npm - @inflexa-ai/harness - Versions diffs - 0.35.8 → 0.36.1 - Mend

@inflexa-ai/harness 0.35.8 → 0.36.1

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Files changed (198) hide show

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

@@ -1,3182 +0,0 @@
-/**
- * Phase 4 — dossier assembly.
- *
- * Calls `assembleDossier` (~3.5K LOC of aggregation over the Phase-3 bundle)
- * and returns the assembled `DossierBody`. The safety-corroboration and
- * claim-investigation sections are stamped by the workflow body between this
- * step and synthesis; the Phase-5 synthesis sections (translational commentary,
- * liability bullets, safety-flags trail) are stamped by the Phase-5 persist
- * step.
- *
- * 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 compute. Replay caching earns its keep here because `annotatorDeps`
- * carries the per-row clinical-consequence annotator's LLM seam: assembly makes
- * bounded model calls for off-target rows that have no cached annotation. Those
- * calls are per-row best-effort — a failure leaves the row's original fallback —
- * and their results are cached in Postgres, so a repeat assessment of the same
- * target reaches them without an LLM call at all.
- */
-import type { Pool } from "pg";
-import { z } from "zod";
-import type { Logger } from "../../lib/logger.js";
-import type { ClinicalConsequenceAnnotatorDeps } from "./lib/clinical-consequence-annotator.js";
-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<{
-        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>;
-            dropped_count: z.ZodOptional<z.ZodNumber>;
-            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.$strip>, z.ZodObject<{
-            coverage: z.ZodLiteral<"filtered">;
-            filter: z.ZodString;
-            dropped_count: z.ZodNumber;
-            inference_path: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>, z.ZodObject<{
-            coverage: z.ZodLiteral<"not_loaded">;
-            reason: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>], "coverage">;
-        entity: z.ZodObject<{
-            canonicalId: z.ZodString;
-            symbol: z.ZodString;
-            displayName: z.ZodString;
-            entityType: z.ZodEnum<{
-                gene: "gene";
-                protein: "protein";
-                rna: "rna";
-                complex: "complex";
-            }>;
-            ontology: z.ZodString;
-            identifiers: z.ZodObject<{
-                hgnc: z.ZodOptional<z.ZodString>;
-                ensembl: z.ZodOptional<z.ZodString>;
-                uniprot: z.ZodOptional<z.ZodString>;
-                chembl: z.ZodOptional<z.ZodString>;
-                ncbiGene: z.ZodOptional<z.ZodString>;
-            }, z.core.$strip>;
-            synonyms: z.ZodDefault<z.ZodArray<z.ZodString>>;
-            proteinFamily: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>;
-        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.ZodEnum<{
-                        hematologic: "hematologic";
-                        metabolic: "metabolic";
-                        immune: "immune";
-                        hepatic: "hepatic";
-                        musculoskeletal: "musculoskeletal";
-                        cns: "cns";
-                        renal: "renal";
-                        reproductive: "reproductive";
-                        respiratory: "respiratory";
-                        cardiac: "cardiac";
-                        vascular: "vascular";
-                        pns: "pns";
-                        gi: "gi";
-                        pancreas: "pancreas";
-                        endocrine_thyroid: "endocrine_thyroid";
-                        dermatologic: "dermatologic";
-                        ocular: "ocular";
-                        oncology: "oncology";
-                    }>>;
-                    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;
-                    metadata: z.ZodOptional<z.ZodObject<{
-                        merged_chembl_ids: z.ZodOptional<z.ZodArray<z.ZodString>>;
-                    }, z.core.$strip>>;
-                    relationship: z.ZodLiteral<"off_target">;
-                    support: z.ZodDiscriminatedUnion<[z.ZodObject<{
-                        state: z.ZodLiteral<"scored">;
-                        evidence: z.ZodArray<z.ZodObject<{
-                            pmid: z.ZodOptional<z.ZodString>;
-                            doi: z.ZodOptional<z.ZodString>;
-                            accession: z.ZodOptional<z.ZodString>;
-                            source: z.ZodString;
-                            predicate: z.ZodOptional<z.ZodString>;
-                            score: z.ZodOptional<z.ZodNumber>;
-                            strength: z.ZodOptional<z.ZodString>;
-                            is_human: z.ZodOptional<z.ZodBoolean>;
-                            is_clinical: z.ZodOptional<z.ZodBoolean>;
-                            excerpt: z.ZodOptional<z.ZodString>;
-                            metadata: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
-                            regulatory_reference: z.ZodOptional<z.ZodObject<{
-                                document: z.ZodString;
-                                section: z.ZodOptional<z.ZodString>;
-                                doc_id: z.ZodOptional<z.ZodString>;
-                                doc_url: z.ZodOptional<z.ZodString>;
-                            }, z.core.$strip>>;
-                        }, z.core.$strip>>;
-                    }, z.core.$strip>, z.ZodObject<{
-                        state: z.ZodLiteral<"unknown">;
-                        reason: z.ZodString;
-                    }, z.core.$strip>], "state">;
-                }, z.core.$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.ZodEnum<{
-                        hematologic: "hematologic";
-                        metabolic: "metabolic";
-                        immune: "immune";
-                        hepatic: "hepatic";
-                        musculoskeletal: "musculoskeletal";
-                        cns: "cns";
-                        renal: "renal";
-                        reproductive: "reproductive";
-                        respiratory: "respiratory";
-                        cardiac: "cardiac";
-                        vascular: "vascular";
-                        pns: "pns";
-                        gi: "gi";
-                        pancreas: "pancreas";
-                        endocrine_thyroid: "endocrine_thyroid";
-                        dermatologic: "dermatologic";
-                        ocular: "ocular";
-                        oncology: "oncology";
-                    }>>;
-                    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.$strip>]>;
-                    selectivity_window_below_threshold: z.ZodBoolean;
-                    metadata: z.ZodOptional<z.ZodObject<{
-                        merged_chembl_ids: z.ZodOptional<z.ZodArray<z.ZodString>>;
-                    }, z.core.$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;
-                    evidence: z.ZodArray<z.ZodObject<{
-                        pmid: z.ZodOptional<z.ZodString>;
-                        doi: z.ZodOptional<z.ZodString>;
-                        accession: 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>;
-            dropped_count: z.ZodOptional<z.ZodNumber>;
-            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.$strip>, z.ZodObject<{
-            coverage: z.ZodLiteral<"filtered">;
-            filter: z.ZodString;
-            dropped_count: z.ZodNumber;
-            inference_path: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>, z.ZodObject<{
-            coverage: z.ZodLiteral<"not_loaded">;
-            reason: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>], "coverage">;
-        liability_summary: z.ZodObject<{
-            liability_bullets: z.ZodArray<z.ZodObject<{
-                text: z.ZodString;
-                rationale: z.ZodString;
-                category: z.ZodEnum<{
-                    other: "other";
-                    fatal_post_market: "fatal_post_market";
-                    class_liability: "class_liability";
-                    off_target_safety: "off_target_safety";
-                    high_safety_organ_expression: "high_safety_organ_expression";
-                    broad_expression: "broad_expression";
-                }>;
-                support: z.ZodDiscriminatedUnion<[z.ZodObject<{
-                    state: z.ZodLiteral<"scored">;
-                    evidence: z.ZodArray<z.ZodObject<{
-                        pmid: z.ZodOptional<z.ZodString>;
-                        doi: z.ZodOptional<z.ZodString>;
-                        accession: z.ZodOptional<z.ZodString>;
-                        source: z.ZodString;
-                        predicate: z.ZodOptional<z.ZodString>;
-                        score: z.ZodOptional<z.ZodNumber>;
-                        strength: z.ZodOptional<z.ZodString>;
-                        is_human: z.ZodOptional<z.ZodBoolean>;
-                        is_clinical: z.ZodOptional<z.ZodBoolean>;
-                        excerpt: z.ZodOptional<z.ZodString>;
-                        metadata: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
-                        regulatory_reference: z.ZodOptional<z.ZodObject<{
-                            document: z.ZodString;
-                            section: z.ZodOptional<z.ZodString>;
-                            doc_id: z.ZodOptional<z.ZodString>;
-                            doc_url: z.ZodOptional<z.ZodString>;
-                        }, z.core.$strip>>;
-                    }, z.core.$strip>>;
-                }, z.core.$strip>, z.ZodObject<{
-                    state: z.ZodLiteral<"unknown">;
-                    reason: z.ZodString;
-                }, z.core.$strip>], "state">;
-            }, z.core.$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>;
-        indications: z.ZodDiscriminatedUnion<[z.ZodObject<{
-            coverage: z.ZodLiteral<"available">;
-            data: z.ZodObject<{
-                rows: z.ZodArray<z.ZodObject<{
-                    disease_id: z.ZodString;
-                    disease_name: z.ZodString;
-                    composite_score: z.ZodNumber;
-                    composite_score_breakdown: z.ZodOptional<z.ZodObject<{
-                        base: z.ZodNumber;
-                        source_bonuses: z.ZodRecord<z.ZodString, z.ZodNumber>;
-                        paper_depth: z.ZodNumber;
-                    }, z.core.$strip>>;
-                    evidence_score: z.ZodNumber;
-                    source_count: z.ZodNumber;
-                    unique_paper_count: z.ZodNumber;
-                    sources: z.ZodArray<z.ZodString>;
-                    evidence: z.ZodArray<z.ZodObject<{
-                        pmid: z.ZodOptional<z.ZodString>;
-                        doi: z.ZodOptional<z.ZodString>;
-                        accession: z.ZodOptional<z.ZodString>;
-                        source: z.ZodString;
-                        predicate: z.ZodOptional<z.ZodString>;
-                        score: z.ZodOptional<z.ZodNumber>;
-                        strength: z.ZodOptional<z.ZodString>;
-                        is_human: z.ZodOptional<z.ZodBoolean>;
-                        is_clinical: z.ZodOptional<z.ZodBoolean>;
-                        excerpt: z.ZodOptional<z.ZodString>;
-                        metadata: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
-                        regulatory_reference: z.ZodOptional<z.ZodObject<{
-                            document: z.ZodString;
-                            section: z.ZodOptional<z.ZodString>;
-                            doc_id: z.ZodOptional<z.ZodString>;
-                            doc_url: z.ZodOptional<z.ZodString>;
-                        }, z.core.$strip>>;
-                    }, z.core.$strip>>;
-                }, z.core.$strip>>;
-                excluded_unsupported_count: z.ZodOptional<z.ZodNumber>;
-                unsupported_associations: z.ZodOptional<z.ZodArray<z.ZodObject<{
-                    disease_id: z.ZodString;
-                    disease_name: z.ZodString;
-                }, z.core.$strip>>>;
-            }, z.core.$strip>;
-            dropped_count: z.ZodOptional<z.ZodNumber>;
-            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.$strip>, z.ZodObject<{
-            coverage: z.ZodLiteral<"filtered">;
-            filter: z.ZodString;
-            dropped_count: z.ZodNumber;
-            inference_path: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>, z.ZodObject<{
-            coverage: z.ZodLiteral<"not_loaded">;
-            reason: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>], "coverage">;
-        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>;
-                        accession: 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.$strip>;
-            dropped_count: z.ZodOptional<z.ZodNumber>;
-            inference_path: z.ZodOptional<z.ZodString>;
-            truncated: z.ZodOptional<z.ZodBoolean>;
-        }, z.core.$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<"filtered">;
-            filter: z.ZodString;
-            dropped_count: z.ZodNumber;
-            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">;
-        clinical_development: z.ZodObject<{
-            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.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.ZodEnum<{
-                            low: "low";
-                            medium: "medium";
-                            high: "high";
-                            off_target: "off_target";
-                        }>;
-                        attribution: z.ZodObject<{
-                            relationship: z.ZodEnum<{
-                                unknown: "unknown";
-                                related_family_target: "related_family_target";
-                                condition_only: "condition_only";
-                                direct_modulator: "direct_modulator";
-                                class_modulator: "class_modulator";
-                                target_biomarker: "target_biomarker";
-                                pathway_biomarker: "pathway_biomarker";
-                                unrelated: "unrelated";
-                            }>;
-                            evidence_role: z.ZodEnum<{
-                                supports_target: "supports_target";
-                                contextual: "contextual";
-                                excluded: "excluded";
-                            }>;
-                            basis: z.ZodArray<z.ZodObject<{
-                                kind: z.ZodEnum<{
-                                    mechanism_target_match: "mechanism_target_match";
-                                    known_class_drug: "known_class_drug";
-                                    therapeutic_program_match: "therapeutic_program_match";
-                                    related_family_target: "related_family_target";
-                                    biomarker_endpoint: "biomarker_endpoint";
-                                    condition_only: "condition_only";
-                                    text_match: "text_match";
-                                    manual: "manual";
-                                }>;
-                                source: z.ZodString;
-                                excerpt: z.ZodOptional<z.ZodString>;
-                                metadata: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
-                            }, z.core.$strip>>;
-                            resolved_interventions: z.ZodDefault<z.ZodArray<z.ZodObject<{
-                                name: z.ZodString;
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-                                chembl_id: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-                                therapeutic_program_id: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-                                target_uniprots: z.ZodDefault<z.ZodArray<z.ZodString>>;
-                                resolver_source: z.ZodString;
-                            }, z.core.$strip>>>;
-                            exclusion_reason: z.ZodOptional<z.ZodString>;
-                        }, z.core.$strip>;
-                        eligible_for_toxicology_aggregation: z.ZodBoolean;
-                    }, z.core.$strip>>>;
-                }, z.core.$strip>;
-                dropped_count: z.ZodOptional<z.ZodNumber>;
-                inference_path: z.ZodOptional<z.ZodString>;
-                truncated: z.ZodOptional<z.ZodBoolean>;
-            }, z.core.$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<"filtered">;
-                filter: z.ZodString;
-                dropped_count: z.ZodNumber;
-                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";
-                        }>;
-                        model_id: z.ZodString;
-                        attempt_count: z.ZodNumber;
-                        retry_critique: z.ZodNullable<z.ZodString>;
-                        output_chars: z.ZodNumber;
-                        probe_verdict: z.ZodEnum<{
-                            skipped: "skipped";
-                            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";
-                            relaxed: "relaxed";
-                        }>;
-                        final_coverage: z.ZodEnum<{
-                            available: "available";
-                            queried_no_data: "queried_no_data";
-                        }>;
-                        error_kind: z.ZodOptional<z.ZodNullable<z.ZodEnum<{
-                            "synthesis-too-shallow": "synthesis-too-shallow";
-                            "synthesis-unavailable": "synthesis-unavailable";
-                            "voice-violation": "voice-violation";
-                        }>>>;
-                        error_message: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-                    }, z.core.$strip>>;
-                }, z.core.$strip>;
-                dropped_count: z.ZodOptional<z.ZodNumber>;
-                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.$strip>, z.ZodObject<{
-                coverage: z.ZodLiteral<"filtered">;
-                filter: z.ZodString;
-                dropped_count: z.ZodNumber;
-                inference_path: z.ZodOptional<z.ZodString>;
-            }, z.core.$strip>, z.ZodObject<{
-                coverage: z.ZodLiteral<"not_loaded">;
-                reason: z.ZodOptional<z.ZodString>;
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-            quality_gates: z.ZodDiscriminatedUnion<[z.ZodObject<{
-                coverage: z.ZodLiteral<"available">;
-                data: z.ZodObject<{
-                    rows: z.ZodArray<z.ZodObject<{
-                        gate_id: z.ZodString;
-                        status: z.ZodEnum<{
-                            blocked: "blocked";
-                            warning: "warning";
-                            pass: "pass";
-                        }>;
-                        message: z.ZodString;
-                        affected_sections: z.ZodDefault<z.ZodArray<z.ZodString>>;
-                        unresolved_count: z.ZodOptional<z.ZodNumber>;
-                        metadata: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
-                    }, z.core.$strip>>;
-                }, z.core.$strip>;
-                dropped_count: z.ZodOptional<z.ZodNumber>;
-                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.$strip>, z.ZodObject<{
-                coverage: z.ZodLiteral<"filtered">;
-                filter: z.ZodString;
-                dropped_count: z.ZodNumber;
-                inference_path: z.ZodOptional<z.ZodString>;
-            }, z.core.$strip>, z.ZodObject<{
-                coverage: z.ZodLiteral<"not_loaded">;
-                reason: z.ZodOptional<z.ZodString>;
-            }, z.core.$strip>], "coverage">;
-            recommendation_audit: z.ZodOptional<z.ZodDiscriminatedUnion<[z.ZodObject<{
-                coverage: z.ZodLiteral<"available">;
-                data: z.ZodObject<{
-                    citations_total: z.ZodNumber;
-                    citations_unresolved: z.ZodArray<z.ZodUnion<readonly [z.ZodObject<{
-                        surface: z.ZodEnum<{
-                            rationale: "rationale";
-                            key_strengths: "key_strengths";
-                            key_risks: "key_risks";
-                            modality_choice: "modality_choice";
-                        }>;
-                        path: z.ZodString;
-                        excerpt: z.ZodString;
-                    }, z.core.$strip>, z.ZodObject<{
-                        surface: z.ZodLiteral<"external_missing">;
-                        id: z.ZodString;
-                        excerpt: z.ZodString;
-                    }, z.core.$strip>, z.ZodObject<{
-                        surface: z.ZodLiteral<"organ_claim_without_probe_pass">;
-                        excerpt: z.ZodString;
-                        bullet_category: z.ZodString;
-                    }, z.core.$strip>, z.ZodObject<{
-                        surface: z.ZodLiteral<"nct_wrong_class">;
-                        id: z.ZodString;
-                        excerpt: z.ZodString;
-                    }, z.core.$strip>, z.ZodObject<{
-                        surface: z.ZodLiteral<"pmid_not_in_key_papers">;
-                        id: z.ZodString;
-                        excerpt: z.ZodString;
-                    }, z.core.$strip>, z.ZodObject<{
-                        surface: z.ZodLiteral<"direction_mismatch">;
-                        pmid: z.ZodString;
-                        excerpt: z.ZodString;
-                        paper_conclusion_direction: z.ZodOptional<z.ZodEnum<{
-                            supports: "supports";
-                            contradicts: "contradicts";
-                            ambiguous: "ambiguous";
-                        }>>;
-                    }, z.core.$strip>, z.ZodObject<{
-                        surface: z.ZodLiteral<"abstract_unavailable">;
-                        pmid: z.ZodString;
-                        excerpt: z.ZodString;
-                    }, z.core.$strip>, z.ZodObject<{
-                        surface: z.ZodLiteral<"off_topic_citation">;
-                        pmid: z.ZodString;
-                        excerpt: z.ZodString;
-                    }, z.core.$strip>]>>;
-                    non_dossier_citations: z.ZodArray<z.ZodObject<{
-                        token: z.ZodString;
-                        source: z.ZodString;
-                    }, z.core.$strip>>;
-                }, z.core.$strip>;
-                dropped_count: z.ZodOptional<z.ZodNumber>;
-                inference_path: z.ZodOptional<z.ZodString>;
-                truncated: z.ZodOptional<z.ZodBoolean>;
-            }, z.core.$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<"filtered">;
-                filter: z.ZodString;
-                dropped_count: z.ZodNumber;
-                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.$strip>;
-        executive_recommendation: z.ZodDiscriminatedUnion<[z.ZodObject<{
-            coverage: z.ZodLiteral<"available">;
-            data: z.ZodObject<{
-                disposition: z.ZodEnum<{
-                    pursue: "pursue";
-                    conditional: "conditional";
-                    de_prioritize: "de_prioritize";
-                    insufficient_evidence: "insufficient_evidence";
-                }>;
-                confidence: z.ZodEnum<{
-                    low: "low";
-                    medium: "medium";
-                    high: "high";
-                }>;
-                rationale: z.ZodString;
-                key_strengths: z.ZodDefault<z.ZodArray<z.ZodString>>;
-                key_risks: z.ZodDefault<z.ZodArray<z.ZodString>>;
-                key_risks_dropped: z.ZodOptional<z.ZodArray<z.ZodObject<{
-                    text: z.ZodString;
-                    reason: z.ZodString;
-                    cited_pmid: z.ZodOptional<z.ZodString>;
-                }, z.core.$strip>>>;
-                modality_choice: z.ZodObject<{
-                    modality: z.ZodString;
-                    rationale: z.ZodString;
-                }, z.core.$strip>;
-                coverage_qualifier: z.ZodObject<{
-                    sections_consulted: z.ZodDefault<z.ZodArray<z.ZodString>>;
-                    sections_unavailable: z.ZodDefault<z.ZodArray<z.ZodString>>;
-                    note: z.ZodString;
-                    unverified_bullets: z.ZodOptional<z.ZodArray<z.ZodObject<{
-                        text: z.ZodString;
-                        bullet_category: z.ZodString;
-                        surface: z.ZodLiteral<"organ_claim_without_probe_pass">;
-                    }, z.core.$strip>>>;
-                }, z.core.$strip>;
-            }, z.core.$strip>;
-            dropped_count: z.ZodOptional<z.ZodNumber>;
-            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.$strip>, z.ZodObject<{
-            coverage: z.ZodLiteral<"filtered">;
-            filter: z.ZodString;
-            dropped_count: z.ZodNumber;
-            inference_path: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>, z.ZodObject<{
-            coverage: z.ZodLiteral<"not_loaded">;
-            reason: z.ZodOptional<z.ZodString>;
-        }, z.core.$strip>], "coverage">;
-        generated_at: z.ZodString;
-    }, z.core.$strip>;
-}, z.core.$strip>;
-export type Phase4Output = z.infer<typeof Phase4OutputSchema>;
-export { Phase3BundleSchema };
-export type { Phase3Bundle };
-/**
- * Run Phase 4 — assemble the dossier body from the Phase-3 bundle.
- * Safely cached on DBOS replay; the caller supplies the annotator seam.
- */
-export declare function phase4Assemble(pool: Pool, phase3: Phase3Bundle, annotatorDeps?: ClinicalConsequenceAnnotatorDeps, logger?: Logger): Promise<Phase4Output>;