@inflexa-ai/harness 0.1.1

package/dist/workflows/target-assessment/phase4-assemble.d.ts

@@ -0,0 +1,1841 @@
+/**
+ * Phase 4 — deterministic dossier assembly.
+ *
+ * Pure function over a Phase-3 bundle. Calls `assembleDossier` (~3.5K LOC
+ * of pure compute) and returns the assembled `DossierV4Body`. The Phase-5
+ * synthesis sections (translational commentary, liability bullets, safety-
+ * flags trail) are stamped by the Phase-5 persist step after this step
+ * completes.
+ *
+ * The DBOS workflow body wraps this in `DBOS.runStep({name: "phase4-assemble"})`
+ * so recovery on a fresh replica replays the cached output without re-running
+ * the ~1-3 sec compute.
+ *
+ * `assembleDossier` accepts an optional `ClinicalConsequenceAnnotatorDeps`
+ * bundle that is threaded through to `annotateOffTargetPanel`. For the
+ * DBOS workflow the parameter is undefined — the annotator falls back to
+ * its DB cache + no-LLM path. Threading a real deps bundle (provider +
+ * session + model) through Phase-4 is a follow-up tracked in §17 cleanup.
+ */
+import type { Pool } from "pg";
+import { z } from "zod";
+import type { Phase3Bundle } from "./steps/phase3-aggregate.js";
+import { Phase3BundleSchema } from "./steps/phase3-aggregate.js";
+export declare const Phase4OutputSchema: z.ZodObject<{
+    assessmentId: z.ZodString;
+    dossier: z.ZodObject<{
+        drug_interactions: z.ZodDiscriminatedUnion<[z.ZodObject<{
+            coverage: z.ZodLiteral<"available">;
+            data: z.ZodObject<{
+                rows: z.ZodArray<z.ZodObject<{
+                    drug_id: z.ZodNullable<z.ZodString>;
+                    drug_name: z.ZodString;
+                    best_score: z.ZodNumber;
+                    predicates: z.ZodArray<z.ZodString>;
+                    sources: z.ZodArray<z.ZodString>;
+                    paper_count: z.ZodNumber;
+                    dominant_direction: z.ZodEnum<{
+                        unknown: "unknown";
+                        positive: "positive";
+                        negative: "negative";
+                        mixed: "mixed";
+                    }>;
+                    has_human_evidence: z.ZodBoolean;
+                    has_clinical_evidence: z.ZodBoolean;
+                    evidence: z.ZodArray<z.ZodObject<{
+                        pmid: z.ZodOptional<z.ZodString>;
+                        doi: z.ZodOptional<z.ZodString>;
+                        source: z.ZodString;
+                        predicate: z.ZodOptional<z.ZodString>;
+                        score: z.ZodOptional<z.ZodNumber>;
+                        strength: z.ZodOptional<z.ZodString>;
+                        is_human: z.ZodOptional<z.ZodBoolean>;
+                        is_clinical: z.ZodOptional<z.ZodBoolean>;
+                        excerpt: z.ZodOptional<z.ZodString>;
+                        metadata: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+                        regulatory_reference: z.ZodOptional<z.ZodObject<{
+                            document: z.ZodString;
+                            section: z.ZodOptional<z.ZodString>;
+                            doc_id: z.ZodOptional<z.ZodString>;
+                            doc_url: z.ZodOptional<z.ZodString>;
+                        }, z.core.$strip>>;
+                    }, z.core.$strip>>;
+                }, z.core.$strip>>;
+            }, z.core.$strip>;
+            inference_path: z.ZodOptional<z.ZodString>;
+            truncated: z.ZodOptional<z.ZodBoolean>;
+        }, z.core.$strip>, z.ZodObject<{
+            coverage: z.ZodLiteral<"queried_no_data">;
+            error: z.ZodOptional<z.ZodObject<{
+                message: z.ZodString;
+                source: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>>;
+            inference_path: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>, z.ZodObject<{
+            coverage: z.ZodLiteral<"not_loaded">;
+            reason: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>], "coverage">;
+        tractability: z.ZodDiscriminatedUnion<[z.ZodObject<{
+            coverage: z.ZodLiteral<"available">;
+            data: z.ZodObject<{
+                modalities: z.ZodArray<z.ZodObject<{
+                    modality: z.ZodEnum<{
+                        small_molecule: "small_molecule";
+                        antibody: "antibody";
+                        protac: "protac";
+                        other_clinical: "other_clinical";
+                        oligonucleotide: "oligonucleotide";
+                        peptide: "peptide";
+                    }>;
+                    levels: z.ZodArray<z.ZodString>;
+                    has_approved_drug: z.ZodBoolean;
+                    has_clinical_stage: z.ZodBoolean;
+                    is_inferred_from_family: z.ZodBoolean;
+                    approved_drug_ids: z.ZodOptional<z.ZodArray<z.ZodString>>;
+                    note: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>>;
+                preferred_modality: z.ZodNullable<z.ZodString>;
+                drug_molecule_types_present: z.ZodDefault<z.ZodArray<z.ZodString>>;
+            }, z.core.$strip>;
+            inference_path: z.ZodOptional<z.ZodString>;
+            truncated: z.ZodOptional<z.ZodBoolean>;
+        }, z.core.$strip>, z.ZodObject<{
+            coverage: z.ZodLiteral<"queried_no_data">;
+            error: z.ZodOptional<z.ZodObject<{
+                message: z.ZodString;
+                source: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>>;
+            inference_path: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>, z.ZodObject<{
+            coverage: z.ZodLiteral<"not_loaded">;
+            reason: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>], "coverage">;
+        schema_version: z.ZodLiteral<"4">;
+        off_target_panel: z.ZodDiscriminatedUnion<[z.ZodObject<{
+            coverage: z.ZodLiteral<"available">;
+            data: z.ZodObject<{
+                rows: z.ZodArray<z.ZodObject<{
+                    off_target_id: z.ZodNullable<z.ZodString>;
+                    off_target_name: z.ZodString;
+                    target_class: z.ZodOptional<z.ZodString>;
+                    pchembl: z.ZodNumber;
+                    is_safety_panel_target: z.ZodBoolean;
+                    organ_system: z.ZodNullable<z.ZodString>;
+                    clinical_consequence: z.ZodNullable<z.ZodString>;
+                    selectivity: z.ZodUnion<readonly [z.ZodObject<{
+                        vs_primary_potency: z.ZodObject<{
+                            primary_pchembl_used: z.ZodNumber;
+                            primary_source: z.ZodEnum<{
+                                chembl_target_drug_indication: "chembl_target_drug_indication";
+                                literature_curated: "literature_curated";
+                            }>;
+                            fold: z.ZodNumber;
+                            log_units: z.ZodNumber;
+                        }, z.core.$strip>;
+                    }, z.core.$strip>, z.ZodObject<{
+                        selectivity_unknown: z.ZodLiteral<true>;
+                        reason: z.ZodString;
+                    }, z.core.$strip>]>;
+                    selectivity_window_below_threshold: z.ZodBoolean;
+                    evidence: z.ZodArray<z.ZodObject<{
+                        pmid: z.ZodOptional<z.ZodString>;
+                        doi: z.ZodOptional<z.ZodString>;
+                        source: z.ZodString;
+                        predicate: z.ZodOptional<z.ZodString>;
+                        score: z.ZodOptional<z.ZodNumber>;
+                        strength: z.ZodOptional<z.ZodString>;
+                        is_human: z.ZodOptional<z.ZodBoolean>;
+                        is_clinical: z.ZodOptional<z.ZodBoolean>;
+                        excerpt: z.ZodOptional<z.ZodString>;
+                        metadata: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+                        regulatory_reference: z.ZodOptional<z.ZodObject<{
+                            document: z.ZodString;
+                            section: z.ZodOptional<z.ZodString>;
+                            doc_id: z.ZodOptional<z.ZodString>;
+                            doc_url: z.ZodOptional<z.ZodString>;
+                        }, z.core.$strip>>;
+                    }, z.core.$strip>>;
+                    metadata: z.ZodOptional<z.ZodObject<{
+                        merged_chembl_ids: z.ZodOptional<z.ZodArray<z.ZodString>>;
+                    }, z.core.$strip>>;
+                    relationship: z.ZodLiteral<"off_target">;
+                }, z.core.$strip>>;
+                excluded_rows: z.ZodArray<z.ZodObject<{
+                    off_target_id: z.ZodNullable<z.ZodString>;
+                    off_target_name: z.ZodString;
+                    target_class: z.ZodOptional<z.ZodString>;
+                    pchembl: z.ZodNumber;
+                    is_safety_panel_target: z.ZodBoolean;
+                    organ_system: z.ZodNullable<z.ZodString>;
+                    clinical_consequence: z.ZodNullable<z.ZodString>;
+                    selectivity: z.ZodUnion<readonly [z.ZodObject<{
+                        vs_primary_potency: z.ZodObject<{
+                            primary_pchembl_used: z.ZodNumber;
+                            primary_source: z.ZodEnum<{
+                                chembl_target_drug_indication: "chembl_target_drug_indication";
+                                literature_curated: "literature_curated";
+                            }>;
+                            fold: z.ZodNumber;
+                            log_units: z.ZodNumber;
+                        }, z.core.$strip>;
+                    }, z.core.$strip>, z.ZodObject<{
+                        selectivity_unknown: z.ZodLiteral<true>;
+                        reason: z.ZodString;
+                    }, z.core.$strip>]>;
+                    selectivity_window_below_threshold: z.ZodBoolean;
+                    evidence: z.ZodArray<z.ZodObject<{
+                        pmid: z.ZodOptional<z.ZodString>;
+                        doi: z.ZodOptional<z.ZodString>;
+                        source: z.ZodString;
+                        predicate: z.ZodOptional<z.ZodString>;
+                        score: z.ZodOptional<z.ZodNumber>;
+                        strength: z.ZodOptional<z.ZodString>;
+                        is_human: z.ZodOptional<z.ZodBoolean>;
+                        is_clinical: z.ZodOptional<z.ZodBoolean>;
+                        excerpt: z.ZodOptional<z.ZodString>;
+                        metadata: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+                        regulatory_reference: z.ZodOptional<z.ZodObject<{
+                            document: z.ZodString;
+                            section: z.ZodOptional<z.ZodString>;
+                            doc_id: z.ZodOptional<z.ZodString>;
+                            doc_url: z.ZodOptional<z.ZodString>;
+                        }, z.core.$strip>>;
+                    }, z.core.$strip>>;
+                    metadata: z.ZodOptional<z.ZodObject<{
+                        merged_chembl_ids: z.ZodOptional<z.ZodArray<z.ZodString>>;
+                    }, z.core.$strip>>;
+                    relationship: z.ZodEnum<{
+                        intended_co_target: "intended_co_target";
+                        on_target_self_hit: "on_target_self_hit";
+                        obligate_cofactor: "obligate_cofactor";
+                    }>;
+                    reason: z.ZodString;
+                }, z.core.$strip>>;
+            }, z.core.$strip>;
+            inference_path: z.ZodOptional<z.ZodString>;
+            truncated: z.ZodOptional<z.ZodBoolean>;
+        }, z.core.$strip>, z.ZodObject<{
+            coverage: z.ZodLiteral<"queried_no_data">;
+            error: z.ZodOptional<z.ZodObject<{
+                message: z.ZodString;
+                source: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>>;
+            inference_path: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>, z.ZodObject<{
+            coverage: z.ZodLiteral<"not_loaded">;
+            reason: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>], "coverage">;
+        liability_summary: z.ZodObject<{
+            liability_bullets: z.ZodArray<z.ZodObject<{
+                text: z.ZodString;
+                rationale: z.ZodString;
+                category: z.ZodEnum<{
+                    other: "other";
+                    fatal_post_market: "fatal_post_market";
+                    class_liability: "class_liability";
+                    off_target_safety: "off_target_safety";
+                    high_safety_organ_expression: "high_safety_organ_expression";
+                    broad_expression: "broad_expression";
+                }>;
+            }, z.core.$strip>>;
+            liability_bullets_dropped: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                text: z.ZodString;
+                rationale: z.ZodString;
+                category: z.ZodEnum<{
+                    other: "other";
+                    fatal_post_market: "fatal_post_market";
+                    class_liability: "class_liability";
+                    off_target_safety: "off_target_safety";
+                    high_safety_organ_expression: "high_safety_organ_expression";
+                    broad_expression: "broad_expression";
+                }>;
+                reason: z.ZodString;
+                cited_pmid: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>>>;
+            modality_recommendation: z.ZodNullable<z.ZodString>;
+            same_class_drug_count: z.ZodNumber;
+            inferred_therapeutic_area: z.ZodNullable<z.ZodString>;
+            no_liabilities_disclosure: z.ZodOptional<z.ZodString>;
+        }, z.core.$strict>;
+        analytics: z.ZodObject<{
+            evidence_conflicts: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                coverage: z.ZodLiteral<"available">;
+                data: z.ZodObject<{
+                    rows: z.ZodArray<z.ZodObject<{
+                        evidence_item_id: z.ZodString;
+                        predicate: z.ZodString;
+                        contradicting_predicates: z.ZodArray<z.ZodString>;
+                        surfaced_in_section: z.ZodString;
+                        evidence: z.ZodArray<z.ZodObject<{
+                            pmid: z.ZodOptional<z.ZodString>;
+                            doi: z.ZodOptional<z.ZodString>;
+                            source: z.ZodString;
+                            predicate: z.ZodOptional<z.ZodString>;
+                            score: z.ZodOptional<z.ZodNumber>;
+                            strength: z.ZodOptional<z.ZodString>;
+                            is_human: z.ZodOptional<z.ZodBoolean>;
+                            is_clinical: z.ZodOptional<z.ZodBoolean>;
+                            excerpt: z.ZodOptional<z.ZodString>;
+                            metadata: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+                            regulatory_reference: z.ZodOptional<z.ZodObject<{
+                                document: z.ZodString;
+                                section: z.ZodOptional<z.ZodString>;
+                                doc_id: z.ZodOptional<z.ZodString>;
+                                doc_url: z.ZodOptional<z.ZodString>;
+                            }, z.core.$strip>>;
+                        }, z.core.$strip>>;
+                    }, z.core.$strip>>;
+                }, z.core.$strip>;
+                inference_path: z.ZodOptional<z.ZodString>;
+                truncated: z.ZodOptional<z.ZodBoolean>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"queried_no_data">;
+                error: z.ZodOptional<z.ZodObject<{
+                    message: z.ZodString;
+                    source: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>>;
+                inference_path: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"not_loaded">;
+                reason: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>], "coverage">;
+            evidence_timeline: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                coverage: z.ZodLiteral<"available">;
+                data: z.ZodObject<{
+                    histogram: z.ZodRecord<z.ZodString, z.ZodNumber>;
+                    first_reported_year: z.ZodNullable<z.ZodNumber>;
+                    last_reported_year: z.ZodNullable<z.ZodNumber>;
+                    trend_labels: z.ZodArray<z.ZodString>;
+                }, z.core.$strip>;
+                inference_path: z.ZodOptional<z.ZodString>;
+                truncated: z.ZodOptional<z.ZodBoolean>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"queried_no_data">;
+                error: z.ZodOptional<z.ZodObject<{
+                    message: z.ZodString;
+                    source: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>>;
+                inference_path: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"not_loaded">;
+                reason: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>], "coverage">;
+            translational_chain: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                coverage: z.ZodLiteral<"available">;
+                data: z.ZodObject<{
+                    tiers: z.ZodArray<z.ZodObject<{
+                        tier: z.ZodEnum<{
+                            computational: "computational";
+                            basic_in_vitro: "basic_in_vitro";
+                            complex_in_vitro: "complex_in_vitro";
+                            in_vivo_animal: "in_vivo_animal";
+                            ex_vivo_human: "ex_vivo_human";
+                            clinical: "clinical";
+                        }>;
+                        claim_count: z.ZodNumber;
+                        paper_count: z.ZodNumber;
+                    }, z.core.$strip>>;
+                    peak_evidence_tier: z.ZodNullable<z.ZodEnum<{
+                        computational: "computational";
+                        basic_in_vitro: "basic_in_vitro";
+                        complex_in_vitro: "complex_in_vitro";
+                        in_vivo_animal: "in_vivo_animal";
+                        ex_vivo_human: "ex_vivo_human";
+                        clinical: "clinical";
+                    }>>;
+                    progression_complete: z.ZodBoolean;
+                    weakest_progression_gap: z.ZodOptional<z.ZodNullable<z.ZodEnum<{
+                        computational: "computational";
+                        basic_in_vitro: "basic_in_vitro";
+                        complex_in_vitro: "complex_in_vitro";
+                        in_vivo_animal: "in_vivo_animal";
+                        ex_vivo_human: "ex_vivo_human";
+                        clinical: "clinical";
+                    }>>>;
+                }, z.core.$strip>;
+                inference_path: z.ZodOptional<z.ZodString>;
+                truncated: z.ZodOptional<z.ZodBoolean>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"queried_no_data">;
+                error: z.ZodOptional<z.ZodObject<{
+                    message: z.ZodString;
+                    source: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>>;
+                inference_path: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"not_loaded">;
+                reason: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>], "coverage">;
+            additional_evidence: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                coverage: z.ZodLiteral<"available">;
+                data: z.ZodObject<{
+                    rows: z.ZodArray<z.ZodObject<{
+                        predicate: z.ZodString;
+                        evidence: z.ZodArray<z.ZodObject<{
+                            pmid: z.ZodOptional<z.ZodString>;
+                            doi: z.ZodOptional<z.ZodString>;
+                            source: z.ZodString;
+                            predicate: z.ZodOptional<z.ZodString>;
+                            score: z.ZodOptional<z.ZodNumber>;
+                            strength: z.ZodOptional<z.ZodString>;
+                            is_human: z.ZodOptional<z.ZodBoolean>;
+                            is_clinical: z.ZodOptional<z.ZodBoolean>;
+                            excerpt: z.ZodOptional<z.ZodString>;
+                            metadata: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+                            regulatory_reference: z.ZodOptional<z.ZodObject<{
+                                document: z.ZodString;
+                                section: z.ZodOptional<z.ZodString>;
+                                doc_id: z.ZodOptional<z.ZodString>;
+                                doc_url: z.ZodOptional<z.ZodString>;
+                            }, z.core.$strip>>;
+                        }, z.core.$strip>>;
+                    }, z.core.$strip>>;
+                    score_floor: z.ZodNumber;
+                }, z.core.$strip>;
+                inference_path: z.ZodOptional<z.ZodString>;
+                truncated: z.ZodOptional<z.ZodBoolean>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"queried_no_data">;
+                error: z.ZodOptional<z.ZodObject<{
+                    message: z.ZodString;
+                    source: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>>;
+                inference_path: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"not_loaded">;
+                reason: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>], "coverage">;
+            discovery_trials: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                coverage: z.ZodLiteral<"available">;
+                data: z.ZodObject<{
+                    rows: z.ZodArray<z.ZodObject<{
+                        nct_id: z.ZodString;
+                        title: z.ZodString;
+                        phase: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+                        status: z.ZodOptional<z.ZodString>;
+                        conditions: z.ZodArray<z.ZodString>;
+                        start_date: z.ZodOptional<z.ZodString>;
+                        completion_date: z.ZodOptional<z.ZodString>;
+                        match_confidence: z.ZodEnum<{
+                            high: "high";
+                            medium: "medium";
+                            low: "low";
+                        }>;
+                        relevance_basis: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                            kind: z.ZodLiteral<"drug_in_class_match">;
+                            drug_id: z.ZodString;
+                            matched_term: z.ZodOptional<z.ZodString>;
+                        }, z.core.$strip>, z.ZodObject<{
+                            kind: z.ZodLiteral<"title_keyword">;
+                            matched_term: z.ZodString;
+                        }, z.core.$strip>, z.ZodObject<{
+                            kind: z.ZodLiteral<"condition_match">;
+                            matched_term: z.ZodOptional<z.ZodString>;
+                        }, z.core.$strip>, z.ZodObject<{
+                            kind: z.ZodLiteral<"manual">;
+                        }, z.core.$strip>], "kind">;
+                    }, z.core.$strip>>;
+                    related_target_trials: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                        nct_id: z.ZodString;
+                        title: z.ZodString;
+                        phase: z.ZodNullable<z.ZodString>;
+                        status: z.ZodString;
+                        conditions: z.ZodArray<z.ZodString>;
+                        start_date: z.ZodNullable<z.ZodString>;
+                        completion_date: z.ZodNullable<z.ZodString>;
+                        match_confidence: z.ZodLiteral<"off_target">;
+                    }, z.core.$strip>>>;
+                    related_receptor: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>;
+                inference_path: z.ZodOptional<z.ZodString>;
+                truncated: z.ZodOptional<z.ZodBoolean>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"queried_no_data">;
+                error: z.ZodOptional<z.ZodObject<{
+                    message: z.ZodString;
+                    source: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>>;
+                inference_path: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"not_loaded">;
+                reason: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>], "coverage">;
+            synthesis_diagnostics: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                coverage: z.ZodLiteral<"available">;
+                data: z.ZodObject<{
+                    rows: z.ZodArray<z.ZodObject<{
+                        step_id: z.ZodEnum<{
+                            "liability-bullets": "liability-bullets";
+                            "safety-flags-trail": "safety-flags-trail";
+                            "translational-commentary": "translational-commentary";
+                            "dossier-recommendation": "dossier-recommendation";
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+                            pass: "pass";
+                            "fail-length": "fail-length";
+                            "fail-section-references": "fail-section-references";
+                            "fail-key-strengths-risks": "fail-key-strengths-risks";
+                            "fail-source-references": "fail-source-references";
+                            "fail-numeric-claim": "fail-numeric-claim";
+                            "fail-voice": "fail-voice";
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+                            "synthesis-too-shallow": "synthesis-too-shallow";
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+                ensembl: z.ZodOptional<z.ZodString>;
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+                        relationship: z.ZodEnum<{
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+                        agency: z.ZodEnum<{
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+                            EMA: "EMA";
+                            MHRA: "MHRA";
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+                            TGA: "TGA";
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+                            withdrawal: "withdrawal";
+                            indication_restriction: "indication_restriction";
+                            REMS: "REMS";
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+                            DHCP: "DHCP";
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+                            rems: "rems";
+                            referral: "referral";
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+                            specificity: z.ZodOptional<z.ZodNumber>;
+                            auc: z.ZodOptional<z.ZodNumber>;
+                            hazard_ratio: z.ZodOptional<z.ZodNumber>;
+                        }, z.core.$strip>;
+                    }, z.core.$strip>>;
+                }, z.core.$strip>;
+                inference_path: z.ZodOptional<z.ZodString>;
+                truncated: z.ZodOptional<z.ZodBoolean>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"queried_no_data">;
+                error: z.ZodOptional<z.ZodObject<{
+                    message: z.ZodString;
+                    source: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>>;
+                inference_path: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"not_loaded">;
+                reason: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>], "coverage">;
+            genetic_alterations: z.ZodObject<{
+                somatic: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                    coverage: z.ZodLiteral<"available">;
+                    data: z.ZodObject<{
+                        rows: z.ZodArray<z.ZodObject<{
+                            cancer_type: z.ZodString;
+                            cohort: z.ZodString;
+                            mutation_count: z.ZodNumber;
+                            total_samples: z.ZodNumber;
+                            frequency: z.ZodNumber;
+                            source: z.ZodString;
+                        }, z.core.$strip>>;
+                    }, z.core.$strip>;
+                    inference_path: z.ZodOptional<z.ZodString>;
+                    truncated: z.ZodOptional<z.ZodBoolean>;
+                }, z.core.$strip>, z.ZodObject<{
+                    coverage: z.ZodLiteral<"queried_no_data">;
+                    error: z.ZodOptional<z.ZodObject<{
+                        message: z.ZodString;
+                        source: z.ZodOptional<z.ZodString>;
+                    }, z.core.$strip>>;
+                    inference_path: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>, z.ZodObject<{
+                    coverage: z.ZodLiteral<"not_loaded">;
+                    reason: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>], "coverage">;
+                clinvar: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                    coverage: z.ZodLiteral<"available">;
+                    data: z.ZodObject<{
+                        rows: z.ZodArray<z.ZodObject<{
+                            variant_id: z.ZodString;
+                            hgvs: z.ZodString;
+                            classification: z.ZodString;
+                            condition: z.ZodString;
+                            review_status: z.ZodString;
+                        }, z.core.$strip>>;
+                    }, z.core.$strip>;
+                    inference_path: z.ZodOptional<z.ZodString>;
+                    truncated: z.ZodOptional<z.ZodBoolean>;
+                }, z.core.$strip>, z.ZodObject<{
+                    coverage: z.ZodLiteral<"queried_no_data">;
+                    error: z.ZodOptional<z.ZodObject<{
+                        message: z.ZodString;
+                        source: z.ZodOptional<z.ZodString>;
+                    }, z.core.$strip>>;
+                    inference_path: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>, z.ZodObject<{
+                    coverage: z.ZodLiteral<"not_loaded">;
+                    reason: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>], "coverage">;
+            }, z.core.$strip>;
+            resistance_evidence: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                coverage: z.ZodLiteral<"available">;
+                data: z.ZodObject<{
+                    rows: z.ZodArray<z.ZodObject<{
+                        partner_id: z.ZodNullable<z.ZodString>;
+                        partner_name: z.ZodString;
+                        predicate: z.ZodString;
+                        best_score: z.ZodNumber;
+                        source_count: z.ZodNumber;
+                        paper_count: z.ZodNumber;
+                        evidence: z.ZodArray<z.ZodObject<{
+                            pmid: z.ZodOptional<z.ZodString>;
+                            doi: z.ZodOptional<z.ZodString>;
+                            source: z.ZodString;
+                            predicate: z.ZodOptional<z.ZodString>;
+                            score: z.ZodOptional<z.ZodNumber>;
+                            strength: z.ZodOptional<z.ZodString>;
+                            is_human: z.ZodOptional<z.ZodBoolean>;
+                            is_clinical: z.ZodOptional<z.ZodBoolean>;
+                            excerpt: z.ZodOptional<z.ZodString>;
+                            metadata: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+                            regulatory_reference: z.ZodOptional<z.ZodObject<{
+                                document: z.ZodString;
+                                section: z.ZodOptional<z.ZodString>;
+                                doc_id: z.ZodOptional<z.ZodString>;
+                                doc_url: z.ZodOptional<z.ZodString>;
+                            }, z.core.$strip>>;
+                        }, z.core.$strip>>;
+                    }, z.core.$strip>>;
+                }, z.core.$strip>;
+                inference_path: z.ZodOptional<z.ZodString>;
+                truncated: z.ZodOptional<z.ZodBoolean>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"queried_no_data">;
+                error: z.ZodOptional<z.ZodObject<{
+                    message: z.ZodString;
+                    source: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>>;
+                inference_path: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"not_loaded">;
+                reason: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>], "coverage">;
+            combination_evidence: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                coverage: z.ZodLiteral<"available">;
+                data: z.ZodObject<{
+                    rows: z.ZodArray<z.ZodObject<{
+                        partner_id: z.ZodNullable<z.ZodString>;
+                        partner_name: z.ZodString;
+                        predicate: z.ZodString;
+                        best_score: z.ZodNumber;
+                        source_count: z.ZodNumber;
+                        paper_count: z.ZodNumber;
+                        evidence: z.ZodArray<z.ZodObject<{
+                            pmid: z.ZodOptional<z.ZodString>;
+                            doi: z.ZodOptional<z.ZodString>;
+                            source: z.ZodString;
+                            predicate: z.ZodOptional<z.ZodString>;
+                            score: z.ZodOptional<z.ZodNumber>;
+                            strength: z.ZodOptional<z.ZodString>;
+                            is_human: z.ZodOptional<z.ZodBoolean>;
+                            is_clinical: z.ZodOptional<z.ZodBoolean>;
+                            excerpt: z.ZodOptional<z.ZodString>;
+                            metadata: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+                            regulatory_reference: z.ZodOptional<z.ZodObject<{
+                                document: z.ZodString;
+                                section: z.ZodOptional<z.ZodString>;
+                                doc_id: z.ZodOptional<z.ZodString>;
+                                doc_url: z.ZodOptional<z.ZodString>;
+                            }, z.core.$strip>>;
+                        }, z.core.$strip>>;
+                    }, z.core.$strip>>;
+                }, z.core.$strip>;
+                inference_path: z.ZodOptional<z.ZodString>;
+                truncated: z.ZodOptional<z.ZodBoolean>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"queried_no_data">;
+                error: z.ZodOptional<z.ZodObject<{
+                    message: z.ZodString;
+                    source: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>>;
+                inference_path: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"not_loaded">;
+                reason: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>], "coverage">;
+            pathway_context: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                coverage: z.ZodLiteral<"available">;
+                data: z.ZodObject<{
+                    rows: z.ZodArray<z.ZodObject<{
+                        pathway_id: z.ZodString;
+                        pathway_name: z.ZodString;
+                        database: z.ZodEnum<{
+                            kegg: "kegg";
+                            reactome: "reactome";
+                            wikipathways: "wikipathways";
+                            msigdb: "msigdb";
+                        }>;
+                        evidence_score: z.ZodNumber;
+                        entity_uniprots: z.ZodOptional<z.ZodArray<z.ZodString>>;
+                        metadata: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+                    }, z.core.$strip>>;
+                    databases_queried: z.ZodArray<z.ZodString>;
+                    databases_skipped: z.ZodArray<z.ZodString>;
+                }, z.core.$strip>;
+                inference_path: z.ZodOptional<z.ZodString>;
+                truncated: z.ZodOptional<z.ZodBoolean>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"queried_no_data">;
+                error: z.ZodOptional<z.ZodObject<{
+                    message: z.ZodString;
+                    source: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>>;
+                inference_path: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"not_loaded">;
+                reason: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>], "coverage">;
+            ppi_network: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                coverage: z.ZodLiteral<"available">;
+                data: z.ZodObject<{
+                    partners: z.ZodArray<z.ZodObject<{
+                        partner_id: z.ZodNullable<z.ZodString>;
+                        partner_name: z.ZodString;
+                        string_score: z.ZodNullable<z.ZodNumber>;
+                        literature_score: z.ZodNullable<z.ZodNumber>;
+                        combined_score: z.ZodNumber;
+                        sources: z.ZodArray<z.ZodString>;
+                        has_human_evidence: z.ZodBoolean;
+                        has_clinical_evidence: z.ZodBoolean;
+                    }, z.core.$strip>>;
+                }, z.core.$strip>;
+                inference_path: z.ZodOptional<z.ZodString>;
+                truncated: z.ZodOptional<z.ZodBoolean>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"queried_no_data">;
+                error: z.ZodOptional<z.ZodObject<{
+                    message: z.ZodString;
+                    source: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>>;
+                inference_path: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"not_loaded">;
+                reason: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>], "coverage">;
+            preclinical: z.ZodObject<{
+                ko_phenotype: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                    coverage: z.ZodLiteral<"available">;
+                    data: z.ZodObject<{
+                        marker_symbol: z.ZodNullable<z.ZodString>;
+                        viability: z.ZodNullable<z.ZodString>;
+                        sex_dimorphism: z.ZodBoolean;
+                        organ_systems_with_phenotype: z.ZodArray<z.ZodString>;
+                        top_mp_terms: z.ZodArray<z.ZodString>;
+                        total_phenotype_count: z.ZodNumber;
+                        pre_weaning_lethal: z.ZodBoolean;
+                        supporting_literature: z.ZodArray<z.ZodObject<{
+                            pmid: z.ZodOptional<z.ZodString>;
+                            doi: z.ZodOptional<z.ZodString>;
+                            source: z.ZodString;
+                            predicate: z.ZodOptional<z.ZodString>;
+                            score: z.ZodOptional<z.ZodNumber>;
+                            strength: z.ZodOptional<z.ZodString>;
+                            is_human: z.ZodOptional<z.ZodBoolean>;
+                            is_clinical: z.ZodOptional<z.ZodBoolean>;
+                            excerpt: z.ZodOptional<z.ZodString>;
+                            metadata: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+                            regulatory_reference: z.ZodOptional<z.ZodObject<{
+                                document: z.ZodString;
+                                section: z.ZodOptional<z.ZodString>;
+                                doc_id: z.ZodOptional<z.ZodString>;
+                                doc_url: z.ZodOptional<z.ZodString>;
+                            }, z.core.$strip>>;
+                        }, z.core.$strip>>;
+                    }, z.core.$strip>;
+                    inference_path: z.ZodOptional<z.ZodString>;
+                    truncated: z.ZodOptional<z.ZodBoolean>;
+                }, z.core.$strip>, z.ZodObject<{
+                    coverage: z.ZodLiteral<"queried_no_data">;
+                    error: z.ZodOptional<z.ZodObject<{
+                        message: z.ZodString;
+                        source: z.ZodOptional<z.ZodString>;
+                    }, z.core.$strip>>;
+                    inference_path: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>, z.ZodObject<{
+                    coverage: z.ZodLiteral<"not_loaded">;
+                    reason: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>], "coverage">;
+                expression_heatmap: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                    coverage: z.ZodLiteral<"available">;
+                    data: z.ZodObject<{
+                        cells: z.ZodArray<z.ZodObject<{
+                            tissue: z.ZodString;
+                            species: z.ZodEnum<{
+                                human: "human";
+                                mouse: "mouse";
+                                rat: "rat";
+                                macaque: "macaque";
+                                dog: "dog";
+                            }>;
+                            rank: z.ZodEnum<{
+                                high: "high";
+                                medium: "medium";
+                                low: "low";
+                                absent: "absent";
+                                not_loaded: "not_loaded";
+                                no_data: "no_data";
+                            }>;
+                        }, z.core.$strip>>;
+                        per_species_coverage: z.ZodRecord<z.ZodString, z.ZodEnum<{
+                            available: "available";
+                            queried_no_data: "queried_no_data";
+                            not_loaded: "not_loaded";
+                        }>>;
+                    }, z.core.$strip>;
+                    inference_path: z.ZodOptional<z.ZodString>;
+                    truncated: z.ZodOptional<z.ZodBoolean>;
+                }, z.core.$strip>, z.ZodObject<{
+                    coverage: z.ZodLiteral<"queried_no_data">;
+                    error: z.ZodOptional<z.ZodObject<{
+                        message: z.ZodString;
+                        source: z.ZodOptional<z.ZodString>;
+                    }, z.core.$strip>>;
+                    inference_path: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>, z.ZodObject<{
+                    coverage: z.ZodLiteral<"not_loaded">;
+                    reason: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>], "coverage">;
+                translational_commentary: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                    coverage: z.ZodLiteral<"available">;
+                    data: z.ZodObject<{
+                        rows: z.ZodArray<z.ZodObject<{
+                            severity: z.ZodEnum<{
+                                ok: "ok";
+                                caution: "caution";
+                                gap: "gap";
+                            }>;
+                            organ: z.ZodOptional<z.ZodString>;
+                            species: z.ZodOptional<z.ZodString>;
+                            text: z.ZodString;
+                        }, z.core.$strip>>;
+                    }, z.core.$strip>;
+                    inference_path: z.ZodOptional<z.ZodString>;
+                    truncated: z.ZodOptional<z.ZodBoolean>;
+                }, z.core.$strip>, z.ZodObject<{
+                    coverage: z.ZodLiteral<"queried_no_data">;
+                    error: z.ZodOptional<z.ZodObject<{
+                        message: z.ZodString;
+                        source: z.ZodOptional<z.ZodString>;
+                    }, z.core.$strip>>;
+                    inference_path: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>, z.ZodObject<{
+                    coverage: z.ZodLiteral<"not_loaded">;
+                    reason: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>], "coverage">;
+                preclinical_literature: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                    coverage: z.ZodLiteral<"available">;
+                    data: z.ZodObject<{
+                        rows: z.ZodArray<z.ZodObject<{
+                            pmid: z.ZodNullable<z.ZodString>;
+                            claim: z.ZodString;
+                            excerpt: z.ZodOptional<z.ZodString>;
+                            model_system: z.ZodString;
+                            species: z.ZodString;
+                        }, z.core.$strip>>;
+                        total_claim_count: z.ZodNumber;
+                        truncated: z.ZodBoolean;
+                    }, z.core.$strip>;
+                    inference_path: z.ZodOptional<z.ZodString>;
+                    truncated: z.ZodOptional<z.ZodBoolean>;
+                }, z.core.$strip>, z.ZodObject<{
+                    coverage: z.ZodLiteral<"queried_no_data">;
+                    error: z.ZodOptional<z.ZodObject<{
+                        message: z.ZodString;
+                        source: z.ZodOptional<z.ZodString>;
+                    }, z.core.$strip>>;
+                    inference_path: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>, z.ZodObject<{
+                    coverage: z.ZodLiteral<"not_loaded">;
+                    reason: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>], "coverage">;
+                data_coverage: z.ZodObject<{
+                    ko: z.ZodEnum<{
+                        none: "none";
+                        available: "available";
+                        queried_no_data: "queried_no_data";
+                        not_loaded: "not_loaded";
+                        no_phenotypes: "no_phenotypes";
+                    }>;
+                    expression: z.ZodEnum<{
+                        available: "available";
+                        queried_no_data: "queried_no_data";
+                        not_loaded: "not_loaded";
+                    }>;
+                    literature: z.ZodEnum<{
+                        available: "available";
+                        queried_no_data: "queried_no_data";
+                        not_loaded: "not_loaded";
+                    }>;
+                    per_species: z.ZodRecord<z.ZodString, z.ZodBoolean>;
+                }, z.core.$strip>;
+            }, z.core.$strip>;
+            key_papers: z.ZodDiscriminatedUnion<[z.ZodObject<{
+                coverage: z.ZodLiteral<"available">;
+                data: z.ZodObject<{
+                    rows: z.ZodArray<z.ZodObject<{
+                        pmid: z.ZodString;
+                        title: z.ZodString;
+                        internal_reference_count: z.ZodNumber;
+                        year: z.ZodOptional<z.ZodNumber>;
+                    }, z.core.$strip>>;
+                }, z.core.$strip>;
+                inference_path: z.ZodOptional<z.ZodString>;
+                truncated: z.ZodOptional<z.ZodBoolean>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"queried_no_data">;
+                error: z.ZodOptional<z.ZodObject<{
+                    message: z.ZodString;
+                    source: z.ZodOptional<z.ZodString>;
+                }, z.core.$strip>>;
+                inference_path: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>, z.ZodObject<{
+                coverage: z.ZodLiteral<"not_loaded">;
+                reason: z.ZodOptional<z.ZodString>;
+            }, z.core.$strip>], "coverage">;
+        }, z.core.$strip>;
+        generated_at: z.ZodString;
+    }, z.core.$strip>;
+}, z.core.$strip>;
+export type Phase4Output = z.infer<typeof Phase4OutputSchema>;
+export { Phase3BundleSchema };
+export type { Phase3Bundle };
+/**
+ * Run Phase 4 — assemble the v4 dossier body from the Phase-3 bundle.
+ * Deterministic over its inputs; safely cached on DBOS replay.
+ */
+export declare function phase4Assemble(pool: Pool, phase3: Phase3Bundle): Promise<Phase4Output>;