@inflexa-ai/harness 0.45.0 → 0.46.0

package/dist/tools/lib/bgee-client.js

@@ -11,6 +11,8 @@
  * field carries `.optional()`, not `.nullable()`.
  */
 import { z } from "zod";
+import { isUnknownArray } from "../../lib/unknown-array.js";
+import { parseUnknownRecord } from "../../lib/unknown-containers.js";
 import { apiFetchValidated, describeApiError, isUnexpectedApiError } from "./api-utils.js";
 const ENSEMBL_BASE = "https://rest.ensembl.org";
 const BGEE_BASE = "https://www.bgee.org/api";
@@ -60,28 +62,32 @@ export const EnsemblHomologyResponseSchema = z.object({
     data: z.array(z.object({ homologies: z.array(z.object({ id: z.string().optional(), type: z.string().optional() })).optional() })).optional(),
 });
 export function parseExpressionResponse(raw) {
-    // `raw` is the untyped Bgee API payload; `.data.calls` is reached defensively and
-    // the `Array.isArray` guard below means a shape mismatch degrades to an empty list.
-    const calls = raw?.data?.calls;
-    if (!Array.isArray(calls))
+    const calls = parseUnknownRecord(parseUnknownRecord(raw)?.data)?.calls;
+    if (!isUnknownArray(calls))
         return [];
     const out = [];
-    for (const call of calls) {
-        const anatName = call?.condition?.anatEntity?.name ?? "";
+    for (const entry of calls) {
+        const call = parseUnknownRecord(entry);
+        if (!call)
+            continue;
+        const condition = parseUnknownRecord(call.condition);
+        const anatEntity = parseUnknownRecord(condition?.anatEntity);
+        const anatName = typeof anatEntity?.name === "string" ? anatEntity.name : "";
         const tissue = anatName.trim().toLowerCase();
         if (!tissue)
             continue;
-        const cellTypeName = call?.condition?.cellType?.name;
+        const cellTypeRecord = parseUnknownRecord(condition?.cellType);
+        const cellTypeName = cellTypeRecord?.name;
         const cellType = typeof cellTypeName === "string" && cellTypeName.trim() !== "" ? cellTypeName.trim().toLowerCase() : null;
-        const rawScore = call?.expressionScore?.expressionScore;
+        const rawScore = parseUnknownRecord(call.expressionScore)?.expressionScore;
         let expressionScore = null;
         if (typeof rawScore === "string" || typeof rawScore === "number") {
             const n = typeof rawScore === "number" ? rawScore : parseFloat(rawScore);
             expressionScore = Number.isFinite(n) ? n : null;
         }
-        const quality = call?.expressionQuality;
+        const quality = call.expressionQuality;
         const confidence = quality === "gold" || quality === "silver" ? quality : null;
-        const stateRaw = call?.expressionState;
+        const stateRaw = call.expressionState;
         const expressionState = stateRaw === "not expressed" ? "not expressed" : "expressed";
         out.push({
             tissue,

package/dist/tools/lib/cbioportal-client.d.ts

@@ -11,19 +11,19 @@
  * not `.nullable()`.
  */
 import { z } from "zod";
-export interface CancerStudy {
+export type CancerStudy = {
     studyId: string;
     cancerType: string;
     cancerTypeName: string;
-}
-export interface MutationFrequency {
+};
+export type MutationFrequency = {
     cancerTypeId: string;
     cancerTypeName: string;
     totalSamples: number;
     mutatedSamples: number;
     frequency: number;
     studies: string[];
-}
+};
 export declare const RawMutationRowSchema: z.ZodObject<{
     studyId: z.ZodString;
     sampleId: z.ZodString;

package/dist/tools/lib/cbioportal-client.js

@@ -12,6 +12,7 @@
  */
 import { z } from "zod";
 import { apiFetchValidated, describeApiError } from "./api-utils.js";
+import { presentGet } from "../../lib/present.js";
 const CBIOPORTAL_BASE = "https://www.cbioportal.org/api";
 const HEADERS = { Accept: "application/json" };
 // Raw cBioPortal wire shapes, validated at the fetch boundary. Fields the code
@@ -52,7 +53,7 @@ async function listStudies() {
     const res = await apiFetchValidated(url, z.array(RawCancerStudySchema), { headers: HEADERS });
     if (res.isErr())
         throw new Error(describeApiError(res.error));
-    return res.value ?? [];
+    return res.value;
 }
 /**
  * The cancer-type vocabulary, keyed by its id. The study SUMMARY projection
@@ -65,7 +66,7 @@ async function cancerTypeNames() {
     const names = new Map();
     if (res.isErr())
         return names;
-    for (const row of res.value ?? []) {
+    for (const row of res.value) {
         if (row.cancerTypeId && row.name)
             names.set(row.cancerTypeId, row.name);
     }
@@ -76,14 +77,14 @@ async function listAllSampleLists() {
     const res = await apiFetchValidated(url, z.array(RawSampleListSchema), { headers: HEADERS });
     if (res.isErr())
         throw new Error(describeApiError(res.error));
-    return res.value ?? [];
+    return res.value;
 }
 async function listMutationProfiles() {
     const url = `${CBIOPORTAL_BASE}/molecular-profiles?projection=SUMMARY&pageSize=10000`;
     const res = await apiFetchValidated(url, z.array(RawMolecularProfileSchema), { headers: HEADERS });
     if (res.isErr())
         throw new Error(describeApiError(res.error));
-    return (res.value ?? []).filter((p) => p.molecularAlterationType === "MUTATION_EXTENDED");
+    return res.value.filter((p) => p.molecularAlterationType === "MUTATION_EXTENDED");
 }
 async function fetchMutationRowsForGene(entrezGeneId, profileIds) {
     if (profileIds.length === 0)
@@ -99,7 +100,7 @@ async function fetchMutationRowsForGene(entrezGeneId, profileIds) {
     });
     if (res.isErr())
         throw new Error(describeApiError(res.error));
-    return res.value ?? [];
+    return res.value;
 }
 /**
  * Resolve a gene symbol to its NCBI Entrez Gene ID via cBioPortal's gene
@@ -111,7 +112,7 @@ async function resolveEntrezId(symbol) {
     const res = await apiFetchValidated(url, z.object({ entrezGeneId: z.number().optional() }), { headers: HEADERS });
     if (res.isErr())
         return null;
-    return res.value?.entrezGeneId ?? null;
+    return res.value.entrezGeneId ?? null;
 }
 /**
  * Compute somatic mutation frequencies for a target across all curated
@@ -145,7 +146,7 @@ export async function getSomaticMutationFrequencies(geneSymbol, options = {}) {
     for (const m of mutations) {
         if (!mutatedStudySamples.has(m.studyId))
             mutatedStudySamples.set(m.studyId, new Set());
-        mutatedStudySamples.get(m.studyId).add(m.sampleId);
+        presentGet(mutatedStudySamples, m.studyId, "the sample set of the study").add(m.sampleId);
     }
     const byCancerType = new Map();
     for (const studyId of studiesWithMutations) {
@@ -163,7 +164,7 @@ export async function getSomaticMutationFrequencies(geneSymbol, options = {}) {
                 studies: new Set(),
             });
         }
-        const bucket = byCancerType.get(cancerTypeId);
+        const bucket = presentGet(byCancerType, cancerTypeId, "the aggregate bucket");
         bucket.total += sampleCount;
         bucket.mutated += mutatedStudySamples.get(studyId)?.size ?? 0;
         bucket.studies.add(studyId);

package/dist/tools/lib/chembl-client.d.ts

@@ -9,24 +9,24 @@
  */
 import { z } from "zod";
 import type { Logger } from "../../lib/logger.js";
-export interface ChemblCompound {
+export type ChemblCompound = {
     chemblId: string;
     preferredCompoundName: string | null;
     canonicalSmiles: string | null;
     molecularWeight: number | null;
     alogp: number | null;
     molecularFormula: string | null;
-}
+};
 /** How `searchCompounds` interprets its query string. */
 export type CompoundSearchType = "target" | "compound" | "smiles";
-export interface ChemblTarget {
+export type ChemblTarget = {
     targetChemblId: string;
     preferredName: string | null;
     targetType: string | null;
     organism: string | null;
     geneNames: string[];
-}
-export interface ChemblActivity {
+};
+export type ChemblActivity = {
     activityId: number | null;
     compoundChemblId: string;
     targetChemblId: string | null;
@@ -36,31 +36,31 @@ export interface ChemblActivity {
     assayChemblId: string | null;
     assayType: string | null;
     pchemblValue: number | null;
-}
-export interface ChemblMechanism {
+};
+export type ChemblMechanism = {
     mechanismOfAction: string | null;
     actionType: string | null;
     targetChemblId: string | null;
     targetName: string | null;
     moleculeChemblId: string;
-}
-export interface ChemblDrug {
+};
+export type ChemblDrug = {
     moleculeChemblId: string;
     preferredName: string | null;
     maxPhase: number | null;
     moleculeType: string | null;
     firstApproval: number | null;
     indication: string | null;
-}
-export interface ChemblModulator {
+};
+export type ChemblModulator = {
     moleculeChemblId: string;
     parentChemblId: string | null;
     preferredName: string | null;
     maxPhase: number | null;
     moleculeType: string | null;
     firstApproval: number | null;
-}
-export interface ChemblPolypharmHit {
+};
+export type ChemblPolypharmHit = {
     moleculeChemblId: string;
     targetChemblId: string;
     targetName: string | null;
@@ -70,7 +70,7 @@ export interface ChemblPolypharmHit {
     standardValue: number | null;
     standardUnits: string | null;
     pchemblValue: number | null;
-}
+};
 export declare const TargetSearchResponseSchema: z.ZodObject<{
     targets: z.ZodOptional<z.ZodArray<z.ZodObject<{
         target_chembl_id: z.ZodOptional<z.ZodString>;

package/dist/tools/lib/chembl-client.js

@@ -9,6 +9,7 @@
  */
 import { z } from "zod";
 import { createNoopLogger } from "../../lib/console-logger.js";
+import { presentAt } from "../../lib/present.js";
 import { apiFetchValidated, describeApiError, isUnexpectedApiError, zWireNumber } from "./api-utils.js";
 import { CHEMBL_BASE, CHEMBL_HEADERS as HEADERS } from "./chembl-config.js";
 /** The `max_phase` of an approved drug. ChEMBL serializes it as the string "4.0". */
@@ -184,7 +185,8 @@ async function searchCompoundsByTarget(query, limit) {
     }
     if (!targetRes.value.targets?.length)
         return [];
-    const targetChemblId = targetRes.value.targets[0].target_chembl_id;
+    const firstTarget = targetRes.value.targets[0];
+    const targetChemblId = firstTarget?.target_chembl_id;
     if (!targetChemblId)
         return [];
     const activityRes = await apiFetchValidated(`${CHEMBL_BASE}/activity.json?target_chembl_id=${targetChemblId}&limit=${limit}`, CompoundActivityIdResponseSchema, {
@@ -439,7 +441,10 @@ async function searchApprovedDrugsByName(query, limit) {
     const approved = (res.value.molecules ?? []).filter((mol) => mol.max_phase != null && mol.max_phase >= APPROVED_MAX_PHASE);
     if (approved.length === 0)
         return [];
-    const moleculeChemblIds = approved.map((mol) => mol.molecule_chembl_id).filter((id) => id !== undefined && id.length > 0);
+    const moleculeChemblIds = approved.flatMap((mol) => {
+        const id = mol.molecule_chembl_id;
+        return id !== undefined && id.length > 0 ? [id] : [];
+    });
     const indications = await fetchIndicationsOf(moleculeChemblIds);
     return approved.map((raw) => mapDrug(raw, indications.get(raw.molecule_chembl_id ?? "") ?? null));
 }
@@ -559,7 +564,7 @@ export async function getModulatorPolypharmacology(moleculeChemblId, options = {
         for (const [idx, id] of batch.entries()) {
             const hit = hits.find((h) => h.targetChemblId === id);
             if (hit)
-                hit.targetName = names[idx];
+                hit.targetName = names[idx] ?? null;
         }
     }
     return hits.sort((a, b) => (b.pchemblValue ?? 0) - (a.pchemblValue ?? 0));
@@ -587,7 +592,9 @@ export async function getModulatorOnTargetPchembl(modulatorChemblId, targetChemb
         return null;
     values.sort((a, b) => a - b);
     const mid = Math.floor(values.length / 2);
-    return values.length % 2 === 1 ? values[mid] : (values[mid - 1] + values[mid]) / 2;
+    return values.length % 2 === 1
+        ? presentAt(values, mid, "the middle activity value")
+        : (presentAt(values, mid - 1, "the lower middle activity value") + presentAt(values, mid, "the middle activity value")) / 2;
 }
 /**
  * Secondary path: fetch clinical-stage small molecules via the activity table.

package/dist/tools/lib/clinical-benchmarks-client.d.ts

@@ -3,21 +3,21 @@
  * absent value. The bundled dataset gives each key, and `getBenchmarks` answers
  * with the "all" baseline for an unknown therapeutic area.
  */
-export interface PhaseTransitions {
+export type PhaseTransitions = {
     phase1_to_phase2: number;
     phase2_to_phase3: number;
     phase3_to_nda: number;
     nda_to_approval: number;
     phase1_to_approval: number;
-}
-export interface BenchmarkResult {
+};
+export type BenchmarkResult = {
     therapeutic_area: string;
     source: "available" | "fallback";
     data_version: string;
     data_window: string;
     attribution: string;
     transitions: PhaseTransitions;
-}
+};
 /**
  * Infer therapeutic area from a list of indication labels using the
  * dataset's pattern map. First match wins.

package/dist/tools/lib/clinical-benchmarks-client.js

@@ -5,9 +5,6 @@
  */
 import benchmarksData from "../../data/clinical-benchmarks.json" with { type: "json" };
 const dataset = benchmarksData;
-if (!dataset.phase_transitions || !dataset.phase_transitions.all) {
-    throw new Error("clinical-benchmarks.json is missing phase_transitions.all baseline");
-}
 function loadDataset() {
     return dataset;
 }
@@ -36,15 +33,15 @@ export function inferTherapeuticArea(indicationLabels) {
  */
 export function getBenchmarks(therapeuticArea) {
     const dataset = loadDataset();
-    const useFallback = !therapeuticArea || !dataset.phase_transitions[therapeuticArea];
-    const ta = useFallback ? "all" : therapeuticArea;
+    const requested = !therapeuticArea ? undefined : dataset.phase_transitions[therapeuticArea];
+    const ta = requested === undefined || therapeuticArea === null ? "all" : therapeuticArea;
     return {
         therapeutic_area: ta,
-        source: useFallback ? "fallback" : "available",
+        source: requested === undefined ? "fallback" : "available",
         data_version: dataset.data_version,
         data_window: dataset.data_window,
         attribution: dataset.source,
-        transitions: dataset.phase_transitions[ta],
+        transitions: requested ?? dataset.phase_transitions.all,
     };
 }
 /** Return the dataset's metadata for transparency. */

package/dist/tools/lib/clinical-trials-client.d.ts

@@ -6,7 +6,7 @@
  * `.optional()`, not `.nullable()`.
  */
 import { z } from "zod";
-export interface ClinicalTrial {
+export type ClinicalTrial = {
     nctId: string;
     title: string;
     officialTitle: string | null;
@@ -24,13 +24,13 @@ export interface ClinicalTrial {
     briefSummary: string | null;
     detailedDescription: string | null;
     sponsor: string | null;
-}
-export interface ClinicalTrialIntervention {
+};
+export type ClinicalTrialIntervention = {
     name: string;
     type: string | null;
     description: string | null;
     otherNames: string[];
-}
+};
 export type OutcomeEffect = {
     kind: "quantitative";
     value: number;
@@ -41,46 +41,46 @@ export type OutcomeEffect = {
     kind: "not_extracted";
     reason: "ctgov_no_numeric_result" | "ctgov_no_result_groups";
 };
-export interface OutcomeMeasure {
+export type OutcomeMeasure = {
     type: "primary" | "secondary" | "other";
     measure: string;
     description: string | null;
     timeFrame: string | null;
     effect: OutcomeEffect;
-}
-export interface AdverseEventGroup {
+};
+export type AdverseEventGroup = {
     groupId: string;
     title: string;
     description: string | null;
-}
-export interface AdverseEventCount {
+};
+export type AdverseEventCount = {
     groupId: string;
     numAffected: number | null;
     numAtRisk: number | null;
-}
-export interface AdverseEvent {
+};
+export type AdverseEvent = {
     serious: boolean;
     term: string;
     organSystem: string | null;
     counts: AdverseEventCount[];
-}
-export interface TrialDetails {
+};
+export type TrialDetails = {
     trial: ClinicalTrial;
     whyStopped: string | null;
     outcomes: OutcomeMeasure[];
     adverseEventGroups: AdverseEventGroup[];
     adverseEvents: AdverseEvent[];
-}
+};
 /**
  * One phase token of `protocolSection.designModule.phases`. `NA` marks a study
  * that runs under no phase, such as an observational study.
  */
 export type TrialPhase = "EARLY_PHASE1" | "PHASE1" | "PHASE2" | "PHASE3" | "PHASE4" | "NA";
-export interface SearchOptions {
+export type SearchOptions = {
     phase?: TrialPhase;
     status?: "RECRUITING" | "ACTIVE_NOT_RECRUITING" | "COMPLETED" | "NOT_YET_RECRUITING" | "TERMINATED" | "WITHDRAWN" | "SUSPENDED";
     limit?: number;
-}
+};
 /** One study record. It is exported so that the golden-fixture table drives it. */
 export declare const CtStudySchema: z.ZodObject<{
     protocolSection: z.ZodOptional<z.ZodObject<{
@@ -121,7 +121,7 @@ export declare const CtStudySchema: z.ZodObject<{
                 name: z.ZodOptional<z.ZodString>;
                 type: z.ZodOptional<z.ZodString>;
                 description: z.ZodOptional<z.ZodString>;
-                otherNames: z.ZodOptional<z.ZodUnknown>;
+                otherNames: z.ZodOptional<z.ZodPipe<z.ZodArray<z.ZodJSONSchema>, z.ZodTransform<string[], z.JSONType[]>>>;
             }, z.core.$strip>>>;
         }, z.core.$strip>>;
         sponsorCollaboratorsModule: z.ZodOptional<z.ZodObject<{
@@ -232,7 +232,7 @@ export declare const CtSearchResponseSchema: z.ZodObject<{
                     name: z.ZodOptional<z.ZodString>;
                     type: z.ZodOptional<z.ZodString>;
                     description: z.ZodOptional<z.ZodString>;
-                    otherNames: z.ZodOptional<z.ZodUnknown>;
+                    otherNames: z.ZodOptional<z.ZodPipe<z.ZodArray<z.ZodJSONSchema>, z.ZodTransform<string[], z.JSONType[]>>>;
                 }, z.core.$strip>>>;
             }, z.core.$strip>>;
             sponsorCollaboratorsModule: z.ZodOptional<z.ZodObject<{

package/dist/tools/lib/clinical-trials-client.js

@@ -17,7 +17,11 @@ const CtInterventionSchema = z.object({
     name: z.string().optional(),
     type: z.string().optional(),
     description: z.string().optional(),
-    otherNames: z.unknown().optional(),
+    // An alias is one name among others; a member that is not a string loses that name, never the study.
+    otherNames: z
+        .array(z.json())
+        .transform((names) => names.flatMap((name) => (typeof name === "string" ? [name] : [])))
+        .optional(),
 });
 const CtOutcomeSchema = z.object({
     measure: z.string().optional(),
@@ -140,7 +144,7 @@ export function mapClinicalTrialStudy(s) {
         name: i.name ?? "Unknown",
         type: i.type ?? null,
         description: i.description ?? null,
-        otherNames: Array.isArray(i.otherNames) ? i.otherNames : [],
+        otherNames: i.otherNames ?? [],
     }));
     const interventions = interventionDetails.map((i) => i.name);
     const sponsor = proto.sponsorCollaboratorsModule?.leadSponsor?.name ?? null;
@@ -195,11 +199,11 @@ export async function searchTrials(query, options = {}) {
     });
     if (res.isErr())
         throw new Error(describeApiError(res.error));
-    const studies = res.value?.studies ?? [];
+    const studies = res.value.studies ?? [];
     const phase = options.phase;
     const selected = phase ? studies.filter((study) => studyHasPhase(study, phase)) : studies;
     const trials = selected.slice(0, limit).map(mapClinicalTrialStudy);
-    return { totalFound: res.value?.totalCount ?? trials.length, trials };
+    return { totalFound: res.value.totalCount ?? trials.length, trials };
 }
 /** Search trials whose intervention or condition mentions the gene/target. */
 export async function searchTrialsForTarget(symbol, options = {}) {
@@ -272,12 +276,8 @@ function extractEffect(resultsMeasure) {
                         kind: "quantitative",
                         value: num,
                         units: resultsMeasure?.unitOfMeasure ?? "",
-                        ...(m.lowerLimit !== undefined && m.lowerLimit !== null && !isNaN(parseFloat(m.lowerLimit))
-                            ? { ci_low: parseFloat(m.lowerLimit) }
-                            : {}),
-                        ...(m.upperLimit !== undefined && m.upperLimit !== null && !isNaN(parseFloat(m.upperLimit))
-                            ? { ci_high: parseFloat(m.upperLimit) }
-                            : {}),
+                        ci_low: m.lowerLimit !== undefined && !isNaN(parseFloat(m.lowerLimit)) ? parseFloat(m.lowerLimit) : undefined,
+                        ci_high: m.upperLimit !== undefined && !isNaN(parseFloat(m.upperLimit)) ? parseFloat(m.upperLimit) : undefined,
                     };
                 }
             }

package/dist/tools/lib/clinvar-client.d.ts

@@ -5,7 +5,7 @@
  */
 import { z } from "zod";
 export type ClinicalSignificance = "pathogenic" | "likely-pathogenic" | "benign" | "likely-benign" | "uncertain";
-export interface ClinvarVariant {
+export type ClinvarVariant = {
     variationId: string;
     title: string;
     clinicalSignificance: string;
@@ -14,7 +14,7 @@ export interface ClinvarVariant {
     molecularConsequence: string;
     conditions: string[];
     accession: string;
-}
+};
 export declare const ClinvarSearchResponseSchema: z.ZodObject<{
     esearchresult: z.ZodOptional<z.ZodObject<{
         idlist: z.ZodOptional<z.ZodArray<z.ZodString>>;

package/dist/tools/lib/clinvar-client.js

@@ -53,10 +53,10 @@ const SIG_MAP = {
 };
 /** Filter out uninformative ClinVar entries (literal "not provided", placeholders). */
 export function filterInformative(variants) {
-    const noise = /^(not provided|not specified|reclassified)$/i;
+    const noise = new Set(["not provided", "not specified", "reclassified"]);
     return variants.filter((v) => {
-        const sig = (v.clinicalSignificance ?? "").trim();
-        if (!sig || noise.test(sig))
+        const sig = v.clinicalSignificance.trim();
+        if (!sig || noise.has(sig.toLowerCase()))
             return false;
         return true;
     });
@@ -76,8 +76,8 @@ export async function searchClinvar(ncbiApiKey, query, options = {}) {
     const searchRes = await apiFetchValidated(searchUrl, ClinvarSearchResponseSchema);
     if (searchRes.isErr())
         throw new Error(describeApiError(searchRes.error));
-    const ids = searchRes.value?.esearchresult?.idlist ?? [];
-    const totalFound = Number(searchRes.value?.esearchresult?.count ?? ids.length);
+    const ids = searchRes.value.esearchresult?.idlist ?? [];
+    const totalFound = Number(searchRes.value.esearchresult?.count ?? ids.length);
     if (ids.length === 0)
         return { totalFound, variants: [] };
     const summaryUrl = ncbiUrl(ncbiApiKey, "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi", {
@@ -98,7 +98,7 @@ export async function searchClinvar(ncbiApiKey, query, options = {}) {
  * golden-fixture table exercises it against a stored payload.
  */
 export function mapClinvarVariants(ids, summary) {
-    const result = summary?.result ?? {};
+    const result = summary.result ?? {};
     const rawUids = result.uids;
     const uids = Array.isArray(rawUids) ? rawUids : ids;
     return uids.map((uid) => {