@inflexa-ai/harness 0.35.7 → 0.36.0

package/dist/workflows/target-assessment/assemblers/orchestrator.d.ts

@@ -1,118 +0,0 @@
-/**
- * Phase-4 deterministic assemblers.
- *
- * Each assembler maps Phase-1 / Phase-2 / Phase-3 outputs onto the
- * corresponding dossier section schema. Coverage is honored end-to-end: an
- * upstream that came back empty or was never consulted yields
- * `queried_no_data` / `not_loaded` rather than a fabricated section.
- *
- * Where a section applies a threshold of its own, the decision runs through
- * `coverageFromFilteredRows` over both counts — what survived and what the
- * threshold discarded — so a section our own filter emptied reports
- * `filtered` rather than an `available` section holding nothing. Deciding
- * coverage first and filtering the payload afterwards is the shape that loses
- * that distinction.
- *
- * Aggregate rows preserve their contributing evidence under `evidence: [...]`
- * arrays.
- */
-import type { DossierBody, Entity, TractabilitySection } from "@inflexa-ai/harness/contracts/target-dossier.js";
-import type { Phase2Bundle } from "../steps/phase2-aggregate.js";
-import type { Phase3Bundle } from "../steps/phase3-aggregate.js";
-import type { ResolvedTarget } from "../schemas.js";
-import type { Pool } from "pg";
-import type { Logger } from "../../../lib/logger.js";
-import type { ClinicalConsequenceAnnotatorDeps } from "../lib/clinical-consequence-annotator.js";
-import { HIGH_EXPRESSION_TPM_THRESHOLD } from "../lib/expression-constants.js";
-export { HIGH_EXPRESSION_TPM_THRESHOLD };
-export declare function assembleEntity(resolved: ResolvedTarget): Entity;
-type OpenTargetsCoverageResult = Phase2Bundle["phase1"]["collectors"]["opentargets"];
-export type DrugForTractability = {
-    drug_id: string;
-    drug_name: string | null;
-    molecule_type: string | null;
-    max_phase: number | null;
-};
-/**
- * Pure helper that flips `has_approved_drug=true` and populates
- * `approved_drug_ids` on any modality that has a max_phase=4 drug in
- * the provided list. Unrecognised molecule_types are silently ignored.
- */
-export declare function enrichTractabilityModalitiesWithApprovals<M extends {
-    modality: "small_molecule" | "antibody" | "other_clinical";
-    has_approved_drug: boolean;
-    approved_drug_ids?: string[];
-}>(modalities: M[], drugs: DrugForTractability[]): (M & {
-    approved_drug_ids?: string[];
-})[];
-export declare function assembleTractability(resolved: ResolvedTarget, ot: OpenTargetsCoverageResult, drugs: DrugForTractability[]): TractabilitySection;
-/**
- * Build a body-only dossier from Phase-2 (and optionally Phase-3)
- * outputs. Synthesis-dependent fields stay `not_loaded` until Phase 5
- * stamps them in `phase5-persist.ts`. The derived sub-tree is NOT
- * attached here — phase5-persist computes it after synthesis is stamped
- * so the final derived values reflect liability bullets and safety flags.
- */
-export declare function assembleDossier(pool: Pool, phase2: Phase2Bundle, phase3?: Phase3Bundle, annotatorDeps?: ClinicalConsequenceAnnotatorDeps, logger?: Logger): Promise<DossierBody>;
-type ReconcileFaersClassPrecedent = {
-    coverage?: "available" | "queried_no_data" | "not_loaded";
-    data?: {
-        per_organ?: Array<{
-            organ?: string;
-            top_aes?: Array<{
-                term?: string;
-                report_count?: number;
-            }>;
-        }>;
-        drugs_in_class?: Array<{
-            drug_id?: string;
-            drug_name?: string;
-        }>;
-    };
-} | undefined;
-type ReconcileFaersOutput = {
-    coverage: "available";
-    data: {
-        total_reports: number;
-        seriousness: {
-            coverage: "queried_no_data";
-            total_reports: number;
-        };
-        top_signals: Array<{
-            meddra_term: string;
-            organ?: string;
-            report_count: number;
-        }>;
-        per_modulator: Array<{
-            modulator: string;
-            modulator_id: string | null;
-            report_count: number;
-            coverage: "queried_no_data";
-        }>;
-    };
-    error?: {
-        message: string;
-    };
-    inference_path: string;
-};
-/**
- * Reconciles target-level FAERS with class_precedent aggregates.
- *
- * When target-level FAERS has data (coverage: "available"), pass through
- * unchanged. When class_precedent has FAERS-derived reports in per_organ,
- * fold them into a class-scoped FAERS summary payload with
- * coverage: "available" and inference_path tagged — rather than leaving
- * the section as queried_no_data, which creates an evidence conflict
- * that the conflict-detector flags. When neither has data, return
- * faers unchanged.
- */
-export declare function reconcileFaersCoverage<TFaers extends {
-    coverage: "available" | "queried_no_data" | "not_loaded";
-    error?: {
-        message: string;
-    };
-    reason?: string;
-}>(input: {
-    faers: TFaers;
-    class_precedent: ReconcileFaersClassPrecedent;
-}): TFaers | ReconcileFaersOutput;