Publish exact composite input blockers and complete patent provenance audit

audits/n1-n5-input-readiness-v1/n5_precursor_mismatches.jsonl

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+{"dataset_id": "n5", "reaction_node_path": [0], "reaction_only": {"N1C(=S)NC(=CC1=O)C": 1}, "reaction_reactants": {"C1CN(CCN1CC)c2c(c(Cl)ccc2)CBr": 1, "N1C(=S)NC(=CC1=O)C": 1}, "recorded_reaction": "[CH2:4]1[CH2:5][N:6]([CH2:24][CH2:25][N:3]1[CH2:2][CH3:1])[c:7]2[c:13]([c:11]([Cl:12])[cH:10][cH:9][cH:8]2)[CH2:14][Br:26].[c:18]1([cH:20][c:21]([OH:22])[n:23][c:16]([n:17]1)[SH:15])[CH3:19]>>[CH2:4]1[CH2:5][N:6]([CH2:24][CH2:25][N:3]1[CH2:2][CH3:1])[c:7]2[cH:8][cH:9][cH:10][c:11]([Cl:12])[c:13]2[CH2:14][S:15][c:16]3[n:23][c:21]([cH:20][c:18]([n:17]3)[CH3:19])[OH:22]", "route_id": "3032", "route_only": {"c1(cc(O)nc(n1)S)C": 1}, "route_precursors": {"C1CN(CCN1CC)c2c(c(Cl)ccc2)CBr": 1, "c1(cc(O)nc(n1)S)C": 1}, "source_record_id": "US20150225423A1;0414;1736056"}
+{"dataset_id": "n5", "reaction_node_path": [0, 0, 0, 0, 0], "reaction_only": {"C1(=O)C(=O)Nc2c(cc(c(c2[N+](=O)[O-])N)Cl)N1": 1}, "reaction_reactants": {"C1(=O)C(=O)Nc2c(cc(c(c2[N+](=O)[O-])N)Cl)N1": 1}, "recorded_reaction": "[c:4]12[c:13]([c:12]([N+:11]([O-:24])=[O:23])[c:8]([c:6]([Cl:7])[cH:5]1)[NH2:9])[n:14][c:15]([OH:16])[c:2]([n:3]2)[OH:1]>>[C:2]1(=[O:1])[C:15](=[O:16])[NH:14][c:13]2[c:4]([cH:5][c:6]([c:8]([c:12]2[N+:11](=[O:23])[O-:24])[NH2:9])[Cl:7])[NH:3]1", "route_id": "9035", "route_only": {"c12c(c([N+]([O-])=O)c(c(Cl)c1)N)nc(O)c(n2)O": 1}, "route_precursors": {"c12c(c([N+]([O-])=O)c(c(Cl)c1)N)nc(O)c(n2)O": 1}, "source_record_id": "US05109001;;249758"}
+{"dataset_id": "n5", "reaction_node_path": [0, 0, 0, 0, 0, 0, 0], "reaction_only": {"C1(=O)C(Nc2c(cc(Cl)c(NC(=O)OCC)c2[N+]([O-])=O)N1)=O": 1}, "reaction_reactants": {"C1(=O)C(Nc2c(cc(Cl)c(NC(=O)OCC)c2[N+]([O-])=O)N1)=O": 1}, "recorded_reaction": "[NH:9]([c:8]1[c:6]([cH:5][c:4]2[c:13]([n:14][c:15]([OH:16])[c:2]([n:3]2)[OH:1])[c:12]1[N+:11](=[O:23])[O-:24])[Cl:7])[C:21](=[O:22])[O:20][CH2:19][CH3:25]>>[c:4]12[c:13]([c:12]([N+:11]([O-:24])=[O:23])[c:8]([c:6]([Cl:7])[cH:5]1)[NH2:9])[n:14][c:15]([OH:16])[c:2]([n:3]2)[OH:1]", "route_id": "9035", "route_only": {"N(c1c(cc2c(nc(O)c(n2)O)c1[N+](=O)[O-])Cl)C(=O)OCC": 1}, "route_precursors": {"N(c1c(cc2c(nc(O)c(n2)O)c1[N+](=O)[O-])Cl)C(=O)OCC": 1}, "source_record_id": "US05109001;;249757"}

audits/n1-n5-input-readiness-v1/n5_reference_errors.jsonl

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+{"dataset_id": "n5", "error": "Reaction reactants disagree with route precursor multiset", "route_id": "3032", "source_identity": "sha256:5a27be2e0199f2bacd66556122f50906a24e27946bb30b1d9472d55d725e71af"}
+{"dataset_id": "n5", "error": "Reaction reactants disagree with route precursor multiset", "route_id": "9035", "source_identity": "sha256:5a27be2e0199f2bacd66556122f50906a24e27946bb30b1d9472d55d725e71af"}

audits/n1-n5-input-readiness-v1/preparation.json

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+{
+  "inputs": [
+    {
+      "path": "/Users/almazgil/Developer/projects/route-inspector/data/clean/n1_routes.json",
+      "sha256": "c1e396cd71228e3ab113412428571d223ef943835c3793f91b994b3341359439"
+    },
+    {
+      "path": "/Users/almazgil/Developer/projects/route-inspector/data/clean/n5_routes.json",
+      "sha256": "5a27be2e0199f2bacd66556122f50906a24e27946bb30b1d9472d55d725e71af"
+    },
+    {
+      "path": "/Users/almazgil/Developer/projects/retrocomposite/src/retrocomposite/selection.py",
+      "sha256": "2b59087f78fa196ea2f520cb11e5c5ee60fe12662f4de748b709fad094753767"
+    },
+    {
+      "path": "/Users/almazgil/Developer/projects/retrocomposite/src/retrocomposite/segments.py",
+      "sha256": "59da9e1c6ecea558da05379a1d40b0a3979d9258aa7cd8ed0b416d3226c601db"
+    }
+  ],
+  "kind": "cohort-input-readiness",
+  "outputs": {
+    "n5_precursor_mismatches.jsonl": "b474d149f59e0ae789efad87b6ef68f302ea63e17cb14c207c05a6829b08320a",
+    "n5_reference_errors.jsonl": "4ae3e9f964e157c6c76b0bd132e623a7d842718edd3f4351275d0ec6bea01797",
+    "patent_provenance.jsonl": "36a0f025f5f2d4eda2bf2d6dfe1d0b8b2dc37b3c6ce1cca2041649c00173858c",
+    "summary.json": "e0dce653155408f8ad3d2d60d14cca9a68af3e39a06922d5c48d18900d9a90e2"
+  },
+  "schema": "retrocomposite-preparation/1",
+  "software": {
+    "SynPlanner": "1.8.0",
+    "chython-synplan": "1.108",
+    "retrocomposite": "0.1.0",
+    "route-inspector": "3.0.0.dev0"
+  },
+  "status": "blocked",
+  "stereo": "ignored"
+}

audits/n1-n5-input-readiness-v1/summary.json

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+{
+  "candidate_composites": {
+    "certified_links": 13121,
+    "eligible_training_cohorts_published": false,
+    "identity_version": 3,
+    "library": "outputs/composite_libraries/n1-retrocomposite-v3-20261025",
+    "uncertified_diagnostics": 1043
+  },
+  "full_occurrence_filtering_completed": false,
+  "invalid_n5_routes": [
+    "3032",
+    "9035"
+  ],
+  "legacy_patent_parser_false_negatives_corrected_n5_routes": 1113,
+  "mismatching_reactions": 3,
+  "patent_disjoint_status": "blocked",
+  "patent_identity_policy": "paroutes-document-identifiers-including-legacy-us-reissue-sir/2",
+  "patent_provenance": {
+    "n1": {
+      "complete": 10000,
+      "routes": 10000
+    },
+    "n5": {
+      "complete": 10000,
+      "routes": 10000
+    }
+  },
+  "primary_status": "blocked",
+  "reason": "Incomplete n5 E3 reference index: three reaction/precursor mismatches in routes 3032 and 9035",
+  "resolution": "Reconcile the three mapped-reaction/route-precursor representations in RouteInspector under an explicit source-chemistry policy; publish matching source/library revisions, then rerun exclusion selection.",
+  "schema": "retrocomposite-cohort-input-readiness/1",
+  "source_input_files_unchanged": true
+}