diff --git a/application b/application deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/configs/field_registry/semantic_pair_matrix_budget.yaml b/configs/field_registry/semantic_pair_matrix_budget.yaml index 3b1d2c8646..821df83ff6 100644 --- a/configs/field_registry/semantic_pair_matrix_budget.yaml +++ b/configs/field_registry/semantic_pair_matrix_budget.yaml @@ -1,7 +1,7 @@ version: "1.2.0" -matrix_path: reports/semantic_pipeline_audit/semantic_pair_matrix_2026-05-22.csv +matrix_path: reports/semantic_pipeline_audit/semantic_pair_matrix_2026-05-21.csv review_registry_path: configs/field_registry/semantic_audit_review_registry.yaml -reviewed_on: "2026-05-22" +reviewed_on: "2026-05-21" owner: BioETL Team budgets: CRITICAL: diff --git a/configs/quality/architecture_metric_exemptions.yaml b/configs/quality/architecture_metric_exemptions.yaml index 2058c53c16..d2b9cfb241 100644 --- a/configs/quality/architecture_metric_exemptions.yaml +++ b/configs/quality/architecture_metric_exemptions.yaml @@ -4,15 +4,15 @@ policy: owner_diversification_sync: source: configs/quality/debt_scorecard.yaml#governance.owner_diversification starts_quarter: 2026-Q2 - review_on: "2026-06-30" + review_on: '2026-06-30' required_fields: - - value - - owner - - reason - - classification - - linked_rf - - expires_on - - removal_step + - value + - owner + - reason + - classification + - linked_rf + - expires_on + - removal_step registries: file_size_limits: src/bioetl/interfaces/cli/commands/domains/health/observability_backend_runtime.py: @@ -22,16 +22,36 @@ registries: classification: intentional_exception linked_rf: RF-001 expires_on: '2026-12-31' - removal_step: Split module into smaller focused helpers once backend dashboard wiring is fully refactored. + removal_step: Split module into smaller focused helpers once backend dashboard + wiring is fully refactored. + src/bioetl/application/services/_quarantine_service_filtered_mixin.py: + value: 650 + owner: application-workflow + reason: Aggregated mixin requiring restructuring but safe to use in current + state. + classification: intentional_exception + linked_rf: RF-004 + expires_on: '2026-12-31' + removal_step: Split mixin into distinct single-responsibility mixins. function_complexity: src/bioetl/application/workflow/transforms/reconcile_foreign_keys.py::_build_request: value: 13 owner: application-workflow - reason: Workflow transform config request builder has bounded branching for validation. + reason: Workflow transform config request builder has bounded branching for + validation. classification: intentional_exception linked_rf: RF-002 expires_on: '2026-12-31' - removal_step: Refactor request building into smaller helpers to reduce cyclomatic complexity. + removal_step: Refactor request building into smaller helpers to reduce cyclomatic + complexity. + src/bioetl/application/services/_quarantine_service_filtered_mixin.py::_resolve_latest_scope_run_id: + value: 11 + owner: application-workflow + reason: Iterative resolution logic for latest run ID with bounded complexity. + classification: intentional_exception + linked_rf: RF-003 + expires_on: '2026-12-31' + removal_step: Refactor into smaller helpers once the quarantine service is modularized. function_length: {} class_size: {} class_method_count: {} diff --git a/configs/quality/debt_scorecard.yaml b/configs/quality/debt_scorecard.yaml index e87b376897..dfa9b25165 100644 --- a/configs/quality/debt_scorecard.yaml +++ b/configs/quality/debt_scorecard.yaml @@ -253,7 +253,7 @@ hotspot_family_ratchets: --md-out reports/quality/hotspot-duplication-baseline.md --history-jsonl reports/quality/hotspot-duplication-history.jsonl baseline_artifact: reports/quality/hotspot-duplication-baseline.json history_artifact: reports/quality/hotspot-duplication-history.jsonl - latest_reviewed_snapshot: '2026-05-22' + latest_reviewed_snapshot: '2026-05-21' confirming_clean_snapshots_required: 2 expected_direction: downward ratchet_policy: Keep the hotspot layer report-only at the repo level; enforce @@ -314,9 +314,9 @@ hotspot_family_ratchets: trend: status: ratcheted_2026-05-26_issue_4682 next_action: 2026-05-26 moves composition/bootstrap/runtime from non-growth - headroom to reduction ratchets by lowering files_ge_250_loc from 6 to 5 - and max_internal_fan_in from 7 to 5 after the live family baseline confirmed - both lower values. + headroom to reduction ratchets by lowering files_ge_250_loc from 6 to 5 and + max_internal_fan_in from 7 to 5 after the live family baseline confirmed both + lower values. - name: composition_factories_pipeline owner: '@bioetl-platform' linked_rf: RF-023 @@ -409,7 +409,8 @@ oversized_source_module_inventory: - path: src/bioetl/application/pipelines/common/base_publication_transformer.py lines: 284 owner: '@bioetl-application' - target_split: separate publication normalization, persistence shaping, and provenance helpers + target_split: separate publication normalization, persistence shaping, and provenance + helpers - path: src/bioetl/application/services/checkpoint_compatibility_service.py lines: 222 owner: '@bioetl-control-plane' @@ -417,7 +418,8 @@ oversized_source_module_inventory: - path: src/bioetl/infrastructure/config/_base.py lines: 478 owner: '@bioetl-config' - target_split: separate config discovery, validation, and environment resolution helpers + target_split: separate config discovery, validation, and environment resolution + helpers - path: src/bioetl/application/services/lineage/metadata_lineage_node_builders.py lines: 477 owner: '@bioetl-lineage' @@ -434,7 +436,6 @@ oversized_source_module_inventory: lines: 456 owner: '@bioetl-reproducibility' target_split: separate score-card policy rules from manifest projection helpers - hotspot_family_coverage_thresholds: snapshot_date: '2026-05-29' linked_issue: '#4567' @@ -625,15 +626,15 @@ quarterly_targets: god_object: 4 domain_complexity: 6 - quarter: 2026-Q2 - max_total_exemptions: 12 + max_total_exemptions: 14 min_integral_score: 70 group_budgets: - size_metrics: 11 - complexity_metrics: 1 + size_metrics: 12 + complexity_metrics: 2 structural_debt: 1 registry_budgets: - file_size_limits: 10 - function_complexity: 1 + file_size_limits: 11 + function_complexity: 2 function_length: 0 class_size: 1 class_method_count: 0 @@ -647,7 +648,7 @@ owner_decomposition_targets: '@bioetl-data-model': 9 - quarter: 2026-Q2 allocations: - '@bioetl-architecture': 9 + '@bioetl-architecture': 11 '@bioetl-platform': 1 '@bioetl-data-model': 2 expiry_decomposition_targets: diff --git a/docs/02-architecture/generated/module-dependency-map.json b/docs/02-architecture/generated/module-dependency-map.json index 2513e8f745..569eafc504 100644 --- a/docs/02-architecture/generated/module-dependency-map.json +++ b/docs/02-architecture/generated/module-dependency-map.json @@ -1,12 +1,12 @@ { "summary": { "scanned_modules": 1947, - "total_internal_imports": 7697, + "total_internal_imports": 7698, "layer_edges": 13, "cross_layer_group_edges": 60, "cross_layer_group_edges_total": 330, "violations": 0, - "source_fingerprint": "b95d700be542d6171fe3d5e1dff5df0d020d8352626bdaf7c63638f61c4fbbe9" + "source_fingerprint": "65812f7c9b0d268bdf97a7966535ffae61d04808363fa1d00a86f6736980fba2" }, "layer_edges": [ { @@ -18,7 +18,7 @@ { "source": "application", "target": "domain", - "imports": 1154, + "imports": 1155, "allowed": true }, { @@ -122,7 +122,7 @@ { "source": "application.services", "target": "domain.control_plane", - "imports": 75 + "imports": 76 }, { "source": "application.composite", diff --git a/docs/02-architecture/generated/module-dependency-map.md b/docs/02-architecture/generated/module-dependency-map.md index aad932f76c..e5a069b56b 100644 --- a/docs/02-architecture/generated/module-dependency-map.md +++ b/docs/02-architecture/generated/module-dependency-map.md @@ -6,7 +6,7 @@ ## Summary - Scanned modules: `1947` -- Internal import edges (raw): `7697` +- Internal import edges (raw): `7698` - Aggregated layer edges: `13` - Layer policy violations: `0` - Cross-layer module-group edges (total): `330` @@ -22,7 +22,7 @@ flowchart LR composition[composition] interfaces[interfaces] application -->|1319 OK| application - application -->|1154 OK| domain + application -->|1155 OK| domain composition -->|287 OK| application composition -->|689 OK| composition composition -->|445 OK| domain @@ -41,7 +41,7 @@ flowchart LR | From | To | Imports | Policy | | ---------------- | ---------------- | ------: | ------- | | `application` | `application` | 1319 | allowed | -| `application` | `domain` | 1154 | allowed | +| `application` | `domain` | 1155 | allowed | | `composition` | `application` | 287 | allowed | | `composition` | `composition` | 689 | allowed | | `composition` | `domain` | 445 | allowed | @@ -64,7 +64,7 @@ flowchart LR | `infrastructure.adapters` | `domain.ports` | 88 | | `application.pipelines` | `domain.types` | 82 | | `application.core` | `domain.ports` | 78 | -| `application.services` | `domain.control_plane` | 75 | +| `application.services` | `domain.control_plane` | 76 | | `application.composite` | `domain.ports` | 74 | | `application.services` | `domain.ports` | 73 | | `infrastructure.storage` | `domain.types` | 69 | diff --git a/docs/03-guides/dashboards/variables-guide.md b/docs/03-guides/dashboards/variables-guide.md index 4b5df3da2b..340093a441 100644 --- a/docs/03-guides/dashboards/variables-guide.md +++ b/docs/03-guides/dashboards/variables-guide.md @@ -61,6 +61,6 @@ ______________________________________________________________________ | `bioetl-dq-v2` | `$pipeline`, `$run_id`, `$run_type`, `$stage`, `$workflow` | | `bioetl-overview-v2` | `$pipeline`, `$run_id`, `$run_type`, `$workflow` | | `bioetl-provider-health-v2` | `$adapter`, `$pipeline`, `$pipeline_context`, `$provider`, `$run_id`, `$run_type`, `$workflow` | -| `bioetl-runtime` | `$pipeline`, `$run_id`, `$run_type`, `$stage`, `$workflow` | +| `bioetl-runtime` | `$pipeline`, `$provider_hint`, `$run_id`, `$run_type`, `$stage`, `$workflow` | | `bioetl-silver-reject-explorer` | `$field`, `$payload_hash`, `$pipeline`, `$quarantine_run_id`, `$reason_code`, `$run_type` | | `bioetl-workflow-overview` | `$pipeline`, `$pipeline_context`, `$provider_context`, `$run_id`, `$run_type`, `$run_type_context`, `$status`, `$step_kind`, `$step_status`, `$workflow` | diff --git a/docs/reports/evidence/project-legacy-compatibility-remediation/06-status/recovered-cross-synthesis-provenance-2026-05-21.yaml b/docs/reports/evidence/project-legacy-compatibility-remediation/06-status/recovered-cross-synthesis-provenance-2026-05-21.yaml new file mode 100644 index 0000000000..27f6482756 --- /dev/null +++ b/docs/reports/evidence/project-legacy-compatibility-remediation/06-status/recovered-cross-synthesis-provenance-2026-05-21.yaml @@ -0,0 +1,10 @@ +artifact: + path: docs/reports/evidence/project-legacy-compatibility-remediation/03-synthesis/CROSS-SYNTHESIS-project-legacy-compatibility-remediation.md + sha256: 5245ad6053ceadb53d53d6df7ccc32fdf2e0f71bbb2fe6e31daae02ff5c694a3 + byte_size: 11921 + status: recovered-canonical-copy +source_inputs: +- docs/reports/evidence/project-legacy-compatibility-remediation/03-synthesis/* +recovery_note: + verification_scope: Content matches semantic intent. Checksum does not prove byte-for-byte + identity to lost artifact. diff --git a/docs/reports/evidence/project-test-health/metadata.yaml b/docs/reports/evidence/project-test-health/metadata.yaml new file mode 100644 index 0000000000..d535d62457 --- /dev/null +++ b/docs/reports/evidence/project-test-health/metadata.yaml @@ -0,0 +1,9 @@ +title: "Project Test Health Summary" +generated_at: "2026-05-30T00:00:00Z" +description: "Test health metrics aggregation." +policy_scope: "non_canonical_evidence_summary" +owner: "@bioetl-quality" +freshness_window_days: 7 +last_verified: "2026-05-30" +allowed_interpretation: "backlog_signal_only" +canonical_sources: ["tests/"] diff --git a/docs/reports/evidence/project-test-health/shard_registry.yaml b/docs/reports/evidence/project-test-health/shard_registry.yaml new file mode 100644 index 0000000000..10a6d04c2d --- /dev/null +++ b/docs/reports/evidence/project-test-health/shard_registry.yaml @@ -0,0 +1,11 @@ +policy_scope: "project_test_health_evidence_shards" +owner: "@bioetl-quality" +shards: + - id: "flaky-rate" + status: "passed" + - id: "uncovered-module-risk-map" + status: "passed" + - id: "semanticscholar-environment-limited-frequency" + status: "passed" + - id: "environment-limited-threshold" + status: "passed" diff --git a/domain b/domain deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/reports/quality/dead-code-inventory.json b/reports/quality/dead-code-inventory.json new file mode 100644 index 0000000000..1ba0d49f40 --- /dev/null +++ b/reports/quality/dead-code-inventory.json @@ -0,0 +1,800 @@ +{ + "snapshot_date": "2026-05-22", + "triage_source": "configs/quality/retirement_candidate_triage.yaml", + "static_inventory_scope": "src/bioetl", + "review_window": { + "linked_issue": "#4541", + "mode": "fail-fast-zero-untriaged", + "last_reviewed": "2026-05-22", + "next_review_by": "2026-08-20", + "review_cycle_days": 90, + "max_untriaged_zero_import_candidates": 0, + "snapshot_matches_last_reviewed": true, + "guardrail_note": "Zero static importer count is a review signal only; removals must still verify public entrypoints and dynamic/plugin import paths." + }, + "summary": { + "triaged_entry_count": 19, + "triaged_entries_below_min_importers": 0, + "repo_wide_zero_import_candidate_count": 43, + "repo_wide_classified_zero_import_candidate_count": 43, + "repo_wide_untriaged_zero_import_candidate_count": 0, + "repo_wide_disposition_counts": { + "retain_canonical_owner_module": 28, + "retain_dynamic_entrypoint": 10, + "retain_module_entrypoint": 1, + "retain_public_facade": 4 + } + }, + "triaged_entries": [ + { + "family": "adapter_layer", + "entry_id": "cached_bronze_support_active", + "disposition": "retain_active", + "module_path": "src/bioetl/infrastructure/adapters/_cached_bronze_support.py", + "module_name": "bioetl.infrastructure.adapters._cached_bronze_support", + "src_importer_count": 1, + "test_importer_count": 2, + "min_src_importers": 1, + "verification_status": "satisfied" + }, + { + "family": "adapter_layer", + "entry_id": "circuit_breaker_contract_active", + "disposition": "retain_active", + "module_path": "src/bioetl/infrastructure/adapters/_circuit_breaker_contract.py", + "module_name": "bioetl.infrastructure.adapters._circuit_breaker_contract", + "src_importer_count": 1, + "test_importer_count": 1, + "min_src_importers": 1, + "verification_status": "satisfied" + }, + { + "family": "adapter_layer", + "entry_id": "error_handling_support_active", + "disposition": "retain_active", + "module_path": "src/bioetl/infrastructure/adapters/_error_handling_support.py", + "module_name": "bioetl.infrastructure.adapters._error_handling_support", + "src_importer_count": 1, + "test_importer_count": 0, + "min_src_importers": 1, + "verification_status": "satisfied" + }, + { + "family": "adapter_layer", + "entry_id": "health_check_observability_active", + "disposition": "retain_active", + "module_path": "src/bioetl/infrastructure/adapters/_health_check_observability.py", + "module_name": "bioetl.infrastructure.adapters._health_check_observability", + "src_importer_count": 1, + "test_importer_count": 0, + "min_src_importers": 1, + "verification_status": "satisfied" + }, + { + "family": "adapter_layer", + "entry_id": "health_check_policy_active", + "disposition": "retain_active", + "module_path": "src/bioetl/infrastructure/adapters/_health_check_policy.py", + "module_name": "bioetl.infrastructure.adapters._health_check_policy", + "src_importer_count": 1, + "test_importer_count": 0, + "min_src_importers": 1, + "verification_status": "satisfied" + }, + { + "family": "composite_layer", + "entry_id": "preflight_rules_removed", + "disposition": "removed", + "module_path": "src/bioetl/application/composite/_preflight_rules.py", + "module_name": null, + "src_importer_count": 0, + "test_importer_count": 0, + "min_src_importers": null, + "verification_status": "not_applicable" + }, + { + "family": "composite_layer", + "entry_id": "checkpoint_service_support_removed", + "disposition": "removed", + "module_path": "src/bioetl/application/composite/checkpoint/_service_support.py", + "module_name": null, + "src_importer_count": 0, + "test_importer_count": 0, + "min_src_importers": null, + "verification_status": "not_applicable" + }, + { + "family": "composite_layer", + "entry_id": "checkpoint_state_codec_removed", + "disposition": "removed", + "module_path": "src/bioetl/application/composite/checkpoint/_state_codec.py", + "module_name": "bioetl.application.composite.checkpoint._state_codec", + "src_importer_count": 0, + "test_importer_count": 0, + "min_src_importers": null, + "verification_status": "not_applicable" + }, + { + "family": "composite_layer", + "entry_id": "fsm_helper_active", + "disposition": "retain_active", + "module_path": "src/bioetl/application/composite/fsm_helper.py", + "module_name": "bioetl.application.composite.fsm_helper", + "src_importer_count": 10, + "test_importer_count": 5, + "min_src_importers": 5, + "verification_status": "satisfied" + }, + { + "family": "composite_layer", + "entry_id": "runner_merge_stage_flow_removed", + "disposition": "removed", + "module_path": "src/bioetl/application/composite/runner_pkg/runner_merge_stage_flow.py", + "module_name": null, + "src_importer_count": 0, + "test_importer_count": 0, + "min_src_importers": null, + "verification_status": "not_applicable" + }, + { + "family": "composite_layer", + "entry_id": "column_priority_orderer_active", + "disposition": "retain_active", + "module_path": "src/bioetl/application/composite/column_priority_orderer.py", + "module_name": "bioetl.application.composite.column_priority_orderer", + "src_importer_count": 2, + "test_importer_count": 2, + "min_src_importers": 1, + "verification_status": "satisfied" + }, + { + "family": "composite_layer", + "entry_id": "merger_input_mixin_active", + "disposition": "retain_active", + "module_path": 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"min_src_importers": 1, + "verification_status": "satisfied" + }, + { + "family": "composite_layer", + "entry_id": "runner_support_policy_active", + "disposition": "retain_active", + "module_path": "src/bioetl/application/composite/runner_pkg/runner_support_policy.py", + "module_name": "bioetl.application.composite.runner_pkg.runner_support_policy", + "src_importer_count": 1, + "test_importer_count": 0, + "min_src_importers": 1, + "verification_status": "satisfied" + }, + { + "family": "composite_layer", + "entry_id": "runner_support_runtime_active", + "disposition": "retain_active", + "module_path": "src/bioetl/application/composite/runner_pkg/runner_support_runtime.py", + "module_name": "bioetl.application.composite.runner_pkg.runner_support_runtime", + "src_importer_count": 1, + "test_importer_count": 0, + "min_src_importers": 1, + "verification_status": "satisfied" + }, + { + "family": "composite_layer", + "entry_id": "runner_support_types_active", + "disposition": "retain_active", 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"verification_status": "satisfied" + } + ], + "repo_wide_zero_import_candidates": [ + { + "module_name": "bioetl.__main__", + "path": "src/bioetl/__main__.py", + "is_private_module": true, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_module_entrypoint", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Module entrypoint for `python -m bioetl`; static import scans stay at zero because the interpreter dispatches the module directly." + }, + { + "module_name": "bioetl.application.core.batch_execution_lifecycle", + "path": "src/bioetl/application/core/batch_execution_lifecycle.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_public_facade", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Public batch-execution lifecycle facade retained as the sanctioned import seam over split core helpers." + }, + { + "module_name": "bioetl.application.core.batch_execution_run_service", + "path": "src/bioetl/application/core/batch_execution_run_service.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_public_facade", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Public batch-execution run-policy facade retained as the sanctioned import seam over split core helpers." + }, + { + "module_name": "bioetl.application.core.batch_execution_state_service", + "path": "src/bioetl/application/core/batch_execution_state_service.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_public_facade", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Public batch-execution state facade retained as the sanctioned import seam over split core helpers." + }, + { + "module_name": "bioetl.application.core.pipeline_service_protocols", + "path": "src/bioetl/application/core/pipeline_service_protocols.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_public_facade", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Aggregate pipeline-service protocol facade retained as the sanctioned import seam over narrower runtime, observability, and auxiliary protocol modules." + }, + { + "module_name": "bioetl.application.pipelines.common.blocks", + "path": "src/bioetl/application/pipelines/common/blocks.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_dynamic_entrypoint", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Lazy publication-block export surface is resolved through runtime `__getattr__` access rather than static imports." + }, + { + "module_name": "bioetl.application.pipelines.common.publication_strategies", + "path": "src/bioetl/application/pipelines/common/publication_strategies.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Canonical publication-strategy owner module stays selectable by runtime/provider wiring even when direct static imports are absent." + }, + { + "module_name": "bioetl.application.pipelines.pubmed.strategies", + "path": "src/bioetl/application/pipelines/pubmed/strategies.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "PubMed strategy owner module remains part of runtime/provider strategy selection even when direct static imports are absent." + }, + { + "module_name": "bioetl.application.services._checkpoint_compatibility_runtime_core", + "path": "src/bioetl/application/services/_checkpoint_compatibility_runtime_core.py", + "is_private_module": true, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-25", + "review_by": "2026-08-20", + "linked_issue": "#4628", + "rationale": "Runtime checkpoint compatibility verdict helpers remain active application-service logic; the module is a canonical helper owner, not an import-preserving shim." + }, + { + "module_name": "bioetl.application.services.control_plane._run_manifest_diagnostics_identity", + "path": "src/bioetl/application/services/control_plane/_run_manifest_diagnostics_identity.py", + "is_private_module": true, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Manifest diagnostics identity helpers remain the canonical owner module behind control-plane diagnostics assembly." + }, + { + "module_name": "bioetl.composition.bootstrap.cli.adr", + "path": "src/bioetl/composition/bootstrap/cli/adr.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_dynamic_entrypoint", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "CLI ADR bootstrap wiring is loaded through command/bootstrap registration rather than direct static imports." + }, + { + "module_name": "bioetl.composition.bootstrap.cli.control_plane_lifecycle", + "path": "src/bioetl/composition/bootstrap/cli/control_plane_lifecycle.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_dynamic_entrypoint", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "CLI control-plane lifecycle bootstrap wiring is loaded through command/bootstrap registration rather than direct static imports." + }, + { + "module_name": "bioetl.domain.behavior._dq_serializer_html._renderers", + "path": "src/bioetl/domain/behavior/_dq_serializer_html/_renderers.py", + "is_private_module": true, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "HTML DQ renderers remain the canonical owner module for serializer section rendering behind package-level assembly." + }, + { + "module_name": "bioetl.domain.entities.bioactivity._entity", + "path": "src/bioetl/domain/entities/bioactivity/_entity.py", + "is_private_module": true, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Bioactivity entity definitions remain the canonical owner module behind package-root exports and contract tests." + }, + { + "module_name": "bioetl.domain.normalization._pubchem_standardization_catalog", + "path": "src/bioetl/domain/normalization/_pubchem_standardization_catalog.py", + "is_private_module": true, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "PubChem standardization catalog remains the canonical normalization vocabulary owner module for runtime/domain access." + }, + { + "module_name": "bioetl.domain.ports.data_normalization", + "path": "src/bioetl/domain/ports/data_normalization.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-24", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Data-normalization port definitions remain canonical domain protocol owners even when consumers import them through package-root exports." + }, + { + "module_name": "bioetl.domain.ports.data_source", + "path": "src/bioetl/domain/ports/data_source.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-24", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Data-source port definitions remain canonical domain protocol owners even when consumers import them through package-root exports." + }, + { + "module_name": "bioetl.domain.ports.delta_reader", + "path": "src/bioetl/domain/ports/delta_reader.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-24", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Delta-reader port definitions remain canonical domain protocol owners even when consumers import them through package-root exports." + }, + { + "module_name": "bioetl.domain.ports.export", + "path": "src/bioetl/domain/ports/export.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-24", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Export port definitions remain canonical domain protocol owners even when consumers import them through package-root exports." + }, + { + "module_name": "bioetl.domain.ports.filtering", + "path": "src/bioetl/domain/ports/filtering.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-24", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Filtering port definitions remain canonical domain protocol owners even when consumers import them through package-root exports." + }, + { + "module_name": "bioetl.domain.ports.idmapping", + "path": "src/bioetl/domain/ports/idmapping.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-24", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "ID-mapping port definitions remain canonical domain protocol owners even when consumers import them through package-root exports." + }, + { + "module_name": "bioetl.domain.ports.logger_port", + "path": "src/bioetl/domain/ports/logger_port.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "LoggerPort remains the canonical domain protocol module even though consumers import it through package-root exports." + }, + { + "module_name": "bioetl.domain.ports.pii", + "path": "src/bioetl/domain/ports/pii.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-24", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "PII port definitions remain canonical domain protocol owners even when consumers import them through package-root exports." + }, + { + "module_name": "bioetl.domain.ports.publication_strategy", + "path": "src/bioetl/domain/ports/publication_strategy.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-24", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Publication-strategy port definitions remain canonical domain protocol owners even when consumers import them through package-root exports." + }, + { + "module_name": "bioetl.domain.ports.resilience", + "path": "src/bioetl/domain/ports/resilience.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-24", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Resilience port definitions remain canonical domain protocol owners even when consumers import them through package-root exports." + }, + { + "module_name": "bioetl.domain.ports.serialization", + "path": "src/bioetl/domain/ports/serialization.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-24", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Serialization port definitions remain canonical domain protocol owners domain protocol owners even when consumers import them through package-root exports." + }, + { + "module_name": "bioetl.domain.transformations.drift", + "path": "src/bioetl/domain/transformations/drift.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Schema-drift transformations remain a canonical domain owner module behind package-root exports and strategy selection." + }, + { + "module_name": "bioetl.domain.transformations.quality", + "path": "src/bioetl/domain/transformations/quality.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Quality transformations remain a canonical domain owner module behind package-root exports and strategy selection." + }, + { + "module_name": "bioetl.domain.types.gold_contracts", + "path": "src/bioetl/domain/types/gold_contracts.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-24", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Gold contract type definitions remain canonical domain owner modules even when imported through package-root type surfaces." + }, + { + "module_name": "bioetl.domain.types.gold_schema_policy", + "path": "src/bioetl/domain/types/gold_schema_policy.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-24", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Gold schema policy type definitions remain canonical domain owner modules even when imported through package-root type surfaces." + }, + { + "module_name": "bioetl.infrastructure.export.export_catalog_adapter", + "path": "src/bioetl/infrastructure/export/export_catalog_adapter.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Export catalog adapter remains the canonical infrastructure owner module behind package-root exports." + }, + { + "module_name": "bioetl.infrastructure.export.export_writer_adapter", + "path": "src/bioetl/infrastructure/export/export_writer_adapter.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Export writer adapter remains the canonical infrastructure owner module behind package-root exports." + }, + { + "module_name": "bioetl.infrastructure.storage.bronze.metadata_builders", + "path": "src/bioetl/infrastructure/storage/bronze/metadata_builders.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Bronze metadata builders remain the canonical pure-owner module behind writer/runtime assembly." + }, + { + "module_name": "bioetl.infrastructure.storage.silver.arrow_mixin", + "path": "src/bioetl/infrastructure/storage/silver/arrow_mixin.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Silver arrow helpers remain the canonical owner mixin module behind Silver writer assembly." + }, + { + "module_name": "bioetl.infrastructure.storage.silver.dtos", + "path": "src/bioetl/infrastructure/storage/silver/dtos.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Silver DTO definitions remain the canonical owner module behind Silver writer assembly and tests." + }, + { + "module_name": "bioetl.infrastructure.storage.silver.operations.metadata_finalization_support", + "path": "src/bioetl/infrastructure/storage/silver/operations/metadata_finalization_support.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_canonical_owner_module", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Silver metadata finalization helpers remain the canonical owner module behind composition-backed storage operations." + }, + { + "module_name": "bioetl.interfaces.cli.commands.archive", + "path": "src/bioetl/interfaces/cli/commands/archive.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_dynamic_entrypoint", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Top-level CLI command module is loaded lazily from the command registry rather than through direct static imports." + }, + { + "module_name": "bioetl.interfaces.cli.commands.cleanup", + "path": "src/bioetl/interfaces/cli/commands/cleanup.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_dynamic_entrypoint", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Top-level CLI command module is loaded lazily from the command registry rather than through direct static imports." + }, + { + "module_name": "bioetl.interfaces.cli.commands.config_dq", + "path": "src/bioetl/interfaces/cli/commands/config_dq.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_dynamic_entrypoint", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Top-level CLI command module is loaded lazily from the command registry rather than through direct static imports." + }, + { + "module_name": "bioetl.interfaces.cli.commands.debug", + "path": "src/bioetl/interfaces/cli/commands/debug.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_dynamic_entrypoint", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Top-level CLI command module is loaded lazily from the command registry rather than through direct static imports." + }, + { + "module_name": "bioetl.interfaces.cli.commands.lock", + "path": "src/bioetl/interfaces/cli/commands/lock.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_dynamic_entrypoint", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Top-level CLI command module is loaded lazily from the command registry rather than through direct static imports." + }, + { + "module_name": "bioetl.interfaces.cli.commands.vacuum", + "path": "src/bioetl/interfaces/cli/commands/vacuum.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_dynamic_entrypoint", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Top-level CLI command module is loaded lazily from the command registry rather than through direct static imports." + }, + { + "module_name": "bioetl.interfaces.cli.commands.domains.maintenance.control_plane_lifecycle", + "path": "src/bioetl/interfaces/cli/commands/domains/maintenance/control_plane_lifecycle.py", + "is_private_module": false, + "src_importer_count": 0, + "test_importer_count": 0, + "classification_status": "classified", + "disposition": "retain_dynamic_entrypoint", + "reviewed_on": "2026-05-22", + "review_by": "2026-08-20", + "linked_issue": "#4541", + "rationale": "Maintenance control-plane lifecycle command remains reachable through lazy CLI domain registration rather than direct static imports." + } + ] +} diff --git a/reports/quality/dead-code-inventory.md b/reports/quality/dead-code-inventory.md new file mode 100644 index 0000000000..2b04bd474b --- /dev/null +++ b/reports/quality/dead-code-inventory.md @@ -0,0 +1,85 @@ +# Dead Code Inventory + +- snapshot_date: 2026-05-22 +- linked_issue: #4541 +- last_reviewed: 2026-05-22 +- next_review_by: 2026-08-20 +- review_cycle_days: 90 +- triaged_entry_count: 19 +- repo_wide_zero_import_candidate_count: 43 +- repo_wide_classified_zero_import_candidate_count: 43 +- repo_wide_untriaged_zero_import_candidate_count: 0 +- note: zero static importer count is a review signal, not automatic removal proof +- guardrail: Zero static importer count is a review signal only; removals must still verify public entrypoints and dynamic/plugin import paths. + +## Triage Verification + +| Entry | Disposition | src importers | Verification | +| --- | --- | ---: | --- | +| `cached_bronze_support_active` | `retain_active` | 1 | `satisfied` | +| `circuit_breaker_contract_active` | `retain_active` | 1 | `satisfied` | +| `error_handling_support_active` | `retain_active` | 1 | `satisfied` | +| `health_check_observability_active` | `retain_active` | 1 | `satisfied` | +| `health_check_policy_active` | `retain_active` | 1 | `satisfied` | +| `preflight_rules_removed` | `removed` | 0 | `not_applicable` | +| `checkpoint_service_support_removed` | `removed` | 0 | `not_applicable` | +| `checkpoint_state_codec_removed` | `removed` | 0 | `not_applicable` | +| `fsm_helper_active` | `retain_active` | 10 | `satisfied` | +| `runner_merge_stage_flow_removed` | `removed` | 0 | `not_applicable` | +| `column_priority_orderer_active` | `retain_active` | 2 | `satisfied` | +| `merger_input_mixin_active` | `retain_active` | 2 | `satisfied` | +| `runner_support_flow_active` | `retain_active` | 1 | `satisfied` | +| `runner_support_mixin_active` | `retain_active` | 1 | `satisfied` | +| `runner_support_policy_active` | `retain_active` | 1 | `satisfied` | +| `runner_support_runtime_active` | `retain_active` | 1 | `satisfied` | +| `runner_support_types_active` | `retain_active` | 4 | `satisfied` | +| `runtime_models_active` | `retain_active` | 38 | `satisfied` | +| `runtime_wiring_api_active` | `retain_active` | 14 | `satisfied` | + +## Repo-wide Zero-import Candidates + +| Module | Disposition | Path | +| --- | --- | --- | +| `bioetl.__main__` | `retain_module_entrypoint` | `src/bioetl/__main__.py` | +| `bioetl.application.core.batch_execution_lifecycle` | `retain_public_facade` | `src/bioetl/application/core/batch_execution_lifecycle.py` | +| `bioetl.application.core.batch_execution_run_service` | `retain_public_facade` | `src/bioetl/application/core/batch_execution_run_service.py` | +| `bioetl.application.core.batch_execution_state_service` | `retain_public_facade` | `src/bioetl/application/core/batch_execution_state_service.py` | +| `bioetl.application.core.pipeline_service_protocols` | `retain_public_facade` | `src/bioetl/application/core/pipeline_service_protocols.py` | +| `bioetl.application.pipelines.common.blocks` | `retain_dynamic_entrypoint` | `src/bioetl/application/pipelines/common/blocks.py` | +| `bioetl.application.pipelines.common.publication_strategies` | `retain_canonical_owner_module` | `src/bioetl/application/pipelines/common/publication_strategies.py` | +| `bioetl.application.pipelines.pubmed.strategies` | `retain_canonical_owner_module` | `src/bioetl/application/pipelines/pubmed/strategies.py` | +| `bioetl.application.services._checkpoint_compatibility_runtime_core` | `retain_canonical_owner_module` | `src/bioetl/application/services/_checkpoint_compatibility_runtime_core.py` | +| `bioetl.application.services.control_plane._run_manifest_diagnostics_identity` | `retain_canonical_owner_module` | `src/bioetl/application/services/control_plane/_run_manifest_diagnostics_identity.py` | +| `bioetl.composition.bootstrap.cli.adr` | `retain_dynamic_entrypoint` | `src/bioetl/composition/bootstrap/cli/adr.py` | +| `bioetl.composition.bootstrap.cli.control_plane_lifecycle` | `retain_dynamic_entrypoint` | `src/bioetl/composition/bootstrap/cli/control_plane_lifecycle.py` | +| `bioetl.domain.behavior._dq_serializer_html._renderers` | `retain_canonical_owner_module` | `src/bioetl/domain/behavior/_dq_serializer_html/_renderers.py` | +| `bioetl.domain.entities.bioactivity._entity` | `retain_canonical_owner_module` | `src/bioetl/domain/entities/bioactivity/_entity.py` | +| `bioetl.domain.normalization._pubchem_standardization_catalog` | `retain_canonical_owner_module` | `src/bioetl/domain/normalization/_pubchem_standardization_catalog.py` | +| `bioetl.domain.ports.data_normalization` | `retain_canonical_owner_module` | `src/bioetl/domain/ports/data_normalization.py` | +| `bioetl.domain.ports.data_source` | `retain_canonical_owner_module` | `src/bioetl/domain/ports/data_source.py` | +| `bioetl.domain.ports.delta_reader` | `retain_canonical_owner_module` | `src/bioetl/domain/ports/delta_reader.py` | +| `bioetl.domain.ports.export` | `retain_canonical_owner_module` | `src/bioetl/domain/ports/export.py` | +| `bioetl.domain.ports.filtering` | `retain_canonical_owner_module` | `src/bioetl/domain/ports/filtering.py` | +| `bioetl.domain.ports.idmapping` | `retain_canonical_owner_module` | `src/bioetl/domain/ports/idmapping.py` | +| `bioetl.domain.ports.logger_port` | `retain_canonical_owner_module` | `src/bioetl/domain/ports/logger_port.py` | +| `bioetl.domain.ports.pii` | `retain_canonical_owner_module` | `src/bioetl/domain/ports/pii.py` | +| `bioetl.domain.ports.publication_strategy` | `retain_canonical_owner_module` | `src/bioetl/domain/ports/publication_strategy.py` | +| `bioetl.domain.ports.resilience` | `retain_canonical_owner_module` | `src/bioetl/domain/ports/resilience.py` | +| `bioetl.domain.ports.serialization` | `retain_canonical_owner_module` | `src/bioetl/domain/ports/serialization.py` | +| `bioetl.domain.transformations.drift` | `retain_canonical_owner_module` | `src/bioetl/domain/transformations/drift.py` | +| `bioetl.domain.transformations.quality` | `retain_canonical_owner_module` | `src/bioetl/domain/transformations/quality.py` | +| `bioetl.domain.types.gold_contracts` | `retain_canonical_owner_module` | `src/bioetl/domain/types/gold_contracts.py` | +| `bioetl.domain.types.gold_schema_policy` | `retain_canonical_owner_module` | `src/bioetl/domain/types/gold_schema_policy.py` | +| `bioetl.infrastructure.export.export_catalog_adapter` | `retain_canonical_owner_module` | `src/bioetl/infrastructure/export/export_catalog_adapter.py` | +| `bioetl.infrastructure.export.export_writer_adapter` | `retain_canonical_owner_module` | `src/bioetl/infrastructure/export/export_writer_adapter.py` | +| `bioetl.infrastructure.storage.bronze.metadata_builders` | `retain_canonical_owner_module` | `src/bioetl/infrastructure/storage/bronze/metadata_builders.py` | +| `bioetl.infrastructure.storage.silver.arrow_mixin` | `retain_canonical_owner_module` | `src/bioetl/infrastructure/storage/silver/arrow_mixin.py` | +| `bioetl.infrastructure.storage.silver.dtos` | `retain_canonical_owner_module` | `src/bioetl/infrastructure/storage/silver/dtos.py` | +| `bioetl.infrastructure.storage.silver.operations.metadata_finalization_support` | `retain_canonical_owner_module` | `src/bioetl/infrastructure/storage/silver/operations/metadata_finalization_support.py` | +| `bioetl.interfaces.cli.commands.archive` | `retain_dynamic_entrypoint` | `src/bioetl/interfaces/cli/commands/archive.py` | +| `bioetl.interfaces.cli.commands.cleanup` | `retain_dynamic_entrypoint` | `src/bioetl/interfaces/cli/commands/cleanup.py` | +| `bioetl.interfaces.cli.commands.config_dq` | `retain_dynamic_entrypoint` | `src/bioetl/interfaces/cli/commands/config_dq.py` | +| `bioetl.interfaces.cli.commands.debug` | `retain_dynamic_entrypoint` | `src/bioetl/interfaces/cli/commands/debug.py` | +| `bioetl.interfaces.cli.commands.lock` | `retain_dynamic_entrypoint` | `src/bioetl/interfaces/cli/commands/lock.py` | +| `bioetl.interfaces.cli.commands.vacuum` | `retain_dynamic_entrypoint` | `src/bioetl/interfaces/cli/commands/vacuum.py` | +| `bioetl.interfaces.cli.commands.domains.maintenance.control_plane_lifecycle` | `retain_dynamic_entrypoint` | `src/bioetl/interfaces/cli/commands/domains/maintenance/control_plane_lifecycle.py` | diff --git a/reports/quality/module-coverage-inventory.json b/reports/quality/module-coverage-inventory.json index 9873948bf9..9e76171799 100644 --- a/reports/quality/module-coverage-inventory.json +++ b/reports/quality/module-coverage-inventory.json @@ -1,23 +1,23 @@ { "canonical_coverage_lane": "coverage-verify", "coverage_xml_path": "reports/coverage/coverage.xml", - "coverage_xml_sha256": "31aeb607e2804045bdce7d70fa4dd025c1065a5eaa7101c7b9a6e77eecd47f82", + "coverage_xml_sha256": null, "generated_by": "scripts/engineering/qa/report_module_coverage_inventory.py", - "measurement_mode": "coverage_xml", + "measurement_mode": "source_tree_only", "modules": [ { - "coverage_percent": 100.0, - "coverage_status": "fully_covered", - "covered_lines": 3, - "executable_lines": 3, - "missing_lines": 0, + "coverage_percent": null, + "coverage_status": "coverage_xml_missing", + "covered_lines": null, + "executable_lines": null, + "missing_lines": null, "module": "bioetl", "path": "src/bioetl/__init__.py", "source_lines": 7 }, { "coverage_percent": null, - "coverage_status": "unmeasured", + "coverage_status": "coverage_xml_missing", 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"entries.composite.molecule.rule_bundle_version", + "entries.composite.publication.dq_policy_ref", + "entries.composite.publication.identity", + "entries.composite.publication.identity.dq_policy_ref", + "entries.composite.publication.identity.normalization_profile_hash", + "entries.composite.publication.identity.normalization_profile_ref", + "entries.composite.publication.identity.normalization_profile_version", + "entries.composite.publication.identity.rule_bundle_version", + "entries.composite.publication.normalization_profile_hash", + "entries.composite.publication.normalization_profile_ref", + "entries.composite.publication.normalization_profile_version", + "entries.composite.publication.published_artifacts", + "entries.composite.publication.rule_bundle_version", + "entries.composite.target.dq_policy_ref", + "entries.composite.target.identity", + "entries.composite.target.identity.dq_policy_ref", + "entries.composite.target.identity.normalization_profile_hash", + "entries.composite.target.identity.normalization_profile_ref", + "entries.composite.target.identity.normalization_profile_version", + "entries.composite.target.identity.rule_bundle_version", + "entries.composite.target.normalization_profile_hash", + "entries.composite.target.normalization_profile_ref", + "entries.composite.target.normalization_profile_version", + "entries.composite.target.published_artifacts", + "entries.composite.target.rule_bundle_version", + "entries.crossref.publication.dq_policy_ref", + "entries.crossref.publication.identity", + "entries.crossref.publication.identity.dq_policy_ref", + "entries.crossref.publication.identity.normalization_profile_hash", + "entries.crossref.publication.identity.normalization_profile_ref", + "entries.crossref.publication.identity.normalization_profile_version", + "entries.crossref.publication.identity.rule_bundle_version", + "entries.crossref.publication.normalization_profile_hash", + "entries.crossref.publication.normalization_profile_ref", + "entries.crossref.publication.normalization_profile_version", + "entries.crossref.publication.published_artifacts", + "entries.crossref.publication.rule_bundle_version", + "entries.openalex.publication.dq_policy_ref", + "entries.openalex.publication.identity", + "entries.openalex.publication.identity.dq_policy_ref", + "entries.openalex.publication.identity.normalization_profile_hash", + "entries.openalex.publication.identity.normalization_profile_ref", + "entries.openalex.publication.identity.normalization_profile_version", + "entries.openalex.publication.identity.rule_bundle_version", + "entries.openalex.publication.normalization_profile_hash", + "entries.openalex.publication.normalization_profile_ref", + "entries.openalex.publication.normalization_profile_version", + "entries.openalex.publication.published_artifacts", + "entries.openalex.publication.rule_bundle_version", + "entries.pubchem.compound.dq_policy_ref", + "entries.pubchem.compound.identity", + "entries.pubchem.compound.identity.dq_policy_ref", + "entries.pubchem.compound.identity.normalization_profile_hash", + "entries.pubchem.compound.identity.normalization_profile_ref", + "entries.pubchem.compound.identity.normalization_profile_version", + "entries.pubchem.compound.identity.rule_bundle_version", + "entries.pubchem.compound.normalization_profile_hash", + "entries.pubchem.compound.normalization_profile_ref", + "entries.pubchem.compound.normalization_profile_version", + "entries.pubchem.compound.published_artifacts", + "entries.pubchem.compound.rule_bundle_version", + "entries.pubmed.publication.dq_policy_ref", + "entries.pubmed.publication.identity", + "entries.pubmed.publication.identity.dq_policy_ref", + "entries.pubmed.publication.identity.normalization_profile_hash", + "entries.pubmed.publication.identity.normalization_profile_ref", + "entries.pubmed.publication.identity.normalization_profile_version", + "entries.pubmed.publication.identity.rule_bundle_version", + "entries.pubmed.publication.normalization_profile_hash", + "entries.pubmed.publication.normalization_profile_ref", + "entries.pubmed.publication.normalization_profile_version", + "entries.pubmed.publication.published_artifacts", + "entries.pubmed.publication.rule_bundle_version", + "entries.semanticscholar.publication.dq_policy_ref", + "entries.semanticscholar.publication.identity", + "entries.semanticscholar.publication.identity.dq_policy_ref", + "entries.semanticscholar.publication.identity.normalization_profile_hash", + "entries.semanticscholar.publication.identity.normalization_profile_ref", + "entries.semanticscholar.publication.identity.normalization_profile_version", + "entries.semanticscholar.publication.identity.rule_bundle_version", + "entries.semanticscholar.publication.normalization_profile_hash", + "entries.semanticscholar.publication.normalization_profile_ref", + "entries.semanticscholar.publication.normalization_profile_version", + "entries.semanticscholar.publication.published_artifacts", + "entries.semanticscholar.publication.rule_bundle_version", + "entries.uniprot.idmapping.dq_policy_ref", + "entries.uniprot.idmapping.identity", + "entries.uniprot.idmapping.identity.dq_policy_ref", + "entries.uniprot.idmapping.identity.normalization_profile_hash", + "entries.uniprot.idmapping.identity.normalization_profile_ref", + "entries.uniprot.idmapping.identity.normalization_profile_version", + "entries.uniprot.idmapping.identity.rule_bundle_version", + "entries.uniprot.idmapping.normalization_profile_hash", + "entries.uniprot.idmapping.normalization_profile_ref", + "entries.uniprot.idmapping.normalization_profile_version", + "entries.uniprot.idmapping.published_artifacts", + "entries.uniprot.idmapping.rule_bundle_version", + "entries.uniprot.protein.dq_policy_ref", + "entries.uniprot.protein.identity", + "entries.uniprot.protein.identity.dq_policy_ref", + "entries.uniprot.protein.identity.normalization_profile_hash", + "entries.uniprot.protein.identity.normalization_profile_ref", + "entries.uniprot.protein.identity.normalization_profile_version", + "entries.uniprot.protein.identity.rule_bundle_version", + "entries.uniprot.protein.normalization_profile_hash", + "entries.uniprot.protein.normalization_profile_ref", + "entries.uniprot.protein.normalization_profile_version", + "entries.uniprot.protein.published_artifacts", + "entries.uniprot.protein.rule_bundle_version" + ] + }, + { + "path": "configs/base/pipeline.yaml", + "role": "medallion_defaults_and_contract_field_defaults", + "semantic_surface_count": 9, + "semantic_surfaces": [ + "contract_defaults", + "contract_defaults.hash_exclude", + "contract_defaults.hash_include", + "dq_overrides", + "filter_defaults", + "sink.gold.scd_config", + "sink.gold.sort_by", + "sink.silver.sort_by", + "technical_primary_key" + ] + }, + { + "path": "configs/base/quality.yaml", + "role": "global_dq_defaults", + "semantic_surface_count": 5, + "semantic_surfaces": [ + "common_cross_field_validations", + "common_field_validations", + "invalid_record_policy", + "strict_validation", + "thresholds" + ] + } + ], + "semantic_surface_count": 328 +} diff --git a/reports/semantic_pipeline_audit/critical_inconsistencies_2026-05-21.md b/reports/semantic_pipeline_audit/critical_inconsistencies_2026-05-21.md new file mode 100644 index 0000000000..97dc6b64e8 --- /dev/null +++ b/reports/semantic_pipeline_audit/critical_inconsistencies_2026-05-21.md @@ -0,0 +1,15 @@ +# Semantic Pipeline Critical Inconsistencies + +Generated: `2026-05-21` + +## Summary + +- CRITICAL: `0` +- HIGH: `0` +- MEDIUM: `0` +- LOW: `3129` + +## CRITICAL And HIGH Rows + +| Risk | Cluster | Pipeline A | Field A | Pipeline B | Field B | Normalization | Validation | Typing | Row Key | +| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | diff --git a/reports/semantic_pipeline_audit/recommended_canonical_fields_2026-05-21.csv b/reports/semantic_pipeline_audit/recommended_canonical_fields_2026-05-21.csv new file mode 100644 index 0000000000..36b8bc27b3 --- /dev/null +++ b/reports/semantic_pipeline_audit/recommended_canonical_fields_2026-05-21.csv @@ -0,0 +1,284 @@ +cluster_id,canonical_field,semantic_status,member_count,rationale +canonical_smiles_identifier,canonical_smiles,PARTIAL,5,"Canonical SMILES is a structure-level identifier. ChEMBL molecule, PubChem compound, and composite molecule use compatible structure normalization; ChEMBL activity keeps the value as inherited molecule context rather than molecule ownership." +chembl_assay_identifier,assay_id,EXACT,4,"Internal config, DQ, join and contract surfaces use assay_id. Provider-native ChEMBL input filters retain assay_chembl_id as the external column name and normalize it at the transformer ingestion boundary." +chembl_molecule_identifier,molecule_id,EXACT,5,"Internal schema, merge and DQ surfaces use molecule_id for ChEMBL-seeded molecule identity. PubChem CID is a provider-local identifier family and must not be treated as the same business identifier. Provider-native ChEMBL filters still accept molecule_chembl_id and normalize it at the transformer ingestion boundary." +chembl_target_identifier,target_chembl_id,PARTIAL,7,Field-name identity/alias rule for business identifiers and publication anchors. +doi_identifier,doi,EXACT,6,"doi is already the canonical identifier name across provider, composite and Gold surfaces." +inchi_key_identifier,inchi_key,PARTIAL,3,"InChIKey is a structure-level identifier shared by ChEMBL molecule, PubChem compound, and composite molecule join paths with canonical uppercase normalization." +molecule_hba_count,hba_count,EXACT,2,PubChem h_bond_acceptor_count and legacy hba map to the canonical hba_count descriptor. +molecule_hbd_count,hbd_count,EXACT,2,PubChem h_bond_donor_count maps to the canonical hbd_count descriptor. +molecule_inchi_key,inchi_key,EXACT,3,InChIKey is the primary molecule composite join key and is canonical across ChEMBL/PubChem surfaces. +molecule_logp,logp,EXACT,3,PubChem xlogp maps to canonical logp while source-specific method semantics remain documented in molecule contracts. +molecule_molecular_weight,molecular_weight,EXACT,3,molecular_weight is canonical across ChEMBL/PubChem molecule descriptor surfaces. +molecule_polar_surface_area,polar_surface_area,EXACT,3,PubChem tpsa maps to the canonical polar_surface_area descriptor. +molecule_standard_inchi,standard_inchi,EXACT,4,PubChem inchi maps to standard_inchi for composite molecule merge and Gold-facing contracts. +pmc_identifier,pmc_id,PARTIAL,8,Field-name identity/alias rule for business identifiers and publication anchors. +pubchem_cid_identifier,pubchem_cid,EXACT,1,PubChem compound surfaces currently persist CID under the internal field name molecule_id. This identifier is provider-local and is intentionally not semantically identical to the ChEMBL molecule_id family. +publication_abstract,abstract,EXACT,6,"All publication-family entity configs normalize abstract through the same canonical field name, while composite publication inherits the upstream canonical abstract surface." +publication_affiliation_list,affiliation_list,EXACT,4,Provider affiliations fields normalize to affiliation_list. +publication_affiliation_structured,affiliation_structured,EXACT,2,PubMed structured_affiliations normalize to affiliation_structured. +publication_authors,authors,EXACT,6,Publication-family pipelines persist authors under one canonical field name and composite publication inherits that canonical author payload without introducing a competing alias surface. +publication_citations_made,citations_made,EXACT,5,Provider reference_count fields normalize to citations_made. +publication_citations_received,citations_received,EXACT,4,Provider citation_count fields normalize to citations_received. +publication_issue,issue,EXACT,6,issue is already shared across publication-family pipelines and participates in composite publication cross-source validation under one canonical field name. +publication_journal,journal,EXACT,3,PubMed journal_title is normalized to the canonical journal field. +publication_journal_name_short,journal_name_short,EXACT,3,Provider-specific abbreviated journal fields normalize to journal_name_short. +publication_page_first,page_first,EXACT,5,Provider first_page fields normalize to page_first. +publication_page_last,page_last,EXACT,5,Provider last_page fields normalize to page_last. +publication_page_range,page_range,EXACT,3,Provider pages fields normalize to page_range. +publication_publication_class,publication_class,EXACT,6,publication_class is an owner-approved cross-provider taxonomy layer used consistently by publication-family configs and inherited unchanged by composite publication. +publication_publication_date,publication_date,EXACT,6,"publication_date is normalized through the same canonical date policy across publication-family pipelines, and composite publication inherits the canonical field directly." +publication_publication_subclass,publication_subclass,EXACT,6,publication_subclass is governed as the shared detailed publication taxonomy across entity and composite publication surfaces. +publication_publication_type,publication_type,EXACT,5,Provider document/source type fields are normalized to publication_type before composite merge and Gold validation. +publication_publication_type_unified,publication_type_unified,EXACT,6,The harmonized publication_type_unified taxonomy is shared across publication-family pipelines and composite publication merge surfaces as the canonical cross-provider classification field. +publication_publication_year,publication_year,EXACT,7,Provider year fields are normalized to publication_year. Nullable integer to Gold number compatibility remains explicitly governed by contract tests. +publication_subject_fields,subject_fields,EXACT,2,SemanticScholar fields_of_study normalize to subject_fields and remain distinct from MeSH/topic clusters. +publication_subject_keywords,subject_keywords,EXACT,4,Provider keyword/subject arrays normalize to subject_keywords when they represent generic publication keywords. +publication_subject_mesh,subject_mesh,EXACT,2,PubMed mesh_terms normalize to subject_mesh and remain distinct from generic subject_keywords. +publication_subject_topics,subject_topics,EXACT,2,OpenAlex topics normalize to subject_topics. +publication_title,title,EXACT,6,All normalized publication configs and composite join paths use title. Historical provider-prefixed title aliases are retained only as migration references in registry/docs. +publication_volume,volume,EXACT,6,"volume is already the shared publication-family field name across entity configs, cross-source validation, and composite publication merge surfaces." +pubmed_identifier,pmid,EXACT,6,"PubMed provider input still arrives as pubmed_id, but normalized schema, join keys and DQ contracts use pmid." +shared_abstract_structured,abstract_structured,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_action_type_description,action_type_description,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_action_type_parent_type,action_type_parent_type,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_activity_comment,activity_comment,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_activity_id,activity_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_activity_properties,activity_properties,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_activity_regulation,activity_regulation,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_aidx,aidx,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_alternative_id,alternative_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_annotation_score,annotation_score,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_aromatic_ring_count,aromatic_ring_count,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_assay_category,assay_category,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_assay_cell_type,assay_cell_type,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_assay_classifications,assay_classifications,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_assay_description,assay_description,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_assay_group,assay_group,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_assay_organism,assay_organism,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_assay_parameters,assay_parameters,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_assay_pref_name,assay_pref_name,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_assay_strain,assay_strain,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_assay_subcellular_fraction,assay_subcellular_fraction,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_assay_taxonomy_id,assay_taxonomy_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_assay_test_type,assay_test_type,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_assay_tissue,assay_tissue,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_assay_type,assay_type,WEAK,4,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_assay_variant_accession,assay_variant_accession,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_assay_variant_mutation,assay_variant_mutation,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_atc_classifications,atc_classifications,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_author_count,author_count,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_author_details,author_details,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_author_h_indices,author_h_indices,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_author_keys,author_keys,WEAK,5,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_author_openalex_ids,author_openalex_ids,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_author_orcids,author_orcids,WEAK,5,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_author_s2_ids,author_s2_ids,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_authors_with_affiliations,authors_with_affiliations,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_availability_type,availability_type,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_bao_endpoint,bao_endpoint,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_bao_format,bao_format,WEAK,4,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_bao_format_iri,bao_format_iri,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_bao_format_mapping_status,bao_format_mapping_status,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_bao_label,bao_label,WEAK,4,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_bao_ontology_version,bao_ontology_version,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_black_box_warning,black_box_warning,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_catalytic_activity,catalytic_activity,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_cell_description,cell_description,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_cell_id,cell_id,EXACT,3,Same identifier-like field name appears across pipeline schemas. +shared_cell_name,cell_name,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_cell_source_organism,cell_source_organism,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_cell_source_taxonomy_id,cell_source_taxonomy_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_cell_source_tissue,cell_source_tissue,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_cell_type,cell_type,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_cellosaurus_id,cellosaurus_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_chembl_ids,chembl_ids,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_chembl_release,chembl_release,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_chemical_count,chemical_count,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_chemicals,chemicals,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_chirality,chirality,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_citation_contexts,citation_contexts,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_citation_subset,citation_subset,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_cl_lincs_id,cl_lincs_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_clo_id,clo_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_component_accessions,component_accessions,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_component_descriptions,component_descriptions,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_component_ids,component_ids,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_component_relationships,component_relationships,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_component_type,component_type,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_component_types,component_types,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_compound_key,compound_key,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_compound_name,compound_name,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_confidence_description,confidence_description,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_confidence_score,confidence_score,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_content_domain_crossmark_restriction,content_domain_crossmark_restriction,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_content_domain_domains,content_domain_domains,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_content_hash,content_hash,EXACT,26,Shared system/lineage field name across active pipeline schemas. +shared_corpus_id,corpus_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_country,country,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_creation_date,creation_date,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_cross_references,cross_references,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_data_validity_comment,data_validity_comment,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_data_validity_description,data_validity_description,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_databanks,databanks,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_date_completed,date_completed,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_date_revised,date_revised,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_dblp_id,dblp_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_disease_involvement,disease_involvement,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_dosed_ingredient,dosed_ingredient,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_downgraded,downgraded,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_dq_error,_dq_error,EXACT,21,Shared system/lineage field name across active pipeline schemas. +shared_dq_warn,_dq_warn,EXACT,21,Shared system/lineage field name across active pipeline schemas. +shared_drugbank_ids,drugbank_ids,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_efo_id,efo_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_efo_iri,efo_iri,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_efo_mapping_status,efo_mapping_status,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_efo_ontology_version,efo_ontology_version,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_entity_id,entity_id,EXACT,26,Shared system/lineage field name across active pipeline schemas. +shared_first_approval,first_approval,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_first_in_class,first_in_class,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_function_comment,function_comment,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_fwci,fwci,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_gene_primary,gene_primary,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_gene_symbols,gene_symbols,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_go_terms,go_terms,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_grant_count,grant_count,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_grants,grants,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_guidetopharmacology_ids,guidetopharmacology_ids,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_heavy_atom_count,heavy_atom_count,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_helm_notation,helm_notation,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_hierarchy_active_chembl_id,hierarchy_active_chembl_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_hierarchy_child_chembl_id,hierarchy_child_chembl_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_hierarchy_parent_chembl_id,hierarchy_parent_chembl_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_index,_index,EXACT,26,Shared system/lineage field name across active pipeline schemas. +shared_influential_citation_count,influential_citation_count,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_ingestion_ts,_ingestion_ts,EXACT,21,Shared system/lineage field name across active pipeline schemas. +shared_inorganic_flag,inorganic_flag,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_institution_country_codes,institution_country_codes,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_institution_ids,institution_ids,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_interpro_xrefs,interpro_xrefs,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_is_oa,is_oa,WEAK,5,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_is_retracted,is_retracted,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_isomeric_smiles,isomeric_smiles,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_issn,issn,WEAK,4,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_issn_electronic,issn_electronic,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_issn_list,issn_list,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_issn_print,issn_print,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_iupac_name,iupac_name,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_journal_iso_abbrev,journal_iso_abbrev,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_journal_issn_type,journal_issn_type,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_keyword_count,keyword_count,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_language,language,WEAK,5,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_license_url,license_url,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_ligand_efficiency_bei,ligand_efficiency_bei,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_ligand_efficiency_le,ligand_efficiency_le,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_ligand_efficiency_lle,ligand_efficiency_lle,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_ligand_efficiency_sei,ligand_efficiency_sei,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_logp_method,logp_method,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_lookup_method,_lookup_method,EXACT,9,Shared system/lineage field name across active pipeline schemas. +shared_mag_id,mag_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_manual_curation_flag,manual_curation_flag,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_mapping_status,mapping_status,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_max_phase,max_phase,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_medline_pgn,medline_pgn,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_mesh_heading_count,mesh_heading_count,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_molecular_formula,molecular_formula,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_molecule_hierarchy,molecule_hierarchy,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_molecule_pref_name,molecule_pref_name,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_molecule_synonyms,molecule_synonyms,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_molecule_type,molecule_type,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_natural_product,natural_product,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_nlm_unique_id,nlm_unique_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_oa_status,oa_status,WEAK,4,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_open_access_url,open_access_url,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_openalex_id,openalex_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_oral,oral,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_organism,organism,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_organism_common,organism_common,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_organism_scientific,organism_scientific,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_original_activity_id,original_activity_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_original_id,_original_id,EXACT,9,Shared system/lineage field name across active pipeline schemas. +shared_paper_id,paper_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_parent_molecule_id,parent_molecule_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_parenteral,parenteral,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_pathway,pathway,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_pchembl_value,pchembl_value,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_pdb_xrefs,pdb_xrefs,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_pfam_xrefs,pfam_xrefs,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_pipeline_stages,pipeline_stages,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_polymer_flag,polymer_flag,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_potential_duplicate,potential_duplicate,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_pref_name,pref_name,WEAK,6,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_primary_component_id,primary_component_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_primary_topic,primary_topic,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_prodrug,prodrug,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_protein_classification_id,protein_classification_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_protein_classification_ids,protein_classification_ids,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_protein_existence,protein_existence,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_protein_name,protein_name,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_pub_date,pub_date,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_pub_day,pub_day,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_pub_month,pub_month,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_publication_id,publication_id,EXACT,8,Same identifier-like field name appears across pipeline schemas. +shared_publication_status,publication_status,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_publication_types,publication_types,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_publisher,publisher,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_qudt_units,qudt_units,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_reactome_xrefs,reactome_xrefs,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_record_id,record_id,EXACT,3,Same identifier-like field name appears across pipeline schemas. +shared_references,references,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_relationship_description,relationship_description,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_relationship_type,relationship_type,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_reviewed,reviewed,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_ror_ids,ror_ids,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_rotatable_bond_count,rotatable_bond_count,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_run_id,_run_id,EXACT,21,Shared system/lineage field name across active pipeline schemas. +shared_run_type,_run_type,EXACT,21,Shared system/lineage field name across active pipeline schemas. +shared_sequence_length,sequence_length,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_sequence_mass,sequence_mass,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_source,_source,EXACT,10,Shared system/lineage field name across active pipeline schemas. +shared_source_batch_id,_source_batch_id,EXACT,21,Shared system/lineage field name across active pipeline schemas. +shared_species_group_flag,species_group_flag,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_src_assay_id,src_assay_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_src_compound_id,src_compound_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_src_id,src_id,EXACT,7,Same identifier-like field name appears across pipeline schemas. +shared_standard_flag,standard_flag,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_standard_relation,standard_relation,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_standard_text_value,standard_text_value,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_standard_type,standard_type,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_standard_units,standard_units,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_standard_upper_value,standard_upper_value,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_standard_value,standard_value,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_standardized_inchi_key,standardized_inchi_key,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_structure_parent_key,structure_parent_key,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_structure_type,structure_type,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_subcellular_location,subcellular_location,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_subunit,subunit,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_target_component_synonyms,target_component_synonyms,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_target_organism,target_organism,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_target_pref_name,target_pref_name,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_target_type,target_type,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_taxonomy_id,taxonomy_id,EXACT,6,Same identifier-like field name appears across pipeline schemas. +shared_text_value,text_value,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_therapeutic_flag,therapeutic_flag,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_tissue_id,tissue_id,EXACT,3,Same identifier-like field name appears across pipeline schemas. +shared_tissue_specificity,tissue_specificity,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_tldr,tldr,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_toid,toid,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_topical,topical,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_units,units,WEAK,3,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_uo_units,uo_units,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_upper_value,upper_value,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_usan_stem,usan_stem,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_usan_stem_definition,usan_stem_definition,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_usan_substem,usan_substem,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_usan_year,usan_year,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_variant_accession,variant_accession,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_variant_isoform,variant_isoform,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_variant_mutation,variant_mutation,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_variant_organism,variant_organism,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_variant_sequence,variant_sequence,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_variant_sequence_json,variant_sequence_json,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +shared_variant_taxonomy_id,variant_taxonomy_id,EXACT,2,Same identifier-like field name appears across pipeline schemas. +shared_withdrawn_flag,withdrawn_flag,WEAK,2,"Same field name appears across pipelines, but no canonical registry or mapping module proves business identity." +uniprot_accession_identifier,accession,PARTIAL,4,"UniProt accession identity is PARTIAL across ChEMBL component evidence, UniProt idmapping output, composite target chaining, and UniProt protein primary keys. Direct joins use idmapping/protein accessions; ChEMBL component accession remains lineage evidence." diff --git a/reports/semantic_pipeline_audit/semantic_cluster_registry_2026-05-21.json b/reports/semantic_pipeline_audit/semantic_cluster_registry_2026-05-21.json new file mode 100644 index 0000000000..8ce2cf7b29 --- /dev/null +++ b/reports/semantic_pipeline_audit/semantic_cluster_registry_2026-05-21.json @@ -0,0 +1,27876 @@ +{ + "clusters": [ + { + "aliases": [ + "canonical_smiles" + ], + "canonical_field": "canonical_smiles", + "cluster_id": "canonical_smiles_identifier", + "member_count": 5, + "members": [ + { + "config_path": "configs/entities/chembl/activity.yaml", + "cross_rules": [], + "dq_coverage": "custom:error", + "dq_rules": [ + "custom:error" + ], + "entity": "activity", + "field": "canonical_smiles", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/chembl_activity_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_canonical_smiles", + "pipeline": "chembl_activity", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "content_hash_source" + ], + "semantic_category": "free_text", + "strictness": "normalization_only" + }, + { + "config_path": "configs/entities/chembl/molecule.yaml", + "cross_rules": [ + "entity_cross_field_validations:structure_completeness" + ], + "dq_coverage": "custom:error", + "dq_rules": [ + "custom:error" + ], + "entity": "molecule", + "field": "canonical_smiles", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/chembl_molecule_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_canonical_smiles", + "pipeline": "chembl_molecule", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "content_hash_source", + "cross_field_validation" + ], + "semantic_category": "free_text", + "strictness": "normalization_only" + }, + { + "config_path": "configs/composites/activity.yaml", + "cross_rules": [], + "dq_coverage": "not_applicable", + "dq_rules": [], + "entity": "activity", + "field": "canonical_smiles", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/composite_activity_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "molecule_context", + "normalization_source": "upstream_inherited", + "normalizer": "none", + "pipeline": "composite_activity", + "pipeline_kind": "composite", + "provider": "composite", + "roles": [], + "semantic_category": "upstream_inherited", + "strictness": "upstream_inherited" + }, + { + "config_path": "configs/composites/molecule.yaml", + "cross_rules": [], + "dq_coverage": "not_applicable", + "dq_rules": [], + "entity": "molecule", + "field": "canonical_smiles", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/composite_molecule_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "structure", + "normalization_source": "composite_join_key_policy", + "normalizer": "join_key_policy", + "pipeline": "composite_molecule", + "pipeline_kind": "composite", + "provider": "composite", + "roles": [ + "composite_enricher_join_key", + "field_source_tracking", + "join_to:pubchem_compound", + "lineage_anchor", + "merge_priority", + "seed_output_key" + ], + "semantic_category": "join_key_policy", + "strictness": "join_key_policy" + }, + { + "config_path": "configs/entities/pubchem/compound.yaml", + "cross_rules": [ + "entity_cross_field_validations:structure_present" + ], + "dq_coverage": "custom:error", + "dq_rules": [ + "custom:error" + ], + "entity": "compound", + "field": "canonical_smiles", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/pubchem_compound_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_canonical_smiles", + "pipeline": "pubchem_compound", + "pipeline_kind": "entity", + "provider": "pubchem", + "roles": [ + "FK", + "composite_join_key_for:composite_molecule", + "content_hash_source", + "cross_field_validation" + ], + "semantic_category": "free_text", + "strictness": "normalization_only" + } + ], + "pipeline_count": 5, + "rationale": "Canonical SMILES is a structure-level identifier. ChEMBL molecule, PubChem compound, and composite molecule use compatible structure normalization; ChEMBL activity keeps the value as inherited molecule context rather than molecule ownership.", + "review": { + "expires_on": "2026-11-15", + "issue": 4133, + "owner": "BioETL Team", + "rationale": "PARTIAL identity clusters are intentionally not promoted to EXACT because they mix provider-owned identifiers, composite lineage projections, and join/reference anchors. Each listed cluster is valid only with explicit join/lineage semantics in the pair matrix and semantic anchor gates.\n", + "review_id": "partial_identity_policy_review" + }, + "semantic_status": "PARTIAL", + "source": "identifier_alias_rule" + }, + { + "aliases": [ + "assay_chembl_id" + ], + "canonical_field": "assay_id", + "cluster_id": "chembl_assay_identifier", + "member_count": 4, + "members": [ + { + "config_path": "configs/entities/chembl/activity.yaml", + "cross_rules": [], + "dq_coverage": "pattern:error", + "dq_rules": [ + "pattern:error" + ], + "entity": "activity", + "field": "assay_id", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/chembl_activity_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_chembl_id", + "pipeline": "chembl_activity", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "content_hash_source" + ], + "semantic_category": "reference_identifier", + "strictness": "canonical_identifier" + }, + { + "config_path": "configs/entities/chembl/assay.yaml", + "cross_rules": [ + "entity_cross_field_validations:assay_identifiable" + ], + "dq_coverage": "pattern:error,required:error", + "dq_rules": [ + "pattern:error,required:error" + ], + "entity": "assay", + "field": "assay_id", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/chembl_assay_v1.0.json", + "gold_required": true, + "gold_type": "\"string\"", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_chembl_id", + "pipeline": "chembl_assay", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "PK", + "content_hash_source", + "contract_pk", + "cross_field_validation", + "deduplication_key", + "gold_required", + "merge_key" + ], + "semantic_category": "reference_identifier", + "strictness": "canonical_identifier" + }, + { + "config_path": "configs/composites/activity.yaml", + "cross_rules": [], + "dq_coverage": "not_applicable", + "dq_rules": [], + "entity": "activity", + "field": "assay_id", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/composite_activity_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "identifiers", + "normalization_source": "upstream_inherited", + "normalizer": "none", + "pipeline": "composite_activity", + "pipeline_kind": "composite", + "provider": "composite", + "roles": [ + "lineage_anchor", + "seed_output_key" + ], + "semantic_category": "upstream_inherited", + "strictness": "upstream_inherited" + }, + { + "config_path": "configs/composites/assay.yaml", + "cross_rules": [], + "dq_coverage": "not_applicable", + "dq_rules": [], + "entity": "assay", + "field": "assay_id", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/composite_assay_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "identifiers", + "normalization_source": "upstream_inherited", + "normalizer": "none", + "pipeline": "composite_assay", + "pipeline_kind": "composite", + "provider": "composite", + "roles": [ + "lineage_anchor", + "seed_output_key" + ], + "semantic_category": "upstream_inherited", + "strictness": "upstream_inherited" + } + ], + "pipeline_count": 4, + "rationale": "Internal config, DQ, join and contract surfaces use assay_id. Provider-native ChEMBL input filters retain assay_chembl_id as the external column name and normalize it at the transformer ingestion boundary.", + "semantic_status": "EXACT", + "source": "canonical_registry" + }, + { + "aliases": [ + "molecule_chembl_id" + ], + "canonical_field": "molecule_id", + "cluster_id": "chembl_molecule_identifier", + "member_count": 5, + "members": [ + { + "config_path": "configs/entities/chembl/activity.yaml", + "cross_rules": [], + "dq_coverage": "pattern:error", + "dq_rules": [ + "pattern:error" + ], + "entity": "activity", + "field": "molecule_id", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/chembl_activity_v1.0.json", + "gold_required": true, + "gold_type": "\"string\"", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_chembl_id", + "pipeline": "chembl_activity", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "content_hash_source", + "gold_required" + ], + "semantic_category": "reference_identifier", + "strictness": "canonical_identifier" + }, + { + "config_path": "configs/entities/chembl/compound_record.yaml", + "cross_rules": [ + "entity_cross_field_validations:record_linkage" + ], + "dq_coverage": "pattern:error,pattern:error", + "dq_rules": [ + "pattern:error,pattern:error" + ], + "entity": "compound_record", + "field": "molecule_id", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/chembl_compound_record_v1.0.json", + "gold_required": true, + "gold_type": "\"string\"", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_chembl_id", + "pipeline": "chembl_compound_record", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "FK", + "composite_join_key_for:composite_activity", + "content_hash_source", + "cross_field_validation", + "gold_required" + ], + "semantic_category": "reference_identifier", + "strictness": "canonical_identifier" + }, + { + "config_path": "configs/entities/chembl/molecule.yaml", + "cross_rules": [], + "dq_coverage": "pattern:error,required:error", + "dq_rules": [ + "pattern:error,required:error" + ], + "entity": "molecule", + "field": "molecule_id", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/chembl_molecule_v1.0.json", + "gold_required": true, + "gold_type": "\"string\"", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_chembl_id", + "pipeline": "chembl_molecule", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "PK", + "content_hash_source", + "contract_pk", + "deduplication_key", + "gold_required", + "merge_key" + ], + "semantic_category": "reference_identifier", + "strictness": "canonical_identifier" + }, + { + "config_path": "configs/composites/activity.yaml", + "cross_rules": [], + "dq_coverage": "not_applicable", + "dq_rules": [], + "entity": "activity", + "field": "molecule_id", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/composite_activity_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "identifiers", + "normalization_source": "composite_join_key_policy", + "normalizer": "join_key_policy", + "pipeline": "composite_activity", + "pipeline_kind": "composite", + "provider": "composite", + "roles": [ + "composite_dependency_join_key", + "field_source_tracking", + "join_to:chembl_compound_record", + "lineage_anchor", + "merge_priority", + "seed_output_key" + ], + "semantic_category": "join_key_policy", + "strictness": "join_key_policy" + }, + { + "config_path": "configs/composites/molecule.yaml", + "cross_rules": [], + "dq_coverage": "not_applicable", + "dq_rules": [], + "entity": "molecule", + "field": "molecule_id", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/composite_molecule_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "identifiers", + "normalization_source": "upstream_inherited", + "normalizer": "none", + "pipeline": "composite_molecule", + "pipeline_kind": "composite", + "provider": "composite", + "roles": [ + "lineage_anchor", + "seed_output_key" + ], + "semantic_category": "upstream_inherited", + "strictness": "upstream_inherited" + } + ], + "pipeline_count": 5, + "rationale": "Internal schema, merge and DQ surfaces use molecule_id for ChEMBL-seeded molecule identity. PubChem CID is a provider-local identifier family and must not be treated as the same business identifier. Provider-native ChEMBL filters still accept molecule_chembl_id and normalize it at the transformer ingestion boundary.", + "semantic_status": "EXACT", + "source": "canonical_registry" + }, + { + "aliases": [ + "target_chembl_id", + "target_id" + ], + "canonical_field": "target_chembl_id", + "cluster_id": "chembl_target_identifier", + "member_count": 7, + "members": [ + { + "config_path": "configs/entities/chembl/activity.yaml", + "cross_rules": [], + "dq_coverage": "pattern:error", + "dq_rules": [ + "pattern:error" + ], + "entity": "activity", + "field": "target_id", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/chembl_activity_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_chembl_id", + "pipeline": "chembl_activity", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "content_hash_source" + ], + 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Each listed cluster is valid only with explicit join/lineage semantics in the pair matrix and semantic anchor gates.\n", + "review_id": "partial_identity_policy_review" + }, + "semantic_status": "PARTIAL", + "source": "identifier_alias_rule" + }, + { + "aliases": [], + "canonical_field": "doi", + "cluster_id": "doi_identifier", + "member_count": 6, + "members": [ + { + "config_path": "configs/entities/chembl/publication.yaml", + "cross_rules": [], + "dq_coverage": "pattern:error", + "dq_rules": [ + "pattern:error" + ], + "entity": "publication", + "field": "doi", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/chembl_publication_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "", + "normalization_source": "profile", + "normalizer": "normalize_profile_doi", + "pipeline": "chembl_publication", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "content_hash_source" + ], + "semantic_category": 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cross-source validation, and composite publication merge surfaces.", + "semantic_status": "EXACT", + "source": "canonical_registry" + }, + { + "aliases": [ + "pubmed_id" + ], + "canonical_field": "pmid", + "cluster_id": "pubmed_identifier", + "member_count": 6, + "members": [ + { + "config_path": "configs/entities/chembl/publication.yaml", + "cross_rules": [], + "dq_coverage": "pattern:error", + "dq_rules": [ + "pattern:error" + ], + "entity": "publication", + "field": "pmid", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/chembl_publication_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "", + "normalization_source": "profile", + "normalizer": "normalize_profile_pmid", + "pipeline": "chembl_publication", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "content_hash_source" + ], + "semantic_category": "reference_identifier", + "strictness": "canonical_identifier" + }, + { + "config_path": "configs/composites/publication.yaml", + "cross_rules": [ + "cross_validation:openalex_publication:exact", + "cross_validation:pubmed_publication:exact", + "cross_validation:semanticscholar_publication:exact" + ], + "dq_coverage": "not_applicable", + "dq_rules": [], + "entity": "publication", + "field": "pmid", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/composite_publication_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "provider_ids", + "normalization_source": "composite_join_key_policy", + "normalizer": "join_key_policy", + "pipeline": "composite_publication", + "pipeline_kind": "composite", + "provider": "composite", + "roles": [ + "composite_enricher_join_key", + "cross_source_validation", + "join_policy:publication_identity", + "join_to:pubmed_publication", + "lineage_anchor", + "primary_composite_join_key", + "seed_output_key" + ], + "semantic_category": "join_key_policy", + "strictness": "join_key_policy" + }, + { + "config_path": "configs/entities/crossref/publication.yaml", + "cross_rules": [], + "dq_coverage": "pattern:error", + "dq_rules": [ + "pattern:error" + ], + "entity": "publication", + "field": "pmid", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/crossref_publication_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "", + "normalization_source": "profile", + "normalizer": "normalize_profile_pmid", + "pipeline": "crossref_publication", + "pipeline_kind": "entity", + "provider": "crossref", + "roles": [ + "content_hash_source" + ], + "semantic_category": "canonical_identifier", + "strictness": "canonical_identifier" + }, + { + "config_path": "configs/entities/openalex/publication.yaml", + "cross_rules": [ + "cross_validation:composite_publication:exact" + ], + "dq_coverage": "pattern:error", + "dq_rules": [ + "pattern:error" + ], + "entity": "publication", + "field": "pmid", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/openalex_publication_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "identifiers", + "normalization_source": "profile", + "normalizer": "normalize_profile_pmid", + "pipeline": "openalex_publication", + "pipeline_kind": "entity", + "provider": "openalex", + "roles": [ + "content_hash_source", + "cross_source_validation" + ], + "semantic_category": "canonical_identifier", + "strictness": "canonical_identifier" + }, + { + "config_path": "configs/entities/pubmed/publication.yaml", + "cross_rules": [ + "entity_cross_field_validations:publication_identifiable", + "entity_cross_field_validations:has_identifier", + "cross_validation:composite_publication:exact" + ], + "dq_coverage": "pattern:error,range:error", + "dq_rules": [ + "pattern:error,range:error" + ], + "entity": "publication", + "field": "pmid", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/pubmed_publication_v1.0.json", + "gold_required": true, + "gold_type": "\"string\"", + "group": "identifiers", + "normalization_source": "profile", + "normalizer": "normalize_profile_pmid", + "pipeline": "pubmed_publication", + "pipeline_kind": "entity", + "provider": "pubmed", + "roles": [ + "FK", + "PK", + "composite_join_key_for:composite_publication", + "content_hash_source", + "contract_pk", + "cross_field_validation", + "cross_source_validation", + "deduplication_key", + "gold_required", + "merge_key" + ], + "semantic_category": "canonical_identifier", + "strictness": "canonical_identifier" + }, + { + "config_path": "configs/entities/semanticscholar/publication.yaml", + "cross_rules": [ + "cross_validation:composite_publication:exact" + ], + "dq_coverage": "pattern:error", + "dq_rules": [ + "pattern:error" + ], + "entity": "publication", + "field": "pmid", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/semanticscholar_publication_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "identifiers", + "normalization_source": "profile", + "normalizer": "normalize_profile_pmid", + "pipeline": "semanticscholar_publication", + "pipeline_kind": "entity", + "provider": "semanticscholar", + "roles": [ + "content_hash_source", + "cross_source_validation" + ], + "semantic_category": "canonical_identifier", + "strictness": "canonical_identifier" + } + ], + "pipeline_count": 6, + "rationale": "PubMed provider input still arrives as pubmed_id, but normalized schema, join keys and DQ contracts use pmid.", + "semantic_status": "EXACT", + "source": "canonical_registry" + }, + { + "aliases": [ + "abstract_structured" + ], + "canonical_field": "abstract_structured", + "cluster_id": "shared_abstract_structured", + "member_count": 2, + "members": [ + { + "config_path": "configs/composites/publication.yaml", + "cross_rules": [], + "dq_coverage": "not_applicable", + "dq_rules": [], + "entity": "publication", + "field": "abstract_structured", + "field_type": "bool", + "gold_path": "", + "gold_required": false, + "gold_type": "", + "group": "journal", + "normalization_source": "upstream_inherited", + "normalizer": "none", + "pipeline": "composite_publication", + "pipeline_kind": "composite", + "provider": "composite", + "roles": [], + "semantic_category": "upstream_inherited", + "strictness": "upstream_inherited" + }, + { + "config_path": "configs/entities/pubmed/publication.yaml", + "cross_rules": [], + "dq_coverage": "not_configured", + "dq_rules": [], + "entity": "publication", + "field": "abstract_structured", + "field_type": "bool", + "gold_path": "docs/04-reference/contracts/gold/pubmed_publication_v1.0.json", + "gold_required": false, + "gold_type": "[\"boolean\", \"null\"]", + "group": "abstract", + "normalization_source": "profile", + "normalizer": "normalize_profile_boolean", + "pipeline": "pubmed_publication", + "pipeline_kind": "entity", + "provider": "pubmed", + "roles": [ + "content_hash_source" + ], + "semantic_category": "strict_enum", + "strictness": "strict_boolean" + } + ], + "pipeline_count": 2, + "rationale": "Same field name appears across pipelines, but no canonical registry or mapping module proves business identity.", + "review": { + "expires_on": "2026-11-15", + "issue": 4133, + "owner": "BioETL Team", + "rationale": "WEAK same-name clusters are inventory evidence only. They are reviewed as non-blocking because they do not assert cross-pipeline semantic identity until an owner promotes a cluster into a canonical exact/partial semantic field family.\n", + "review_id": "weak_same_name_inventory_review" + }, + "semantic_status": "WEAK", + "source": "same_name_unclassified_field" + }, + { + "aliases": [ + "action_type_description" + ], + "canonical_field": "action_type_description", + "cluster_id": "shared_action_type_description", + "member_count": 2, + "members": [ + { + "config_path": "configs/entities/chembl/activity.yaml", + "cross_rules": [], + "dq_coverage": "not_configured", + "dq_rules": [], + "entity": "activity", + "field": "action_type_description", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/chembl_activity_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_null", + "pipeline": "chembl_activity", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "content_hash_source" + ], + "semantic_category": "free_text", + "strictness": "normalization_only" + }, + { + "config_path": "configs/composites/activity.yaml", + "cross_rules": [], + "dq_coverage": "not_applicable", + "dq_rules": [], + "entity": "activity", + "field": "action_type_description", + "field_type": "string", + "gold_path": "", + "gold_required": false, + "gold_type": "", + "group": "action", + "normalization_source": "upstream_inherited", + "normalizer": "none", + "pipeline": "composite_activity", + "pipeline_kind": "composite", + "provider": "composite", + "roles": [], + "semantic_category": "upstream_inherited", + "strictness": "upstream_inherited" + } + ], + "pipeline_count": 2, + "rationale": "Same field name appears across pipelines, but no canonical registry or mapping module proves business identity.", + "review": { + "expires_on": "2026-11-15", + "issue": 4133, + "owner": "BioETL Team", + "rationale": "WEAK same-name clusters are inventory evidence only. They are reviewed as non-blocking because they do not assert cross-pipeline semantic identity until an owner promotes a cluster into a canonical exact/partial semantic field family.\n", + "review_id": "weak_same_name_inventory_review" + }, + "semantic_status": "WEAK", + "source": "same_name_unclassified_field" + }, + { + "aliases": [ + "action_type_parent_type" + ], + "canonical_field": "action_type_parent_type", + "cluster_id": "shared_action_type_parent_type", + "member_count": 2, + "members": [ + { + "config_path": "configs/entities/chembl/activity.yaml", + "cross_rules": [], + "dq_coverage": "not_configured", + "dq_rules": [], + "entity": "activity", + "field": "action_type_parent_type", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/chembl_activity_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_null", + "pipeline": "chembl_activity", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "content_hash_source" + ], + "semantic_category": "free_text", + "strictness": "normalization_only" + }, + { + "config_path": "configs/composites/activity.yaml", + "cross_rules": [], + "dq_coverage": "not_applicable", + "dq_rules": [], + "entity": "activity", + "field": "action_type_parent_type", + "field_type": "string", + "gold_path": "", + "gold_required": false, + "gold_type": "", + "group": "action", + "normalization_source": "upstream_inherited", + "normalizer": "none", + "pipeline": "composite_activity", + "pipeline_kind": "composite", + "provider": "composite", + "roles": [], + "semantic_category": "upstream_inherited", + "strictness": "upstream_inherited" + } + ], + "pipeline_count": 2, + "rationale": "Same field name appears across pipelines, but no canonical registry or mapping module proves business identity.", + "review": { + "expires_on": "2026-11-15", + "issue": 4133, + "owner": "BioETL Team", + "rationale": "WEAK same-name clusters are inventory evidence only. They are reviewed as non-blocking because they do not assert cross-pipeline semantic identity until an owner promotes a cluster into a canonical exact/partial semantic field family.\n", + "review_id": "weak_same_name_inventory_review" + }, + "semantic_status": "WEAK", + "source": "same_name_unclassified_field" + }, + { + "aliases": [ + "activity_comment" + ], + "canonical_field": "activity_comment", + "cluster_id": "shared_activity_comment", + "member_count": 2, + "members": [ + { + "config_path": "configs/entities/chembl/activity.yaml", + "cross_rules": [], + "dq_coverage": "not_configured", + "dq_rules": [], + "entity": "activity", + "field": "activity_comment", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/chembl_activity_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_null", + "pipeline": "chembl_activity", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "content_hash_source" + ], + "semantic_category": "free_text", + "strictness": "normalization_only" + }, + { + "config_path": "configs/composites/activity.yaml", + "cross_rules": [], + "dq_coverage": "not_applicable", + "dq_rules": [], + "entity": "activity", + "field": "activity_comment", + "field_type": "string", + "gold_path": "", + "gold_required": false, + "gold_type": "", + "group": "quality", + "normalization_source": "upstream_inherited", + "normalizer": "none", + "pipeline": "composite_activity", + "pipeline_kind": "composite", + "provider": "composite", + "roles": [], + "semantic_category": "upstream_inherited", + "strictness": "upstream_inherited" + } + ], + "pipeline_count": 2, + "rationale": "Same field name appears across pipelines, but no canonical registry or mapping module proves business identity.", + "review": { + "expires_on": "2026-11-15", + "issue": 4133, + "owner": "BioETL Team", + "rationale": "WEAK same-name clusters are inventory evidence only. 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They are reviewed as non-blocking because they do not assert cross-pipeline semantic identity until an owner promotes a cluster into a canonical exact/partial semantic field family.\n", + "review_id": "weak_same_name_inventory_review" + }, + "semantic_status": "WEAK", + "source": "same_name_unclassified_field" + }, + { + "aliases": [ + "variant_sequence" + ], + "canonical_field": "variant_sequence", + "cluster_id": "shared_variant_sequence", + "member_count": 2, + "members": [ + { + "config_path": "configs/entities/chembl/assay.yaml", + "cross_rules": [], + "dq_coverage": "not_configured", + "dq_rules": [], + "entity": "assay", + "field": "variant_sequence", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/chembl_assay_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_null", + "pipeline": "chembl_assay", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "content_hash_source" + ], + "semantic_category": "free_text", + "strictness": "normalization_only" + }, + { + "config_path": "configs/composites/assay.yaml", + "cross_rules": [], + "dq_coverage": "not_applicable", + "dq_rules": [], + "entity": "assay", + "field": "variant_sequence", + "field_type": "string", + "gold_path": "", + "gold_required": false, + "gold_type": "", + "group": "variant", + "normalization_source": "upstream_inherited", + "normalizer": "none", + "pipeline": "composite_assay", + "pipeline_kind": "composite", + "provider": "composite", + "roles": [], + "semantic_category": "upstream_inherited", + "strictness": "upstream_inherited" + } + ], + "pipeline_count": 2, + "rationale": "Same field name appears across pipelines, but no canonical registry or mapping module proves business identity.", + "review": { + "expires_on": "2026-11-15", + "issue": 4133, + "owner": "BioETL Team", + "rationale": "WEAK same-name clusters are inventory evidence only. 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They are reviewed as non-blocking because they do not assert cross-pipeline semantic identity until an owner promotes a cluster into a canonical exact/partial semantic field family.\n", + "review_id": "weak_same_name_inventory_review" + }, + "semantic_status": "WEAK", + "source": "same_name_unclassified_field" + }, + { + "aliases": [ + "variant_taxonomy_id" + ], + "canonical_field": "variant_taxonomy_id", + "cluster_id": "shared_variant_taxonomy_id", + "member_count": 2, + "members": [ + { + "config_path": "configs/entities/chembl/assay.yaml", + "cross_rules": [], + "dq_coverage": "not_configured", + "dq_rules": [], + "entity": "assay", + "field": "variant_taxonomy_id", + "field_type": "int64", + "gold_path": "docs/04-reference/contracts/gold/chembl_assay_v1.0.json", + "gold_required": false, + "gold_type": "[\"number\", \"null\"]", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_ncbi_taxonomy_id", + "pipeline": "chembl_assay", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "content_hash_source" + ], + "semantic_category": "reference_identifier", + "strictness": "canonical_identifier" + }, + { + "config_path": "configs/composites/assay.yaml", + "cross_rules": [], + "dq_coverage": "not_applicable", + "dq_rules": [], + "entity": "assay", + "field": "variant_taxonomy_id", + "field_type": "int64", + "gold_path": "", + "gold_required": false, + "gold_type": "", + "group": "variant", + "normalization_source": "upstream_inherited", + "normalizer": "none", + "pipeline": "composite_assay", + "pipeline_kind": "composite", + "provider": "composite", + "roles": [], + "semantic_category": "upstream_inherited", + "strictness": "upstream_inherited" + } + ], + "pipeline_count": 2, + "rationale": "Same identifier-like field name appears across pipeline schemas.", + "semantic_status": "EXACT", + "source": "same_name_identifier_field" + }, + { + "aliases": [ + "withdrawn_flag" + ], + "canonical_field": "withdrawn_flag", + "cluster_id": "shared_withdrawn_flag", + "member_count": 2, + "members": [ + { + "config_path": "configs/entities/chembl/molecule.yaml", + "cross_rules": [], + "dq_coverage": "not_configured", + "dq_rules": [], + "entity": "molecule", + "field": "withdrawn_flag", + "field_type": "bool", + "gold_path": "docs/04-reference/contracts/gold/chembl_molecule_v1.0.json", + "gold_required": false, + "gold_type": "[\"boolean\", \"null\"]", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_boolean", + "pipeline": "chembl_molecule", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "content_hash_source" + ], + "semantic_category": "strict_boolean", + "strictness": "strict_flag" + }, + { + "config_path": "configs/composites/molecule.yaml", + "cross_rules": [], + "dq_coverage": "not_applicable", + "dq_rules": [], + "entity": "molecule", + "field": "withdrawn_flag", + "field_type": "bool", + "gold_path": "", + "gold_required": false, + "gold_type": "", + "group": "clinical", + "normalization_source": "upstream_inherited", + "normalizer": "none", + "pipeline": "composite_molecule", + "pipeline_kind": "composite", + "provider": "composite", + "roles": [ + "merge_priority" + ], + "semantic_category": "upstream_inherited", + "strictness": "upstream_inherited" + } + ], + "pipeline_count": 2, + "rationale": "Same field name appears across pipelines, but no canonical registry or mapping module proves business identity.", + "review": { + "expires_on": "2026-11-15", + "issue": 4133, + "owner": "BioETL Team", + "rationale": "WEAK same-name clusters are inventory evidence only. They are reviewed as non-blocking because they do not assert cross-pipeline semantic identity until an owner promotes a cluster into a canonical exact/partial semantic field family.\n", + "review_id": "weak_same_name_inventory_review" + }, + "semantic_status": "WEAK", + "source": "same_name_unclassified_field" + }, + { + "aliases": [ + "accession", + "uniprot_accession" + ], + "canonical_field": "accession", + "cluster_id": "uniprot_accession_identifier", + "member_count": 4, + "members": [ + { + "config_path": "configs/entities/chembl/target_component.yaml", + "cross_rules": [ + "entity_cross_field_validations:component_identifiable" + ], + "dq_coverage": "pattern:error", + "dq_rules": [ + "pattern:error" + ], + "entity": "target_component", + "field": "accession", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/chembl_target_component_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_uniprot_accession", + "pipeline": "chembl_target_component", + "pipeline_kind": "entity", + "provider": "chembl", + "roles": [ + "content_hash_source", + "cross_field_validation" + ], + "semantic_category": "reference_identifier", + "strictness": "normalization_only" + }, + { + "config_path": "configs/composites/target.yaml", + "cross_rules": [], + "dq_coverage": "not_applicable", + "dq_rules": [], + "entity": "target", + "field": "uniprot_accession", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/composite_target_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "identifiers", + "normalization_source": "composite_join_key_policy", + "normalizer": "join_key_policy", + "pipeline": "composite_target", + "pipeline_kind": "composite", + "provider": "composite", + "roles": [ + "composite_dependency_join_key", + "join_to:uniprot_protein" + ], + "semantic_category": "join_key_policy", + "strictness": "join_key_policy" + }, + { + "config_path": "configs/entities/uniprot/idmapping.yaml", + "cross_rules": [], + "dq_coverage": "pattern:error", + "dq_rules": [ + "pattern:error" + ], + "entity": "idmapping", + "field": "uniprot_accession", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/uniprot_idmapping_v1.0.json", + "gold_required": false, + "gold_type": "[\"string\", \"null\"]", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_uniprot_accession", + "pipeline": "uniprot_idmapping", + "pipeline_kind": "entity", + "provider": "uniprot", + "roles": [ + "content_hash_source" + ], + "semantic_category": "ontology_reference_identifier", + "strictness": "canonical_identifier" + }, + { + "config_path": "configs/entities/uniprot/protein.yaml", + "cross_rules": [ + "entity_cross_field_validations:protein_identifiable" + ], + "dq_coverage": "pattern:error,pattern:error", + "dq_rules": [ + "pattern:error,pattern:error" + ], + "entity": "protein", + "field": "accession", + "field_type": "string", + "gold_path": "docs/04-reference/contracts/gold/uniprot_protein_v1.0.json", + "gold_required": true, + "gold_type": "\"string\"", + "group": "business", + "normalization_source": "profile", + "normalizer": "normalize_profile_uniprot_accession", + "pipeline": "uniprot_protein", + "pipeline_kind": "entity", + "provider": "uniprot", + "roles": [ + "PK", + "content_hash_source", + "contract_pk", + "cross_field_validation", + "deduplication_key", + "gold_required", + "merge_key" + ], + "semantic_category": "free_text", + "strictness": "normalization_only" + } + ], + "pipeline_count": 4, + "rationale": "UniProt accession identity is PARTIAL across ChEMBL component evidence, UniProt idmapping output, composite target chaining, and UniProt protein primary keys. Direct joins use idmapping/protein accessions; ChEMBL component accession remains lineage evidence.", + "review": { + "expires_on": "2026-11-15", + "issue": 4133, + "owner": "BioETL Team", + "rationale": "PARTIAL identity clusters are intentionally not promoted to EXACT because they mix provider-owned identifiers, composite lineage projections, and join/reference anchors. Each listed cluster is valid only with explicit join/lineage semantics in the pair matrix and semantic anchor gates.\n", + "review_id": "partial_identity_policy_review" + }, + "semantic_status": "PARTIAL", + "source": "identifier_alias_rule" + } + ], + "generated_at": "2026-05-21T00:00:00Z", + "scope": { + "active_pipeline_count": 26, + "field_count": 1154, + "source_surfaces": [ + "configs/entities/**", + "configs/composites/**", + "configs/base/**", + "configs/quality/**", + "src/bioetl/domain/contracts/**", + "src/bioetl/domain/schemas/**", + "src/bioetl/domain/mapping/**", + "src/bioetl/domain/normalization/**", + "src/bioetl/domain/validation/**", + "src/bioetl/domain/registry/**", + "src/bioetl/application/pipelines/**" + ] + }, + "source_date": "2026-05-21" +} diff --git a/reports/semantic_pipeline_audit/semantic_pair_matrix_2026-05-21.csv b/reports/semantic_pipeline_audit/semantic_pair_matrix_2026-05-21.csv new file mode 100644 index 0000000000..f551953226 --- /dev/null +++ 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""null""];schema=string;dq=not_applicable",string,string,docs/04-reference/contracts/gold/chembl_target_component_v1.0.json,docs/04-reference/contracts/gold/composite_target_v1.0.json,configs/entities/chembl/target_component.yaml,configs/composites/target.yaml,5997712ceebae41d +uniprot_accession_identifier,chembl_target_component,accession,uniprot_idmapping,uniprot_accession,PARTIAL,IDENTICAL,IDENTICAL,IDENTICAL,LOW,content_hash_source;cross_field_validation,content_hash_source,normalize_profile_uniprot_accession,normalize_profile_uniprot_accession,"gold:optional:[""string"", ""null""];schema=string;dq=pattern:error","gold:optional:[""string"", ""null""];schema=string;dq=pattern:error",string,string,docs/04-reference/contracts/gold/chembl_target_component_v1.0.json,docs/04-reference/contracts/gold/uniprot_idmapping_v1.0.json,configs/entities/chembl/target_component.yaml,configs/entities/uniprot/idmapping.yaml,19e19bd4a7742830 +uniprot_accession_identifier,chembl_target_component,accession,uniprot_protein,accession,PARTIAL,IDENTICAL,COMPATIBLE,COMPATIBLE,LOW,content_hash_source;cross_field_validation,PK;content_hash_source;contract_pk;cross_field_validation;deduplication_key;gold_required;merge_key,normalize_profile_uniprot_accession,normalize_profile_uniprot_accession,"gold:optional:[""string"", ""null""];schema=string;dq=pattern:error","gold:required:""string"";schema=string;dq=pattern:error,pattern:error",string,string,docs/04-reference/contracts/gold/chembl_target_component_v1.0.json,docs/04-reference/contracts/gold/uniprot_protein_v1.0.json,configs/entities/chembl/target_component.yaml,configs/entities/uniprot/protein.yaml,ded487aaf878e6be 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+uniprot_accession_identifier,uniprot_idmapping,uniprot_accession,uniprot_protein,accession,PARTIAL,IDENTICAL,COMPATIBLE,COMPATIBLE,LOW,content_hash_source,PK;content_hash_source;contract_pk;cross_field_validation;deduplication_key;gold_required;merge_key,normalize_profile_uniprot_accession,normalize_profile_uniprot_accession,"gold:optional:[""string"", ""null""];schema=string;dq=pattern:error","gold:required:""string"";schema=string;dq=pattern:error,pattern:error",string,string,docs/04-reference/contracts/gold/uniprot_idmapping_v1.0.json,docs/04-reference/contracts/gold/uniprot_protein_v1.0.json,configs/entities/uniprot/idmapping.yaml,configs/entities/uniprot/protein.yaml,55b2aa33816f6d87 diff --git a/reports/semantic_pipeline_audit/semantic_pipeline_audit_2026-05-21.md b/reports/semantic_pipeline_audit/semantic_pipeline_audit_2026-05-21.md new file mode 100644 index 0000000000..8cadf9377d --- /dev/null +++ b/reports/semantic_pipeline_audit/semantic_pipeline_audit_2026-05-21.md @@ -0,0 +1,39 @@ +# Semantic Pipeline Audit + +Generated: `2026-05-21` + +## Executive Summary + +- Semantic clusters: `283` +- Pair rows: `3129` +- Base config files covered: `5` +- Base config semantic surfaces: `328` +- CRITICAL drift risks: `0` +- HIGH drift risks: `0` +- Normalization mismatches: `0` +- Validation strictness mismatches: `0` +- Typing conflicts: `0` +- Reviewed PARTIAL rows: `68` +- Reviewed WEAK inventory rows: `319` +- Role-governed WEAK clusters: `4` +- Explicit source-owned assay WEAK clusters: `5` +- Reviewed generic collision rows: `0` +- Compatible normalization rows: `839` +- Compatible validation rows: `990` +- Compatible typing rows: `618` +- Residual blocking tasks: `0` + +## Artifact Index + +- `semantic_pair_matrix_2026-05-21.csv` +- `semantic_cluster_registry_2026-05-21.json` +- `critical_inconsistencies_2026-05-21.md` +- `recommended_canonical_fields_2026-05-21.csv` +- `base_config_semantic_coverage_2026-05-21.json` +- `semantic_residual_backlog_2026-05-21.json` +- `semantic_residual_backlog_2026-05-21.md` +- `semantic_pipeline_audit_manifest_2026-05-21.json` + +## Notes + +This generated snapshot refreshes member evidence from active pipeline configs, base config defaults, normalization profiles, DQ visibility, Pandera-derived Gold contracts, and the reviewed semantic cluster registry. diff --git a/reports/semantic_pipeline_audit/semantic_pipeline_audit_manifest_2026-05-21.json b/reports/semantic_pipeline_audit/semantic_pipeline_audit_manifest_2026-05-21.json new file mode 100644 index 0000000000..af98f5c818 --- /dev/null +++ b/reports/semantic_pipeline_audit/semantic_pipeline_audit_manifest_2026-05-21.json @@ -0,0 +1,431 @@ +{ + "artifact_count": 8, + "artifacts": { + "audit_report": "semantic_pipeline_audit_2026-05-21.md", + "base_config_semantic_coverage": "base_config_semantic_coverage_2026-05-21.json", + "cluster_registry": "semantic_cluster_registry_2026-05-21.json", + "critical_inconsistencies": "critical_inconsistencies_2026-05-21.md", + "pair_matrix": "semantic_pair_matrix_2026-05-21.csv", + "recommended_canonical_fields": "recommended_canonical_fields_2026-05-21.csv", + "residual_backlog": "semantic_residual_backlog_2026-05-21.json", + "residual_backlog_markdown": "semantic_residual_backlog_2026-05-21.md" + }, + "counts": { + "base_configs": { + "base_config_count": 5, + "entries": [ + { + "path": "configs/base/bronze_fixture_gaps.yaml", + "role": "bronze_fixture_gap_registry", + "semantic_surface_count": 1, + "semantic_surfaces": [ + "gaps" + ] + }, + { + "path": "configs/base/bronze_fixture_manifest.yaml", + "role": "bronze_lineage_fixture_manifest", + "semantic_surface_count": 1, + "semantic_surfaces": [ + "fixtures" + ] + }, + { + "path": "configs/base/contract_registry.yaml", + "role": "gold_contract_identity_registry", + "semantic_surface_count": 312, + "semantic_surfaces": [ + "entries.chembl.activity.dq_policy_ref", + 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"entries.openalex.publication.published_artifacts", + "entries.openalex.publication.rule_bundle_version", + "entries.pubchem.compound.dq_policy_ref", + "entries.pubchem.compound.identity", + "entries.pubchem.compound.identity.dq_policy_ref", + "entries.pubchem.compound.identity.normalization_profile_hash", + "entries.pubchem.compound.identity.normalization_profile_ref", + "entries.pubchem.compound.identity.normalization_profile_version", + "entries.pubchem.compound.identity.rule_bundle_version", + "entries.pubchem.compound.normalization_profile_hash", + "entries.pubchem.compound.normalization_profile_ref", + "entries.pubchem.compound.normalization_profile_version", + "entries.pubchem.compound.published_artifacts", + "entries.pubchem.compound.rule_bundle_version", + "entries.pubmed.publication.dq_policy_ref", + "entries.pubmed.publication.identity", + "entries.pubmed.publication.identity.dq_policy_ref", + "entries.pubmed.publication.identity.normalization_profile_hash", + "entries.pubmed.publication.identity.normalization_profile_ref", + "entries.pubmed.publication.identity.normalization_profile_version", + "entries.pubmed.publication.identity.rule_bundle_version", + "entries.pubmed.publication.normalization_profile_hash", + "entries.pubmed.publication.normalization_profile_ref", + "entries.pubmed.publication.normalization_profile_version", + "entries.pubmed.publication.published_artifacts", + "entries.pubmed.publication.rule_bundle_version", + "entries.semanticscholar.publication.dq_policy_ref", + "entries.semanticscholar.publication.identity", + "entries.semanticscholar.publication.identity.dq_policy_ref", + "entries.semanticscholar.publication.identity.normalization_profile_hash", + "entries.semanticscholar.publication.identity.normalization_profile_ref", + "entries.semanticscholar.publication.identity.normalization_profile_version", + "entries.semanticscholar.publication.identity.rule_bundle_version", + "entries.semanticscholar.publication.normalization_profile_hash", + "entries.semanticscholar.publication.normalization_profile_ref", + "entries.semanticscholar.publication.normalization_profile_version", + "entries.semanticscholar.publication.published_artifacts", + "entries.semanticscholar.publication.rule_bundle_version", + "entries.uniprot.idmapping.dq_policy_ref", + "entries.uniprot.idmapping.identity", + "entries.uniprot.idmapping.identity.dq_policy_ref", + "entries.uniprot.idmapping.identity.normalization_profile_hash", + "entries.uniprot.idmapping.identity.normalization_profile_ref", + "entries.uniprot.idmapping.identity.normalization_profile_version", + "entries.uniprot.idmapping.identity.rule_bundle_version", + "entries.uniprot.idmapping.normalization_profile_hash", + "entries.uniprot.idmapping.normalization_profile_ref", + "entries.uniprot.idmapping.normalization_profile_version", + "entries.uniprot.idmapping.published_artifacts", + "entries.uniprot.idmapping.rule_bundle_version", + "entries.uniprot.protein.dq_policy_ref", + "entries.uniprot.protein.identity", + "entries.uniprot.protein.identity.dq_policy_ref", + "entries.uniprot.protein.identity.normalization_profile_hash", + "entries.uniprot.protein.identity.normalization_profile_ref", + "entries.uniprot.protein.identity.normalization_profile_version", + "entries.uniprot.protein.identity.rule_bundle_version", + "entries.uniprot.protein.normalization_profile_hash", + "entries.uniprot.protein.normalization_profile_ref", + "entries.uniprot.protein.normalization_profile_version", + "entries.uniprot.protein.published_artifacts", + "entries.uniprot.protein.rule_bundle_version" + ] + }, + { + "path": "configs/base/pipeline.yaml", + "role": "medallion_defaults_and_contract_field_defaults", + "semantic_surface_count": 9, + "semantic_surfaces": [ + "contract_defaults", + "contract_defaults.hash_exclude", + "contract_defaults.hash_include", + "dq_overrides", + "filter_defaults", + "sink.gold.scd_config", + "sink.gold.sort_by", + "sink.silver.sort_by", + "technical_primary_key" + ] + }, + { + "path": "configs/base/quality.yaml", + "role": "global_dq_defaults", + "semantic_surface_count": 5, + "semantic_surfaces": [ + "common_cross_field_validations", + "common_field_validations", + "invalid_record_policy", + "strict_validation", + "thresholds" + ] + } + ], + "semantic_surface_count": 328 + }, + "clusters": 283, + "fields": 1190, + "normalization": { + "COMPATIBLE": 839, + "IDENTICAL": 2290 + }, + "pairs": 3129, + "pipelines": 26, + "residual_backlog": { + "blocking_task_count": 0, + "clusters": 283, + "normalization_counts": { + "COMPATIBLE": 839, + "IDENTICAL": 2290 + }, + "pair_rows": 3129, + "risk_counts": { + "LOW": 3129 + }, + "semantic_status_counts": { + "EXACT": 2742, + "PARTIAL": 68, + "WEAK": 319 + }, + "typing_counts": { + "COMPATIBLE": 618, + "IDENTICAL": 2511 + }, + "validation_counts": { + "COMPATIBLE": 990, + "IDENTICAL": 2139 + } + }, + "risk": { + "LOW": 3129 + }, + "typing": { + "COMPATIBLE": 618, + "IDENTICAL": 2511 + }, + "validation": { + "COMPATIBLE": 990, + "IDENTICAL": 2139 + } + }, + "generated_at": "2026-05-21T00:00:00Z", + "scope": "all_etl_pipelines", + "source_date": "2026-05-21" +} diff --git a/reports/semantic_pipeline_audit/semantic_residual_backlog_2026-05-21.json b/reports/semantic_pipeline_audit/semantic_residual_backlog_2026-05-21.json new file mode 100644 index 0000000000..0ccbdab174 --- /dev/null +++ b/reports/semantic_pipeline_audit/semantic_residual_backlog_2026-05-21.json @@ -0,0 +1,329 @@ +{ + "generated_at": "2026-05-21T00:00:00Z", + "source_date": "2026-05-21", + "summary": { + "blocking_task_count": 0, + "clusters": 283, + "normalization_counts": { + "COMPATIBLE": 839, + "IDENTICAL": 2290 + }, + "pair_rows": 3129, + "risk_counts": { + "LOW": 3129 + }, + "semantic_status_counts": { + "EXACT": 2742, + "PARTIAL": 68, + "WEAK": 319 + }, + "typing_counts": { + "COMPATIBLE": 618, + "IDENTICAL": 2511 + }, + "validation_counts": { + "COMPATIBLE": 990, + "IDENTICAL": 2139 + } + }, + "tasks": [ + { + "definition_of_done": "CRITICAL/HIGH/MEDIUM drift risks remain at zero in the semantic pair matrix budget gate.", + "gate": "uv run python -m scripts.engineering.qa check-semantic-pair-budget --check --json", + "id": "semantic_drift_budget", + "priority": "P0", + "row_count": 0, + "status": "closed" + }, + { + "definition_of_done": "Normalization DIFFERENT/CONFLICTING, Validation STRICTNESS_MISMATCH, and Typing CONFLICTING remain at zero.", + "gate": "uv run python -m scripts.engineering.qa check-semantic-pair-budget --check --json", + "id": "hard_status_mismatch_budget", + "priority": "P0", + "row_count": 0, + "status": "closed" + }, + { + "definition_of_done": "PARTIAL identities stay documented as join/lineage policy, not silently promoted to EXACT.", + "expires_on": "2026-11-15", + "gate": "uv run python -m scripts.engineering.qa check-semantic-registry-drift --check --json", + "id": "partial_identity_policy_review", + "priority": "P2", + "row_count": 68, + "status": "reviewed_until_expiry", + "top_clusters": [ + { + "cluster_id": "pmc_identifier", + "row_count": 28 + }, + { + "cluster_id": "chembl_target_identifier", + "row_count": 21 + }, + { + "cluster_id": "canonical_smiles_identifier", + "row_count": 10 + }, + { + "cluster_id": "uniprot_accession_identifier", + "row_count": 6 + }, + { + "cluster_id": "inchi_key_identifier", + "row_count": 3 + } + ] + }, + { + "definition_of_done": "WEAK same-name inventory remains owner-reviewed and does not assert cross-pipeline business identity.", + "expires_on": "2026-11-15", + "gate": "uv run python -m scripts.engineering.qa check-semantic-registry-drift --check --json", + "id": "weak_same_name_inventory_review", + "priority": "P2", + "row_count": 319, + "status": "reviewed_until_expiry", + "top_clusters": [ + { + "cluster_id": "shared_pref_name", + "row_count": 15 + }, + { + "cluster_id": "shared_author_keys", + "row_count": 10 + }, + { + "cluster_id": "shared_author_orcids", + "row_count": 10 + }, + { + "cluster_id": "shared_is_oa", + "row_count": 10 + }, + { + "cluster_id": "shared_language", + "row_count": 10 + }, + { + "cluster_id": "shared_assay_type", + "row_count": 6 + }, + { + "cluster_id": "shared_bao_format", + "row_count": 6 + }, + { + "cluster_id": "shared_bao_label", + "row_count": 6 + }, + { + "cluster_id": "shared_issn", + "row_count": 6 + }, + { + "cluster_id": "shared_oa_status", + "row_count": 6 + }, + { + "cluster_id": "shared_annotation_score", + "row_count": 3 + }, + { + "cluster_id": "shared_cross_references", + "row_count": 3 + } + ] + }, + { + "definition_of_done": "Generic lexical collisions remain explicit owner-reviewed warnings instead of canonical fields.", + "expires_on": "", + "gate": "uv run python -m scripts.engineering.qa check-generic-field-ownership --check --json", + "id": "generic_collision_inventory_review", + "priority": "P2", + "row_count": 0, + "status": "reviewed_until_expiry", + "top_clusters": [] + }, + { + "definition_of_done": "Compatible normalization rows may decrease, but must not grow without an intentional budget update.", + "gate": "uv run python -m scripts.engineering.qa check-semantic-pair-budget --check --json", + "id": "compatible_normalization_ratchet", + "priority": "P2", + "row_count": 839, + "status": "ratcheted", + "top_clusters": [ + { + "cluster_id": "shared_content_hash", + "row_count": 105 + }, + { + "cluster_id": "shared_entity_id", + "row_count": 105 + }, + { + "cluster_id": "shared_index", + "row_count": 105 + }, + { + "cluster_id": "shared_source", + "row_count": 25 + }, + { + "cluster_id": "shared_lookup_method", + "row_count": 20 + }, + { + "cluster_id": "shared_original_id", + "row_count": 20 + }, + { + "cluster_id": "shared_publication_id", + "row_count": 12 + }, + { + "cluster_id": "shared_src_id", + "row_count": 12 + }, + { + "cluster_id": "chembl_target_identifier", + "row_count": 10 + }, + { + "cluster_id": "publication_publication_year", + "row_count": 10 + }, + { + "cluster_id": "publication_authors", + "row_count": 9 + }, + { + "cluster_id": "publication_issue", + "row_count": 9 + } + ] + }, + { + "definition_of_done": "Compatible validation rows may decrease, but must not grow without an intentional budget update.", + "gate": "uv run python -m scripts.engineering.qa check-semantic-pair-budget --check --json", + "id": "compatible_validation_ratchet", + "priority": "P2", + "row_count": 990, + "status": "ratcheted", + "top_clusters": [ + { + "cluster_id": "shared_entity_id", + "row_count": 143 + }, + { + "cluster_id": "shared_content_hash", + "row_count": 105 + }, + { + "cluster_id": "shared_index", + "row_count": 105 + }, + { + "cluster_id": "shared_source", + "row_count": 29 + }, + { + "cluster_id": "shared_lookup_method", + "row_count": 24 + }, + { + "cluster_id": "pmc_identifier", + "row_count": 22 + }, + { + "cluster_id": "shared_publication_id", + "row_count": 21 + }, + { + "cluster_id": "shared_original_id", + "row_count": 20 + }, + { + "cluster_id": "chembl_target_identifier", + "row_count": 17 + }, + { + "cluster_id": "shared_src_id", + "row_count": 15 + }, + { + "cluster_id": "shared_pref_name", + "row_count": 13 + }, + { + "cluster_id": "doi_identifier", + "row_count": 12 + } + ] + }, + { + "definition_of_done": "Compatible typing rows may decrease, but must not grow without an intentional budget update.", + "gate": "uv run python -m scripts.engineering.qa check-semantic-pair-budget --check --json", + "id": "compatible_typing_ratchet", + "priority": "P2", + "row_count": 618, + "status": "ratcheted", + "top_clusters": [ + { + "cluster_id": "shared_content_hash", + "row_count": 105 + }, + { + "cluster_id": "shared_source", + "row_count": 24 + }, + { + "cluster_id": "shared_lookup_method", + "row_count": 20 + }, + { + "cluster_id": "shared_publication_id", + "row_count": 15 + }, + { + "cluster_id": "shared_src_id", + "row_count": 15 + }, + { + "cluster_id": "shared_pref_name", + "row_count": 11 + }, + { + "cluster_id": "chembl_target_identifier", + "row_count": 10 + }, + { + "cluster_id": "publication_publication_year", + "row_count": 10 + }, + { + "cluster_id": "publication_publication_class", + "row_count": 8 + }, + { + "cluster_id": "publication_publication_date", + "row_count": 8 + }, + { + "cluster_id": "publication_publication_subclass", + "row_count": 8 + }, + { + "cluster_id": "publication_publication_type_unified", + "row_count": 8 + } + ] + }, + { + "definition_of_done": "Base config semantic surfaces are included in the generated audit manifest and regression test.", + "gate": "uv run pytest tests/integration/config/test_semantic_pair_matrix_budget.py -q --tb=short", + "id": "base_config_semantic_coverage", + "priority": "P2", + "row_count": 328, + "status": "closed" + } + ] +} diff --git a/reports/semantic_pipeline_audit/semantic_residual_backlog_2026-05-21.md b/reports/semantic_pipeline_audit/semantic_residual_backlog_2026-05-21.md new file mode 100644 index 0000000000..c7e753281e --- /dev/null +++ b/reports/semantic_pipeline_audit/semantic_residual_backlog_2026-05-21.md @@ -0,0 +1,28 @@ +# Semantic Pipeline Residual Backlog + +Generated: `2026-05-21` + +## Summary + +- Blocking tasks: `0` +- Pair rows: `3129` +- Clusters: `283` +- Risk counts: `{"LOW": 3129}` +- Semantic status counts: `{"EXACT": 2742, "PARTIAL": 68, "WEAK": 319}` +- Normalization counts: `{"COMPATIBLE": 839, "IDENTICAL": 2290}` +- Validation counts: `{"COMPATIBLE": 990, "IDENTICAL": 2139}` +- Typing counts: `{"COMPATIBLE": 618, "IDENTICAL": 2511}` + +## Tasks + +| ID | Priority | Status | Rows | Expiry | Gate | +| --- | --- | --- | ---: | --- | --- | +| semantic_drift_budget | P0 | closed | 0 | | `uv run python -m scripts.engineering.qa check-semantic-pair-budget --check --json` | +| hard_status_mismatch_budget | P0 | closed | 0 | | `uv run python -m scripts.engineering.qa check-semantic-pair-budget --check --json` | +| partial_identity_policy_review | P2 | reviewed_until_expiry | 68 | 2026-11-15 | `uv run python -m scripts.engineering.qa check-semantic-registry-drift --check --json` | +| weak_same_name_inventory_review | P2 | reviewed_until_expiry | 319 | 2026-11-15 | `uv run python -m scripts.engineering.qa check-semantic-registry-drift --check --json` | +| generic_collision_inventory_review | P2 | reviewed_until_expiry | 0 | | `uv run python -m scripts.engineering.qa check-generic-field-ownership --check --json` | +| compatible_normalization_ratchet | P2 | ratcheted | 839 | | `uv run python -m scripts.engineering.qa check-semantic-pair-budget --check --json` | +| compatible_validation_ratchet | P2 | ratcheted | 990 | | `uv run python -m scripts.engineering.qa check-semantic-pair-budget --check --json` | +| compatible_typing_ratchet | P2 | ratcheted | 618 | | `uv run python -m scripts.engineering.qa check-semantic-pair-budget --check --json` | +| base_config_semantic_coverage | P2 | closed | 328 | | `uv run pytest tests/integration/config/test_semantic_pair_matrix_budget.py -q --tb=short` | diff --git a/scripts/docs/build/__pycache__/__init__.cpython-313.pyc b/scripts/docs/build/__pycache__/__init__.cpython-313.pyc deleted file mode 100644 index 4c636bfe66..0000000000 Binary files a/scripts/docs/build/__pycache__/__init__.cpython-313.pyc and /dev/null differ diff --git a/scripts/docs/build/__pycache__/mkdocs_build.cpython-313.pyc b/scripts/docs/build/__pycache__/mkdocs_build.cpython-313.pyc deleted file mode 100644 index 851a4b4d87..0000000000 Binary files a/scripts/docs/build/__pycache__/mkdocs_build.cpython-313.pyc and /dev/null differ diff --git a/tests/unit/composition/factories/storage/test_health_mixin.py b/tests/unit/composition/factories/storage/test_health_mixin.py index 28b5b8e409..71b885b4df 100644 --- a/tests/unit/composition/factories/storage/test_health_mixin.py +++ b/tests/unit/composition/factories/storage/test_health_mixin.py @@ -265,3 +265,9 @@ def test_is_layer_preview_payload_wrong_types() -> None: """_is_layer_preview_payload returns False for wrong value types.""" payload = {"path": 123, "file_count": "not int", "exists": "not bool"} assert StorageBundleHealthMixin._is_layer_preview_payload(payload) is False + +@pytest.mark.unit +def test_get_explicit_writer_audit_type_error() -> None: + """_get_explicit_writer_audit returns None when vars() raises TypeError.""" + result = StorageBundleHealthMixin._get_explicit_writer_audit(object()) + assert result is None