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

Task 1 Implementation Report

Status

DONE_WITH_CONCERNS

The reusable job-local reference alias parser is implemented within the Task 1 file boundary. The only concern is an environment-level RequestsDependencyWarning emitted by pytest startup; the Task 1 module itself is standard-library-only and all focused tests pass.

Files changed

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

No PPI execution, canonical member IDs, Ortholog relationships, contracts, manifests, frontend/backend execution, or diagnostic code was changed. No Git commit was attempted because the workspace has no Git metadata.

RED evidence

Command:

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

Observed before creating gfa_core/id_resolution.py:

• Exit code: 2.
• Collected: 0 items / 1 error.
• Expected failure: ModuleNotFoundError: No module named 'gfa_core.id_resolution' while collecting tests/unit/test_id_resolution.py.
• Pytest summary: ERROR tests/unit/test_id_resolution.py and 1 error in 0.09s.

This was the intended RED failure: the tests imported the required public API before the production module existed.

GREEN evidence

Command:

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

Observed after the minimum implementation:

• Exit code: 0.
• Collected: 10 items.
• Exact pass count: 10 passed in 0.02s.

Self-review findings

• IdAliasCandidate is immutable (dataclass(frozen=True, slots=True)).
• IdResolutionError exposes a stable code plus structured details for missing files, invalid columns/rows, species mismatch, invalid GeneID evidence, exact evidence ambiguity, and versionless ambiguity.
• The parser requires the six legacy columns and optionally consumes ncbi_gene_id.
• Legacy numeric GeneID extraction uses only exact [db_xref=GeneID:<digits>] evidence when the explicit column is absent.
• Candidate priority is accession, numeric NCBI GeneID, then gene symbol; duplicate values retain the first deterministic provenance record.
• Exact accessions are preferred. Versionless matching is exact on the accession base and rejects collisions that do not converge on one GeneID or gene symbol entity.
• Every populated row is checked against the declared species; one mismatch invalidates the complete file.
• Unknown/substring IDs return no candidates; there is no similarity inference.
• Imports are limited to the Python standard library. No network, subprocess, external database, canonical-ID rewrite, or Ortholog-as-alias behavior exists.
• Validation used focused synthetic job-local TSV fixtures, as required for this isolated parser task; no PPI stage or service restart was required.

Concerns or remaining risks

• Pytest startup emits an unrelated RequestsDependencyWarning for the environment's urllib3 and character-detection package versions. It does not originate from or affect gfa_core.id_resolution, but means the requested test command's output is not warning-free.
• End-to-end PPI use and real-job evidence validation are intentionally deferred; the binding brief explicitly excludes PPI execution changes from Task 1.

Independent review fixes

The independent review identified one lookup-invariant defect and one diagnostic omission. Both were reproduced with new regression tests before production changes.

Review-fix RED evidence

Command:

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

Observed after adding the two review regression tests and before changing the parser:

• Exit code: 1.
• Collected: 12 items.
• Summary: 2 failed, 10 passed in 0.05s.
• test_exact_unversioned_key_does_not_bypass_conflicting_versioned_rows failed with DID NOT RAISE IdResolutionError, proving the exact-unversioned branch bypassed group convergence.
• test_symbol_only_version_conflict_reports_evidence_and_index_provenance failed with KeyError: 'gene_symbols', proving the ambiguity payload omitted the conflicting symbol evidence and index provenance.

Review-fix implementation

• Exact-first lookup is now unconditional only for version-suffixed queries.
• A versionless group now includes a same-named exact unversioned row, when present, and all matching versioned rows must converge before candidates are returned.
• The index retains its source path and declared species.
• ambiguous_versionless details now include gene_symbols, source_path, and declared_species in addition to the existing raw ID, matching accessions, and GeneIDs.
• Existing candidate ordering, deduplication, species scoping, immutable candidate API, and offline-only behavior were preserved.

Review-fix GREEN evidence

Focused tests:

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

• Exit code: 0.
• Collected: 12 items.
• Exact pass count: 12 passed in 0.02s.
• The same unrelated environment-level RequestsDependencyWarning remains.

Syntax compilation:

/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/stderr output.