# 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

```bash
/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

```bash
/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

```bash
/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.