@inflexa-ai/harness 0.35.7 → 0.36.0

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

@@ -1,281 +0,0 @@
-import type { ClinicalTrialAttribution, DiscoveryTrials, EvidenceItem } 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 { HIGH_EXPRESSION_TPM_THRESHOLD } from "../lib/expression-constants.js";
-export { HIGH_EXPRESSION_TPM_THRESHOLD };
-type FanoutResults = Phase3Bundle["fanout"];
-export declare function assemblePreclinicalLiterature(phase2: Phase2Bundle): {
-    rows: {
-        pmid: string;
-        claim: string;
-        excerpt: undefined;
-        model_system: string;
-        species: string;
-    }[];
-    total_claim_count: number;
-    truncated: boolean;
-} | null;
-export declare function assembleKeyPapers(phase2: Phase2Bundle, internalRefCounts: Map<string, number>): {
-    pmid: string;
-    title: string;
-    internal_reference_count: number;
-    year: number | undefined;
-}[] | null;
-export declare function tallyInternalReferences(evidenceArrays: EvidenceItem[][]): Map<string, number>;
-export declare function looksLikeKoLiterature(title: string): boolean;
-export declare function assembleKoSupportingLiterature(phase2: Phase2Bundle): EvidenceItem[];
-type PpiSource = "string" | "literature";
-type PpiInputPartner = {
-    proteinA: string;
-    proteinB: string;
-    score: number;
-    experimentalScore?: number;
-    databaseScore?: number;
-    textminingScore?: number;
-};
-export declare function assembleMolecularInteractions(phase2: Phase2Bundle, fanout: FanoutResults | undefined): {
-    partner_id: string | null;
-    partner_name: string;
-    predicate: string;
-    best_score: number;
-    source_count: number;
-    paper_count: number;
-    evidence: EvidenceItem[];
-}[] | null;
-export declare function assembleBiomarkerPotential(phase2: Phase2Bundle): {
-    partner_id: string | null;
-    partner_name: string;
-    predicate: string;
-    best_score: number;
-    source_count: number;
-    paper_count: number;
-    evidence: EvidenceItem[];
-    metrics: Record<string, never>;
-}[] | null;
-export declare function assembleResistanceEvidence(phase2: Phase2Bundle): {
-    partner_id: null;
-    partner_name: string;
-    predicate: string;
-    best_score: number;
-    source_count: number;
-    paper_count: number;
-    evidence: {
-        source: string;
-        predicate: string;
-        pmid: string;
-        excerpt: string;
-        metadata: {
-            year: string;
-            journal: string;
-        };
-    }[];
-}[] | null;
-export declare function assembleCombinationEvidence(phase2: Phase2Bundle): {
-    partner_id: null;
-    partner_name: string;
-    predicate: string;
-    best_score: number;
-    source_count: number;
-    paper_count: number;
-    evidence: {
-        source: string;
-        predicate: string;
-        pmid: string;
-        excerpt: string;
-        metadata: {
-            year: string;
-            journal: string;
-        };
-    }[];
-}[] | null;
-export declare function assembleEvidenceConflicts(phase2: Phase2Bundle): {
-    evidence_item_id: string;
-    predicate: string;
-    contradicting_predicates: string[];
-    surfaced_in_section: string;
-    evidence: EvidenceItem[];
-}[] | null;
-export declare function assembleAdditionalEvidence(phase2: Phase2Bundle): {
-    rows: {
-        predicate: string;
-        evidence: {
-            source: string;
-            pmid?: string | undefined;
-            doi?: string | undefined;
-            accession?: string | undefined;
-            predicate?: string | undefined;
-            score?: number | undefined;
-            strength?: string | undefined;
-            is_human?: boolean | undefined;
-            is_clinical?: boolean | undefined;
-            excerpt?: string | undefined;
-            metadata?: Record<string, unknown> | undefined;
-            regulatory_reference?: {
-                document: string;
-                section?: string | undefined;
-                doc_id?: string | undefined;
-                doc_url?: string | undefined;
-            } | undefined;
-        }[];
-    }[];
-    score_floor: number;
-} | null;
-export declare function dedupePpiPartners(partners: PpiInputPartner[]): {
-    partner_id: string | null;
-    partner_name: string;
-    string_score: number | null;
-    literature_score: number | null;
-    combined_score: number;
-    sources: PpiSource[];
-    has_human_evidence: boolean;
-    has_clinical_evidence: boolean;
-}[];
-export declare function isClinicalMeasurement(name: string): boolean;
-/**
- * Produce a discriminated `failure_category` block. The "safety" branch
- * uses `safety_evidence_excerpt`; all other branches use
- * `category_evidence_excerpt`.
- */
-export declare function buildFailureCategoryDiscriminated(whyStopped: string): {
-    category: "safety";
-    safety_evidence_excerpt: string;
-} | {
-    category: "efficacy";
-    category_evidence_excerpt: string;
-} | {
-    category: "strategic";
-    category_evidence_excerpt: string;
-} | {
-    category: "operational";
-    category_evidence_excerpt: string;
-};
-export declare function isSelfReference(canonicalId: string, diseaseId: string, symbol: string, diseaseName: string): boolean;
-export declare const SOURCE_WEIGHTS: Record<string, number>;
-export declare function indicationCompositeScore(evidenceScore: number, sources: string[], paperCount: number): {
-    composite: number;
-    breakdown: {
-        base: number;
-        source_bonuses: Record<string, number>;
-        paper_depth: number;
-    };
-};
-export declare function deterministicTranslationalCommentary(phase2: Phase2Bundle): Array<{
-    severity: "ok" | "caution" | "gap";
-    organ?: string;
-    species?: string;
-    text: string;
-}>;
-/**
- * Dependency-injected context for resolving drug-to-target mappings.
- * Allows tests to substitute a fake resolver without hitting ChEMBL APIs.
- */
-export type AttributionContext = {
-    assessmentUniprot: string;
-    assessmentSymbol: string;
-    familyUniprots: string[];
-    drugTargetResolver: (chemblId: string) => Promise<string[]>;
-};
-/**
- * Partition a list of trials into primary (on-target or unresolved) and
- * related (off-target via a related family receptor). Each trial's
- * `match_confidence` is derived from ChEMBL mechanism resolution via
- * `classifyTrialAttribution`. When no `drugChemblId` is present on an
- * intervention (because the upstream ctgov bundle carries only drug names),
- * resolution is skipped and the trial lands in primary with confidence "low".
- */
-export declare function partitionTrialsByAttribution<T extends {
-    nctId: string;
-    title: string;
-    interventions?: string[] | Array<{
-        drugChemblId: string | null;
-        name: string;
-    }>;
-    conditions?: string[];
-}>(trials: T[], ctx: AttributionContext): Promise<{
-    primary: Array<T & {
-        match_confidence: "high" | "medium" | "low";
-    }>;
-    related: Array<T & {
-        match_confidence: "off_target";
-    }>;
-}>;
-type RelevanceBasis = {
-    kind: "drug_in_class_match";
-    drug_id: string;
-    matched_term: string;
-} | {
-    kind: "title_keyword";
-    matched_term: string;
-} | {
-    kind: "condition_match";
-    matched_term?: string;
-};
-/**
- * Classify why a candidate trial is considered relevant to the assessment.
- * Checks interventions against known class drug names first (strongest signal),
- * then falls back to title keyword matching, then condition match (weakest).
- *
- * Rows with match_confidence="low" and kind="condition_match" are unreliable
- * (they may be in the same broad disease area but use a completely different
- * drug class — e.g., SGLT2 inhibitors appearing in a GLP-1R dossier).
- * These rows are dropped by the caller before they reach the dossier.
- */
-export declare function classifyRelevanceBasis(trial: {
-    interventions?: string[];
-    conditions?: string[];
-    title: string;
-}, knownClassDrugNames: Set<string>, titleKeywordRx: RegExp): RelevanceBasis;
-/**
- * Classify match confidence for a clinical trial row in the
- * `clinical_development.trials` section.
- *
- * Priority order:
- * 1. "high"   — gene symbol appears in intervention name or trial title.
- * 2. "medium" — intervention name matches a known class drug (drug-in-class).
- * 3. "medium" — gene symbol appears in a condition string.
- * 4. "low"    — no match on any signal.
- *
- * Drug-in-class matching uses case-insensitive substring comparison against
- * `knownClassDrugNames` (uppercase strings from ChEMBL modulators). This
- * promotes calcitonin-class interventions (e.g. "Calcitonin-salmon", "SMC021")
- * for a CALCR assessment even when the gene symbol itself is absent from the
- * intervention name.
- */
-export declare function classifyClinicalTrialConfidence(trial: {
-    interventions?: string[];
-    conditions?: string[];
-    title: string;
-}, geneSymbol: string, knownClassDrugNames: Set<string>): "high" | "medium" | "low";
-export declare function assembleDiscoveryTrials(phase2: Phase2Bundle, symbol: string, attrCtx: AttributionContext, knownClassDrugNames: Set<string>, attachAttribution: <T extends {
-    nct_id: string;
-}>(row: T) => T & {
-    attribution: ClinicalTrialAttribution;
-    eligible_for_toxicology_aggregation: boolean;
-}): Promise<DiscoveryTrials>;
-export declare function assembleEvidenceTimeline(phase2: Phase2Bundle): {
-    histogram: Record<string, number>;
-    first_reported_year: number | null;
-    last_reported_year: number | null;
-    trend_labels: string[];
-} | null;
-declare const TIER_ORDER: readonly ["computational", "basic_in_vitro", "complex_in_vitro", "in_vivo_animal", "ex_vivo_human", "clinical"];
-type Tier = (typeof TIER_ORDER)[number];
-export declare function computeTranslationalChainSummary(tiers: Array<{
-    tier: Tier;
-    claim_count: number;
-    paper_count: number;
-}>): {
-    peak_evidence_tier: Tier | null;
-    progression_complete: boolean;
-    weakest_progression_gap: Tier | null;
-};
-export declare function assembleTranslationalChain(phase2: Phase2Bundle): {
-    tiers: {
-        tier: "computational" | "basic_in_vitro" | "complex_in_vitro" | "in_vivo_animal" | "ex_vivo_human" | "clinical";
-        claim_count: number;
-        paper_count: number;
-    }[];
-    peak_evidence_tier: "computational" | "basic_in_vitro" | "complex_in_vitro" | "in_vivo_animal" | "ex_vivo_human" | "clinical" | null;
-    progression_complete: boolean;
-    weakest_progression_gap: "computational" | "basic_in_vitro" | "complex_in_vitro" | "in_vivo_animal" | "ex_vivo_human" | "clinical" | null;
-} | null;