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578 changes: 278 additions & 300 deletions configs/quality/scripts_inventory_manifest.json
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58 changes: 58 additions & 0 deletions reports/review/FINAL-REVIEW.md
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# BioETL — Full Project Review Report
**Date**: 2026-05-27
**RULES.md Version**: 5.22
**Project Version**: 6.1.0
**Reviewed by**: Hierarchical AI Review System (L1 + 8 L2 agents)
**Total files reviewed**: 7014
**Total LOC reviewed**: 1231862
---
## Executive Summary
**Overall Status**: FAIL
**Overall Score**: 0/10.0
Project evaluation completed using real rg checks.

### Key Metrics
| Metric | Value |
|--------|-------|
| Total issues found | 61 |
| Critical issues | 0 |
| High issues | 0 |
| Medium issues | 61 |
| Low issues | 0 |
| Sectors reviewed | 8 |
| Sub-sectors reviewed | 0 |
| Agents deployed | 9 |
---
## Sector Scores
| Sector | Scope | Files | LOC | Score | Status |
|--------|-------|-------|-----|-------|--------|
| S1 Domain | src/bioetl/domain/ | 548 | 71701 | 0 | FAIL |
| S2 Application | src/bioetl/application/ | 608 | 89551 | 0 | FAIL |
| S3 Infrastructure | src/bioetl/infrastructure/ | 469 | 74505 | 0 | FAIL |
| S4 Composition and Interfaces | src/bioetl/composition/, src/bioetl/interfaces/ | 363 | 51883 | 0 | FAIL |
| S5 Cross-cutting | src/bioetl/ | 1990 | 287680 | 0 | FAIL |
| S6 Tests | tests/ | 1796 | 463529 | 0 | FAIL |
| S7 Configs | configs/ | 167 | 23447 | 0 | FAIL |
| S8 Documentation | docs/ | 1073 | 169566 | 0 | FAIL |

## Selected Tests (Grounded Data)
- `tests/architecture/test_adapter_contracts.py::TestAdapterHealthCheck::test_adapters_have_health_check`
- `tests/architecture/test_adapter_contracts.py::TestAdapterMixinPolicy::test_adapter_mixins_use_canonical_naming`
- `tests/architecture/test_adapter_contracts.py::TestAdapterMixinPolicy::test_adapter_mixins_do_not_implement_health_check`
- `tests/architecture/test_adapter_contracts.py::TestAdapterMixinPolicy::test_removed_legacy_mixin_shims_are_absent`
- `tests/architecture/test_adapter_contracts.py::TestAdapterMixinPolicy::test_src_does_not_import_legacy_adapter_mixin_modules`
- `tests/architecture/test_adapter_contracts.py::TestAdapterMixinPolicy::test_src_does_not_use_legacy_adapter_mixin_symbols`
- `tests/architecture/test_adapter_contracts.py::TestAdapterPortCompliance::test_infrastructure_imports_domain_ports`
- `tests/architecture/test_adapter_contracts.py::TestAdapterPortCompliance::test_filterable_adapters_implement_protocol`
- `tests/architecture/test_adapter_contracts.py::TestAdapterPortCompliance::test_filterable_adapters_runtime_isinstance_protocol[bioetl.infrastructure.adapters.chembl.client-ChemblAdapter-bioetl/infrastructure/adapters/chembl/client.py-contract_markers0]`
- `tests/architecture/test_adapter_contracts.py::TestAdapterPortCompliance::test_filterable_adapters_runtime_isinstance_protocol[bioetl.infrastructure.adapters.crossref.client-CrossRefAdapter-bioetl/infrastructure/adapters/crossref/client.py-contract_markers1]`

## Category Scores (aggregated across all sectors)
| Category | Weight | Score | Issues | Status |
|----------|--------|-------|--------|--------|
| Architecture (ARCH) | 30% | 10.0 | 0 | FAIL |
| Anti-Patterns (AP) | 25% | -20.5 | 61 | FAIL |
| DI Violations (DI) | 20% | 10.0 | 0 | PASS |
| Naming (NAME) | 10% | 10.0 | 0 | PASS |
| Types (TYPE) | 10% | 10.0 | 0 | PASS |
| Testing (TEST) | 5% | 10.0 | 0 | PASS |
18 changes: 18 additions & 0 deletions reports/review/S1-Domain.md
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# Code Review Report — S1: Domain
**Date**: 2026-05-27
**Scope**: src/bioetl/domain/
**Files reviewed**: 548
**Total LOC**: 71701
**Status**: FAIL
**Score**: 0/10.0
---
## Summary
| Category | Issues | CRIT | HIGH | MED | LOW | Score |
|----------|--------|------|------|-----|-----|-------|
| Architecture | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Anti-Patterns | 61 | 0 | 0 | 61 | 0 | -20.5 |
| DI Violations | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Naming | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Types | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Testing | 0 | 0 | 0 | 0 | 0 | 10.0 |
| **TOTAL** | **61** | **0** | **0** | **61** | **0** | **0** |
18 changes: 18 additions & 0 deletions reports/review/S2-Application.md
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# Code Review Report — S2: Application
**Date**: 2026-05-27
**Scope**: src/bioetl/application/
**Files reviewed**: 608
**Total LOC**: 89551
**Status**: FAIL
**Score**: 0/10.0
---
## Summary
| Category | Issues | CRIT | HIGH | MED | LOW | Score |
|----------|--------|------|------|-----|-----|-------|
| Architecture | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Anti-Patterns | 61 | 0 | 0 | 61 | 0 | -20.5 |
| DI Violations | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Naming | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Types | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Testing | 0 | 0 | 0 | 0 | 0 | 10.0 |
| **TOTAL** | **61** | **0** | **0** | **61** | **0** | **0** |
18 changes: 18 additions & 0 deletions reports/review/S3-Infrastructure.md
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# Code Review Report — S3: Infrastructure
**Date**: 2026-05-27
**Scope**: src/bioetl/infrastructure/
**Files reviewed**: 469
**Total LOC**: 74505
**Status**: FAIL
**Score**: 0/10.0
---
## Summary
| Category | Issues | CRIT | HIGH | MED | LOW | Score |
|----------|--------|------|------|-----|-----|-------|
| Architecture | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Anti-Patterns | 61 | 0 | 0 | 61 | 0 | -20.5 |
| DI Violations | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Naming | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Types | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Testing | 0 | 0 | 0 | 0 | 0 | 10.0 |
| **TOTAL** | **61** | **0** | **0** | **61** | **0** | **0** |
18 changes: 18 additions & 0 deletions reports/review/S4-CompositionandInterfaces.md
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# Code Review Report — S4: Composition and Interfaces
**Date**: 2026-05-27
**Scope**: src/bioetl/composition/, src/bioetl/interfaces/
**Files reviewed**: 363
**Total LOC**: 51883
**Status**: FAIL
**Score**: 0/10.0
---
## Summary
| Category | Issues | CRIT | HIGH | MED | LOW | Score |
|----------|--------|------|------|-----|-----|-------|
| Architecture | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Anti-Patterns | 61 | 0 | 0 | 61 | 0 | -20.5 |
| DI Violations | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Naming | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Types | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Testing | 0 | 0 | 0 | 0 | 0 | 10.0 |
| **TOTAL** | **61** | **0** | **0** | **61** | **0** | **0** |
18 changes: 18 additions & 0 deletions reports/review/S5-Cross-cutting.md
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# Code Review Report — S5: Cross-cutting
**Date**: 2026-05-27
**Scope**: src/bioetl/
**Files reviewed**: 1990
**Total LOC**: 287680
**Status**: FAIL
**Score**: 0/10.0
---
## Summary
| Category | Issues | CRIT | HIGH | MED | LOW | Score |
|----------|--------|------|------|-----|-----|-------|
| Architecture | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Anti-Patterns | 61 | 0 | 0 | 61 | 0 | -20.5 |
| DI Violations | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Naming | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Types | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Testing | 0 | 0 | 0 | 0 | 0 | 10.0 |
| **TOTAL** | **61** | **0** | **0** | **61** | **0** | **0** |
18 changes: 18 additions & 0 deletions reports/review/S6-Tests.md
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# Code Review Report — S6: Tests
**Date**: 2026-05-27
**Scope**: tests/
**Files reviewed**: 1796
**Total LOC**: 463529
**Status**: FAIL
**Score**: 0/10.0
---
## Summary
| Category | Issues | CRIT | HIGH | MED | LOW | Score |
|----------|--------|------|------|-----|-----|-------|
| Architecture | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Anti-Patterns | 61 | 0 | 0 | 61 | 0 | -20.5 |
| DI Violations | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Naming | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Types | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Testing | 0 | 0 | 0 | 0 | 0 | 10.0 |
| **TOTAL** | **61** | **0** | **0** | **61** | **0** | **0** |
18 changes: 18 additions & 0 deletions reports/review/S7-Configs.md
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# Code Review Report — S7: Configs
**Date**: 2026-05-27
**Scope**: configs/
**Files reviewed**: 167
**Total LOC**: 23447
**Status**: FAIL
**Score**: 0/10.0
---
## Summary
| Category | Issues | CRIT | HIGH | MED | LOW | Score |
|----------|--------|------|------|-----|-----|-------|
| Architecture | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Anti-Patterns | 61 | 0 | 0 | 61 | 0 | -20.5 |
| DI Violations | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Naming | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Types | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Testing | 0 | 0 | 0 | 0 | 0 | 10.0 |
| **TOTAL** | **61** | **0** | **0** | **61** | **0** | **0** |
18 changes: 18 additions & 0 deletions reports/review/S8-Documentation.md
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# Code Review Report — S8: Documentation
**Date**: 2026-05-27
**Scope**: docs/
**Files reviewed**: 1073
**Total LOC**: 169566
**Status**: FAIL
**Score**: 0/10.0
---
## Summary
| Category | Issues | CRIT | HIGH | MED | LOW | Score |
|----------|--------|------|------|-----|-----|-------|
| Architecture | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Anti-Patterns | 61 | 0 | 0 | 61 | 0 | -20.5 |
| DI Violations | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Naming | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Types | 0 | 0 | 0 | 0 | 0 | 10.0 |
| Testing | 0 | 0 | 0 | 0 | 0 | 10.0 |
| **TOTAL** | **61** | **0** | **0** | **61** | **0** | **0** |
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{"files_changed": 7014, "module": "all", "test_count": 10}
1 change: 1 addition & 0 deletions reports/review/telemetry.jsonl
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{"event": "review_complete", "level": "L1", "shard_scope": "all", "tests_found": 10}
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