@inflexa-ai/harness 0.35.8 → 0.36.1

package/dist/workflows/target-assessment/lib/target-identity-filter.d.ts

@@ -1,59 +0,0 @@
-/**
- * Trial-attribution classifier + UniProt-backed identity resolvers.
- *
- * `resolveOnTargetChemblIds` and `resolveFamilySiblingUniprots` fetch from
- * authoritative sources at assembly time — UniProt for ChEMBL cross-references,
- * IUPHAR Guide to Pharmacology for receptor-family siblings — so assessing a
- * new HGNC target needs no per-target curation here.
- *
- * The actual loop-level checks (`isOnTargetChemblId` etc.) take the
- * resolved arrays as plain inputs so the per-row assembly path stays
- * synchronous after a single upfront await.
- */
-import type { Logger } from "../../../lib/logger.js";
-export type TrialAttributionInput = {
-    assessmentUniprot: string;
-    /** UniProts of related family receptors (resolved from IUPHAR family siblings). */
-    familyUniprots: string[];
-    interventions: Array<{
-        drugChemblId: string | null;
-        name: string;
-    }>;
-    conditions: string[];
-    drugTargetResolver: (chemblId: string) => Promise<string[]>;
-};
-export type TrialAttributionResult = {
-    match_confidence: "high" | "low" | "off_target";
-    intervention_target_uniprots: string[];
-    related_target_uniprots: string[];
-};
-/**
- * Classify how strongly a trial pertains to the assessment target based on
- * the intervention drug's mechanism target.
- */
-export declare function classifyTrialAttribution(input: TrialAttributionInput): Promise<TrialAttributionResult>;
-/**
- * Resolve every ChEMBL target id that UniProt links to the given accession.
- * The result is used as a positive list for on-target self-hit detection —
- * a polypharm row whose off_target_id is in this list is the assessment
- * target itself (alternate ChEMBL entry), not an off-target liability.
- *
- * Returns [] when the accession is missing or UniProt has no ChEMBL xrefs.
- * Network failures are surfaced as an empty list so the assembler degrades
- * to "no alternate-id filtering" rather than blocking the run.
- */
-export declare function resolveOnTargetChemblIds(assessmentUniprot: string, logger?: Logger): Promise<string[]>;
-/**
- * Resolve UniProt accessions of sibling receptors in the same IUPHAR family
- * as the assessment target. Used by `classifyTrialAttribution` so a trial
- * whose intervention hits a paralog (e.g., CALCRL when CALCR is the
- * assessment target) lands in the related bucket rather than the
- * primary trials list.
- */
-export declare function resolveFamilySiblingUniprots(uniprotOrGeneSymbol: string, logger?: Logger): Promise<string[]>;
-/**
- * Returns true if `chemblId` is among the supplied list of on-target ChEMBL
- * ids for the assessment protein. Caller is responsible for resolving the
- * list once via `resolveOnTargetChemblIds` and reusing it across rows.
- */
-export declare function isOnTargetChemblId(chemblId: string, onTargetChemblIds: string[]): boolean;

package/dist/workflows/target-assessment/lib/target-identity-filter.js

@@ -1,95 +0,0 @@
-/**
- * Trial-attribution classifier + UniProt-backed identity resolvers.
- *
- * `resolveOnTargetChemblIds` and `resolveFamilySiblingUniprots` fetch from
- * authoritative sources at assembly time — UniProt for ChEMBL cross-references,
- * IUPHAR Guide to Pharmacology for receptor-family siblings — so assessing a
- * new HGNC target needs no per-target curation here.
- *
- * The actual loop-level checks (`isOnTargetChemblId` etc.) take the
- * resolved arrays as plain inputs so the per-row assembly path stays
- * synchronous after a single upfront await.
- */
-import { createNoopLogger } from "../../../lib/console-logger.js";
-import { withHost } from "../../../lib/host-concurrency.js";
-import { getFamilySiblingUniprots } from "../../../tools/lib/iuphar-client.js";
-import { getChemblIdsByUniProt } from "../../../tools/lib/uniprot-client.js";
-/**
- * Classify how strongly a trial pertains to the assessment target based on
- * the intervention drug's mechanism target.
- */
-export async function classifyTrialAttribution(input) {
-    const interventionTargets = new Set();
-    for (const iv of input.interventions) {
-        if (!iv.drugChemblId)
-            continue;
-        const accs = await input.drugTargetResolver(iv.drugChemblId);
-        for (const a of accs)
-            interventionTargets.add(a);
-    }
-    const intervention_target_uniprots = [...interventionTargets];
-    const hitsAssessment = interventionTargets.has(input.assessmentUniprot);
-    const related_target_uniprots = [...interventionTargets].filter((a) => input.familyUniprots.includes(a) && a !== input.assessmentUniprot);
-    if (hitsAssessment) {
-        return { match_confidence: "high", intervention_target_uniprots, related_target_uniprots };
-    }
-    if (related_target_uniprots.length > 0) {
-        return { match_confidence: "off_target", intervention_target_uniprots, related_target_uniprots };
-    }
-    return { match_confidence: "low", intervention_target_uniprots, related_target_uniprots };
-}
-/**
- * Resolve every ChEMBL target id that UniProt links to the given accession.
- * The result is used as a positive list for on-target self-hit detection —
- * a polypharm row whose off_target_id is in this list is the assessment
- * target itself (alternate ChEMBL entry), not an off-target liability.
- *
- * Returns [] when the accession is missing or UniProt has no ChEMBL xrefs.
- * Network failures are surfaced as an empty list so the assembler degrades
- * to "no alternate-id filtering" rather than blocking the run.
- */
-export async function resolveOnTargetChemblIds(assessmentUniprot, logger) {
-    if (!assessmentUniprot)
-        return [];
-    try {
-        return await withHost("uniprot", () => getChemblIdsByUniProt(assessmentUniprot));
-    }
-    catch (err) {
-        // UniProt answers an unknown accession with a 404, and the client maps that
-        // to an empty record. Thus a throw here is always an unexpected cause, and
-        // the empty list silently turns off the self-hit filter of the panel.
-        const log = (logger ?? createNoopLogger()).named("ta-identity.on-target-chembl");
-        log.error("UniProt ChEMBL cross-reference lookup failed", { uniprot: assessmentUniprot, ...log.errorFields(err) });
-        return [];
-    }
-}
-/**
- * Resolve UniProt accessions of sibling receptors in the same IUPHAR family
- * as the assessment target. Used by `classifyTrialAttribution` so a trial
- * whose intervention hits a paralog (e.g., CALCRL when CALCR is the
- * assessment target) lands in the related bucket rather than the
- * primary trials list.
- */
-export async function resolveFamilySiblingUniprots(uniprotOrGeneSymbol, logger) {
-    if (!uniprotOrGeneSymbol)
-        return [];
-    const log = (logger ?? createNoopLogger()).named("ta-identity.family-siblings");
-    try {
-        return await withHost("iuphar", () => getFamilySiblingUniprots(uniprotOrGeneSymbol, log));
-    }
-    catch (err) {
-        // IUPHAR answers an unknown target with an empty list, thus a throw here is
-        // always an unexpected cause. The empty list then routes a paralog trial into
-        // the primary trials list, which is the defect that this resolver prevents.
-        log.error("IUPHAR family-sibling lookup failed", { query: uniprotOrGeneSymbol, ...log.errorFields(err) });
-        return [];
-    }
-}
-/**
- * Returns true if `chemblId` is among the supplied list of on-target ChEMBL
- * ids for the assessment protein. Caller is responsible for resolving the
- * list once via `resolveOnTargetChemblIds` and reusing it across rows.
- */
-export function isOnTargetChemblId(chemblId, onTargetChemblIds) {
-    return onTargetChemblIds.includes(chemblId);
-}

package/dist/workflows/target-assessment/lib/therapeutic-programs.d.ts

@@ -1,20 +0,0 @@
-import type { EvidenceItem } from "@inflexa-ai/harness/contracts/target-dossier.js";
-export type TherapeuticProgramRow = {
-    programId: string;
-    name: string;
-    targetSymbol: string;
-    targetUniprot: string | null;
-    modality: string;
-    sponsor: string | null;
-    mechanism: string;
-    status: string;
-    nctIds: string[];
-    pmids: string[];
-    evidence: EvidenceItem[];
-    confidence: "high" | "medium" | "low";
-};
-export type TherapeuticProgramTarget = {
-    geneSymbol: string;
-    uniprot: string | null;
-};
-export declare function findTherapeuticProgramsForTarget(target: TherapeuticProgramTarget): TherapeuticProgramRow[];

package/dist/workflows/target-assessment/lib/therapeutic-programs.js

@@ -1,68 +0,0 @@
-const PROGRAM_REGISTRY = [
-    {
-        programId: "AL002",
-        name: "AL002",
-        targetSymbol: "TREM2",
-        targetUniprot: "Q9NZC2",
-        modality: "agonistic monoclonal antibody",
-        sponsor: "Alector",
-        mechanism: "TREM2 agonistic antibody intended to activate microglial TREM2 signaling",
-        status: "Phase 2 completed; negative efficacy result reported",
-        nctIds: ["NCT03635047", "NCT04592874"],
-        pmids: ["39444037", "41787076"],
-        confidence: "high",
-        evidence: [
-            {
-                source: "pubmed",
-                pmid: "39444037",
-                predicate: "phase_1_target_engagement",
-                is_human: true,
-                is_clinical: true,
-            },
-            {
-                source: "pubmed",
-                pmid: "41787076",
-                predicate: "phase_2_negative_trial",
-                is_human: true,
-                is_clinical: true,
-            },
-            {
-                source: "clinicaltrials.gov",
-                predicate: "registered_trial",
-                metadata: { nct_ids: ["NCT03635047", "NCT04592874"] },
-                is_human: true,
-                is_clinical: true,
-            },
-        ],
-    },
-    {
-        programId: "VHB937",
-        name: "VHB937",
-        targetSymbol: "TREM2",
-        targetUniprot: "Q9NZC2",
-        modality: "TREM2-stabilizing monoclonal antibody",
-        sponsor: "Novartis",
-        mechanism: "TREM2 antibody program in early Alzheimer disease",
-        status: "Phase 2 recruiting",
-        nctIds: ["NCT07094516"],
-        pmids: [],
-        confidence: "medium",
-        evidence: [
-            {
-                source: "clinicaltrials.gov",
-                predicate: "registered_trial",
-                metadata: { nct_ids: ["NCT07094516"] },
-                is_human: true,
-                is_clinical: true,
-            },
-        ],
-    },
-];
-export function findTherapeuticProgramsForTarget(target) {
-    const symbol = target.geneSymbol.toUpperCase();
-    return PROGRAM_REGISTRY.filter((program) => {
-        if (program.targetSymbol.toUpperCase() === symbol)
-            return true;
-        return Boolean(target.uniprot && program.targetUniprot === target.uniprot);
-    });
-}

package/dist/workflows/target-assessment/metrics.d.ts

@@ -1,16 +0,0 @@
-/**
- * OpenTelemetry counters for the target-assessment DBOS workflow.
- *
- * Surfaces two signals:
- *  - `cortex.harness.ta.workflow.terminal_reason` — per terminal path; the
- *    alert in §16.5/§16.6 reads this. `reason` ∈ {completed,
- *    target-unresolved, schema-violation, derived-invariant-violation,
- *    unexpected-throw, suspended-on-402, operator-cancelled}.
- *  - billing cache_hit/_miss live in `harness/billing/target-assessment-resolver.ts`.
- *
- * Memoised meter so a re-imported module in tests doesn't recreate the
- * instruments against the same MeterProvider (which would log noisy
- * "duplicate instrument" warnings).
- */
-export type TaTerminalReason = "completed" | "target-unresolved" | "schema-violation" | "derived-invariant-violation" | "unexpected-throw" | "suspended-on-402" | "operator-cancelled" | "deleted";
-export declare function recordTerminalReason(reason: TaTerminalReason): void;

package/dist/workflows/target-assessment/metrics.js

@@ -1,30 +0,0 @@
-/**
- * OpenTelemetry counters for the target-assessment DBOS workflow.
- *
- * Surfaces two signals:
- *  - `cortex.harness.ta.workflow.terminal_reason` — per terminal path; the
- *    alert in §16.5/§16.6 reads this. `reason` ∈ {completed,
- *    target-unresolved, schema-violation, derived-invariant-violation,
- *    unexpected-throw, suspended-on-402, operator-cancelled}.
- *  - billing cache_hit/_miss live in `harness/billing/target-assessment-resolver.ts`.
- *
- * Memoised meter so a re-imported module in tests doesn't recreate the
- * instruments against the same MeterProvider (which would log noisy
- * "duplicate instrument" warnings).
- */
-import { metrics } from "@opentelemetry/api";
-let _instruments;
-function getInstruments() {
-    if (_instruments === undefined) {
-        const meter = metrics.getMeter("cortex.harness.ta");
-        _instruments = {
-            terminalReason: meter.createCounter("cortex.harness.ta.workflow.terminal_reason", {
-                description: "TA workflow terminal dispatches by reason (alert source)",
-            }),
-        };
-    }
-    return _instruments;
-}
-export function recordTerminalReason(reason) {
-    getInstruments().terminalReason.add(1, { reason });
-}