and character-detection package versions do not match the versions supported by that requests installation. No warning originated from gfa_core.id_resolution.

Syntax check

/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
• Output: none

Public import check

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

• Exit code: 0
• Output: IdAliasCandidate IdResolutionError ReferenceAliasIndex

Requirement evidence

• IdResolutionError, immutable IdAliasCandidate, ReferenceAliasIndex.from_tsv, and ReferenceAliasIndex.candidates are present with the required surface.
• The six legacy columns are required; ncbi_gene_id is optional. Missing files and unusable columns raise structured errors.
• Header extraction is restricted to exact [db_xref=GeneID:<digits>] evidence when the explicit GeneID column is absent.
• The legacy/versionless XP test returns exactly three candidates in order: XP_021867507.1, 110806180, LOC110806180.
• Exact versioned accessions are primary. Conflicting versionless entities raise ambiguous_versionless; duplicate same-entity rows deduplicate deterministically.
• Declared-species and mixed-species mismatches invalidate the complete file.
• Unknown substring lookups return no candidates. The module contains no online query, subprocess, ortholog-as-alias, or canonical-ID mutation behavior and imports only the Python standard library.

Real-data note and remaining risk

The actual SOE pep_cds_idmap.tsv could not be located in the currently visible filesystem; only pytest-generated synthetic fixtures were found. Per Task 1's isolated parser scope, this is not a blocking defect. Real-job SOE parsing and end-to-end PPI integration remain intentionally unvalidated/deferred. No backend or Celery restart was required.