@inflexa-ai/harness 0.35.7 → 0.36.0

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

@@ -1,30 +0,0 @@
-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 };
-import type { AttributionContext } from "./literature.js";
-type FanoutResults = Phase3Bundle["fanout"];
-export type TrialOutcomeFilter = {
-    /** Confidence level per NCT ID, as determined by partitionTrialsByAttribution. */
-    attributionByNct: Map<string, "high" | "medium" | "low" | "off_target">;
-    /** NCT IDs that are low-confidence and matched only via condition string — these are off-class contaminants. */
-    lowConditionOnlyNcts: Set<string>;
-};
-export declare function aggregateTrialOutcomes(fanout: FanoutResults | undefined, filter: TrialOutcomeFilter | undefined): {
-    nct_id: string;
-    outcome_type: "primary" | "secondary" | "other";
-    measure: string;
-    description?: string;
-    time_frame?: string;
-    effect: {
-        kind: "quantitative";
-        value: number;
-        units: string;
-        ci_low?: number;
-        ci_high?: number;
-    } | {
-        kind: "not_extracted";
-        reason: "ctgov_no_numeric_result" | "ctgov_no_result_groups";
-    };
-}[] | null;
-export declare function buildTrialOutcomeFilter(phase2: Phase2Bundle, attrCtx: AttributionContext, knownClassDrugNames: Set<string>, symbol: string): Promise<TrialOutcomeFilter>;

package/dist/workflows/target-assessment/assemblers/trials.js

@@ -1,75 +0,0 @@
-import { HIGH_EXPRESSION_TPM_THRESHOLD } from "../lib/expression-constants.js";
-export { HIGH_EXPRESSION_TPM_THRESHOLD };
-import { partitionTrialsByAttribution, classifyRelevanceBasis } from "./literature.js";
-export function aggregateTrialOutcomes(fanout, filter) {
-    if (!fanout)
-        return null;
-    const items = fanout.perTrialAes.results;
-    const rows = [];
-    for (const item of items) {
-        if (item.coverage !== "available")
-            continue;
-        if (filter) {
-            const conf = filter.attributionByNct.get(item.data.nctId);
-            // Drop paralog/off-target trials entirely.
-            if (conf === "off_target")
-                continue;
-            // Drop low-confidence trials whose only relevance basis is a generic condition string.
-            if (conf === "low" && filter.lowConditionOnlyNcts.has(item.data.nctId))
-                continue;
-            // Pass-through path: an NCT ID seen in the fanout but absent from the
-            // attribution map. In normal operation the filter is built from the same
-            // [active, failed] trial set the fanout iterates, so this branch should
-            // never fire. We keep the row rather than drop silently so a future
-            // upstream change that adds NCTs to the fanout without re-running
-            // classification produces visible data rather than silent loss.
-        }
-        for (const o of item.data.outcomes ?? []) {
-            const outcome_type = o.type === "primary" ? "primary" : o.type === "secondary" ? "secondary" : "other";
-            rows.push({
-                nct_id: item.data.nctId,
-                outcome_type,
-                measure: o.measure,
-                description: o.description ?? undefined,
-                time_frame: o.timeFrame ?? undefined,
-                effect: o.effect,
-            });
-        }
-    }
-    rows.sort((a, b) => {
-        const order = { primary: 0, secondary: 1, other: 2 };
-        return order[a.outcome_type] - order[b.outcome_type];
-    });
-    if (rows.length === 0)
-        return null;
-    return rows.slice(0, 200);
-}
-export async function buildTrialOutcomeFilter(phase2, attrCtx, knownClassDrugNames, symbol) {
-    if (phase2.phase1.collectors.ctgov.coverage !== "available") {
-        return { attributionByNct: new Map(), lowConditionOnlyNcts: new Set() };
-    }
-    const ctgov = phase2.phase1.collectors.ctgov;
-    const allTrials = [...ctgov.data.active, ...ctgov.data.failed];
-    const partitioned = await partitionTrialsByAttribution(allTrials, attrCtx);
-    const attributionByNct = new Map();
-    for (const t of partitioned.primary) {
-        attributionByNct.set(t.nctId, t.match_confidence);
-    }
-    for (const t of partitioned.related) {
-        attributionByNct.set(t.nctId, "off_target");
-    }
-    // Collect NCT IDs that are low-confidence and matched only via a generic
-    // condition string — these are wrong-class contaminants (e.g. an SGLT2
-    // trial appearing in a GLP1R dossier because it shares a diabetes indication).
-    const escapedSym = symbol.replace(/[-]/g, "[-\\s]?").replace(/\d+/, "\\d+");
-    const titleKeywordRx = new RegExp(`\\b${escapedSym}\\b`, "i");
-    const lowConditionOnlyNcts = new Set(partitioned.primary
-        .filter((t) => {
-        if (t.match_confidence !== "low")
-            return false;
-        const basis = classifyRelevanceBasis(t, knownClassDrugNames, titleKeywordRx);
-        return basis.kind === "condition_match";
-    })
-        .map((t) => t.nctId));
-    return { attributionByNct, lowConditionOnlyNcts };
-}

package/dist/workflows/target-assessment/collectors/index.d.ts

@@ -1,114 +0,0 @@
-/**
- * Phase-1 collector functions for the harness DBOS workflow.
- *
- * Each collector is a pure async function `(input: ResolvedTarget) =>
- * Promise<CoverageBundle>`. Bodies: try/catch wraps a `withHost`-
- * guarded tool-client call (or a couple in parallel) and returns
- * `{coverage: "available", data}` on success or `{coverage: "queried_no_data",
- * error}` on failure. A handful of collectors return
- * `{coverage: "not_loaded", reason}` when a required upstream identifier is
- * missing — that signals "we never tried" vs. "we tried and got nothing."
- *
- * No collector throws — coverage is the failure mode. The DBOS workflow body
- * wraps each call in `DBOS.runStep({name: "ta-collector:{collectorId}"})` so
- * recovery on a fresh replica replays the cached coverage envelope instead
- * of re-issuing the HTTP call.
- *
- * No `deps` parameter is threaded through today (collectors call the tool
- * clients directly) — every external request goes through the global
- * `withHost(...)` semaphore. The function signature reserves the future
- * `deps` slot for test injection without churning callers.
- */
-import type { Logger } from "../../../lib/logger.js";
-/** Per-run context threaded to collectors that hit keyed external APIs. */
-export interface CollectorCtx {
-    readonly ncbiApiKey?: string;
-    /**
-     * The diagnostics seam of the run. A collector degrades to a coverage
-     * envelope, thus an unexpected cause is invisible without a record here.
-     */
-    readonly logger?: Logger;
-}
-import type { SerializedError } from "../coverage.js";
-import type { CbioportalBundle, ChemblModulatorsBundle, ClinvarBundle, CtgovBundle, ExpressionHumanBundle, ExpressionMultiSpeciesBundle, FaersByTargetBundle, FamilyComplexesBundle, ImpcBundle, MonarchBundle, OpenTargetsBundle, PathwaysBundle, PubmedIndexBundle, ResolvedTarget, StringPpiBundle, TherapeuticProgramsBundle } from "../schemas.js";
-type CoverageAvailable<T> = {
-    coverage: "available";
-    data: T;
-};
-type CoverageQueriedNoData = {
-    coverage: "queried_no_data";
-    error?: SerializedError;
-};
-type CoverageNotLoaded = {
-    coverage: "not_loaded";
-    reason?: string;
-};
-type CoverageEnvelope<T> = CoverageAvailable<T> | CoverageQueriedNoData | CoverageNotLoaded;
-export declare function collectCbioportal(input: ResolvedTarget): Promise<CoverageEnvelope<CbioportalBundle>>;
-export declare function collectChemblModulators(input: ResolvedTarget, ctx: CollectorCtx): Promise<CoverageEnvelope<ChemblModulatorsBundle>>;
-export declare function collectClinvar(input: ResolvedTarget, ctx: CollectorCtx): Promise<CoverageEnvelope<ClinvarBundle>>;
-export declare function collectCtgov(input: ResolvedTarget): Promise<CoverageEnvelope<CtgovBundle>>;
-export declare function collectExpressionHuman(input: ResolvedTarget): Promise<CoverageEnvelope<ExpressionHumanBundle>>;
-export declare function collectExpressionMultiSpecies(input: ResolvedTarget): Promise<CoverageEnvelope<ExpressionMultiSpeciesBundle>>;
-export declare function collectFaersByTarget(input: ResolvedTarget): Promise<CoverageEnvelope<FaersByTargetBundle>>;
-export declare function collectFamilyComplexes(input: ResolvedTarget, ctx: CollectorCtx): Promise<CoverageEnvelope<FamilyComplexesBundle>>;
-export declare function collectImpc(input: ResolvedTarget): Promise<CoverageEnvelope<ImpcBundle>>;
-export declare function collectMonarch(input: ResolvedTarget): Promise<CoverageEnvelope<MonarchBundle>>;
-export declare function collectOpenTargets(input: ResolvedTarget): Promise<CoverageEnvelope<OpenTargetsBundle>>;
-export declare function collectPathways(input: ResolvedTarget): Promise<CoverageEnvelope<PathwaysBundle>>;
-export declare function collectPubmedIndex(input: ResolvedTarget, ctx: CollectorCtx): Promise<CoverageEnvelope<PubmedIndexBundle>>;
-export declare function collectStringPpi(input: ResolvedTarget): Promise<CoverageEnvelope<StringPpiBundle>>;
-export declare function collectTherapeuticPrograms(input: ResolvedTarget): Promise<CoverageEnvelope<TherapeuticProgramsBundle>>;
-/**
- * Stable id used as the durable-step name suffix —
- * `ta-collector:{collectorId}`. The DBOS workflow body iterates this
- * manifest so adding a collector is one entry here + one new exported
- * function above, with no scheduler edits.
- */
-export declare const COLLECTOR_MANIFEST: readonly [{
-    readonly id: "cbioportal";
-    readonly run: typeof collectCbioportal;
-}, {
-    readonly id: "chembl-modulators";
-    readonly run: typeof collectChemblModulators;
-}, {
-    readonly id: "clinvar";
-    readonly run: typeof collectClinvar;
-}, {
-    readonly id: "ctgov";
-    readonly run: typeof collectCtgov;
-}, {
-    readonly id: "expression-human";
-    readonly run: typeof collectExpressionHuman;
-}, {
-    readonly id: "expression-multi-species";
-    readonly run: typeof collectExpressionMultiSpecies;
-}, {
-    readonly id: "faers-by-target";
-    readonly run: typeof collectFaersByTarget;
-}, {
-    readonly id: "family-complexes";
-    readonly run: typeof collectFamilyComplexes;
-}, {
-    readonly id: "impc";
-    readonly run: typeof collectImpc;
-}, {
-    readonly id: "monarch";
-    readonly run: typeof collectMonarch;
-}, {
-    readonly id: "opentargets";
-    readonly run: typeof collectOpenTargets;
-}, {
-    readonly id: "pathways";
-    readonly run: typeof collectPathways;
-}, {
-    readonly id: "pubmed-index";
-    readonly run: typeof collectPubmedIndex;
-}, {
-    readonly id: "string-ppi";
-    readonly run: typeof collectStringPpi;
-}, {
-    readonly id: "therapeutic-programs";
-    readonly run: typeof collectTherapeuticPrograms;
-}];
-export {};