@inflexa-ai/harness 0.45.1 → 0.46.2

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) => {

package/dist/tools/lib/ctx-ops.d.ts

@@ -22,11 +22,11 @@
  * `.nullable()` and `.optional()`.
  */
 import { z } from "zod";
-export interface CtxResolved {
+export type CtxResolved = {
     dtxsid: string;
     preferredName: string;
     casrn: string | null;
-}
+};
 export declare const CtxChemicalSearchRowSchema: z.ZodObject<{
     dtxsid: z.ZodOptional<z.ZodNullable<z.ZodString>>;
     preferredName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
@@ -34,7 +34,7 @@ export declare const CtxChemicalSearchRowSchema: z.ZodObject<{
 }, z.core.$strip>;
 /** Resolve a DTXSID / CASRN / name to a chemical. `null` = no match (valid no-data). */
 export declare function resolveDtxsid(query: string, headers: Record<string, string>): Promise<CtxResolved | null>;
-export interface ToxcastAssayResult {
+export type ToxcastAssayResult = {
     aeid: number;
     assayEndpoint: string;
     ac50: number | null;
@@ -42,13 +42,13 @@ export interface ToxcastAssayResult {
     maxMean: number | null;
     model: string;
     flags: string[];
-}
-export interface ToxcastBioactivity {
+};
+export type ToxcastBioactivity = {
     totalAssays: number;
     activeAssays: number;
     activeHitRate: number;
     results: ToxcastAssayResult[];
-}
+};
 export declare const ToxcastBioactivityRowSchema: z.ZodObject<{
     aeid: z.ZodOptional<z.ZodNumber>;
     hitc: z.ZodOptional<z.ZodNumber>;
@@ -59,7 +59,7 @@ export declare const ToxcastBioactivityRowSchema: z.ZodObject<{
         acc: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>>;
     mc6Param: z.ZodOptional<z.ZodNullable<z.ZodObject<{
-        flag: z.ZodOptional<z.ZodUnknown>;
+        flag: z.ZodOptional<z.ZodJSONSchema>;
     }, z.core.$strip>>>;
 }, z.core.$strip>;
 /**
@@ -159,11 +159,11 @@ export declare const CancerSchema: z.ZodPipe<z.ZodObject<{
 }>>;
 export type CancerSummary = z.infer<typeof CancerSchema>;
 export type CtxHazardDataType = "toxval" | "genetox" | "cancer" | "all";
-export interface CtxHazardData {
+export type CtxHazardData = {
     toxval?: ToxValEntry[];
     genetox?: GenetoxSummary[];
     cancer?: CancerSummary[];
-}
+};
 /**
  * In-vivo hazard data for a chemical. `limit` caps toxval and genetox only —
  * cancer classifications always come back whole.
@@ -172,7 +172,7 @@ export declare function fetchCtxHazardData(dtxsid: string, headers: Record<strin
     dataType: CtxHazardDataType;
     limit: number;
 }): Promise<CtxHazardData>;
-export interface ChemicalDetail {
+export type ChemicalDetail = {
     dtxsid: string;
     dtxcid: string;
     casrn: string | null;
@@ -189,8 +189,8 @@ export interface ChemicalDetail {
     pubchemCid: number | null;
     pubmedCount: number | null;
     sourcesCount: number | null;
-}
-export interface PropertySummary {
+};
+export type PropertySummary = {
     propName: string;
     unit: string;
     experimentalCount: number | null;
@@ -201,7 +201,7 @@ export interface PropertySummary {
     predictedMedian: number | null;
     predictedMin: number | null;
     predictedMax: number | null;
-}
+};
 export declare const RawChemicalDetailSchema: z.ZodObject<{
     dtxsid: z.ZodOptional<z.ZodString>;
     dtxcid: z.ZodOptional<z.ZodNullable<z.ZodString>>;
@@ -224,7 +224,7 @@ export declare const RawChemicalDetailSchema: z.ZodObject<{
 export declare function fetchCtxChemicalDetail(dtxsid: string, headers: Record<string, string>): Promise<ChemicalDetail>;
 /** Experimental + predicted physicochemical property summaries. `undefined` = none served. */
 export declare function fetchCtxChemicalProperties(dtxsid: string, headers: Record<string, string>): Promise<PropertySummary[] | undefined>;
-export interface SeemPrediction {
+export type SeemPrediction = {
     dtxsid: string;
     productionVolume: number | null;
     units: string;
@@ -232,8 +232,8 @@ export interface SeemPrediction {
     probabilityResidential: number | null;
     probabilityPesticide: number | null;
     probabilityIndustrial: number | null;
-}
-export interface HttkParameter {
+};
+export type HttkParameter = {
     parameter: string;
     measured: number | null;
     predicted: number | null;
@@ -241,20 +241,20 @@ export interface HttkParameter {
     model: string;
     species: string;
     reference: string;
-}
-export interface FunctionalUse {
+};
+export type FunctionalUse = {
     functionCategory: string;
     reportedFunction: string;
     docTitle: string;
-}
-export interface ProductData {
+};
+export type ProductData = {
     productName: string;
     generalCategory: string;
     productFamily: string;
     productType: string;
     centralWeightFraction: number | null;
     weightFractionType: string;
-}
+};
 export declare const RawSeemPredictionSchema: z.ZodObject<{
     dtxsid: z.ZodOptional<z.ZodString>;
     productionVolume: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
@@ -279,12 +279,12 @@ export declare const RawFunctionalUseRowSchema: z.ZodObject<{
     doctitle: z.ZodOptional<z.ZodNullable<z.ZodString>>;
 }, z.core.$strip>;
 export type CtxExposureDataType = "seem" | "httk" | "functional-use" | "product-data" | "all";
-export interface CtxExposureData {
+export type CtxExposureData = {
     seem?: SeemPrediction;
     httk?: HttkParameter[];
     functionalUse?: FunctionalUse[];
     productData?: ProductData[];
-}
+};
 /**
  * Human-exposure data for a chemical. `limit` caps functional-use and
  * product-data only — seem and httk always come back whole.

package/dist/tools/lib/ctx-ops.js

@@ -22,6 +22,9 @@
  * `.nullable()` and `.optional()`.
  */
 import { z } from "zod";
+import { isUnknownArray } from "../../lib/unknown-array.js";
+import { parseUnknownRecord } from "../../lib/unknown-containers.js";
+import { parseJsonAs } from "../../lib/parse-json.js";
 import { apiFetchValidated, describeApiError, zWireNumber } from "./api-utils.js";
 import { EPA_CCTE_BASE } from "./toxcast-config.js";
 // A row of the chemical-search endpoint. `dtxsid` is nullable, because a search
@@ -44,11 +47,11 @@ function isNoMatchProblemDetail(error) {
     if (error.type !== "http_status" || error.status !== 400)
         return false;
     try {
-        const body = JSON.parse(error.body);
+        const body = parseUnknownRecord(parseJsonAs(error.body, z.json()));
         // `suggestions` separates the no-match answer from a generic 400
         // `ProblemDetail`, which carries `title` and `detail` alone. Without it,
         // a malformed request reads as a clean no-match.
-        return typeof body === "object" && body !== null && "detail" in body && "title" in body && "suggestions" in body;
+        return body !== undefined && "detail" in body && "title" in body && "suggestions" in body;
     }
     catch {
         return false;
@@ -66,7 +69,7 @@ export async function resolveDtxsid(query, headers) {
             return null;
         throw new Error(describeApiError(res.error));
     }
-    const chem = (res.value ?? []).find((row) => row.dtxsid);
+    const chem = res.value.find((row) => row.dtxsid);
     if (!chem?.dtxsid)
         return null;
     return {
@@ -82,7 +85,7 @@ const ToxcastMc5ParamSchema = z.object({
     acc: z.number().optional(),
 });
 const ToxcastMc6ParamSchema = z.object({
-    flag: z.unknown().optional(),
+    flag: z.json().optional(),
 });
 export const ToxcastBioactivityRowSchema = z.object({
     aeid: z.number().optional(),
@@ -116,7 +119,7 @@ export async function fetchToxcastBioactivity(dtxsid, headers, opts) {
     const bioRes = await apiFetchValidated(bioUrl, z.array(ToxcastBioactivityRowSchema), { headers });
     if (bioRes.isErr())
         throw new Error(describeApiError(bioRes.error));
-    const allResults = bioRes.value ?? [];
+    const allResults = bioRes.value;
     const totalAssays = allResults.length;
     const activeAssays = allResults.filter(isActive).length;
     const filtered = opts.activeOnly ? allResults.filter(isActive) : allResults;
@@ -128,7 +131,7 @@ export async function fetchToxcastBioactivity(dtxsid, headers, opts) {
     const results = page.map((r) => {
         const aeid = r.aeid ?? 0;
         const mc6 = r.mc6Param ?? {};
-        const flags = Array.isArray(mc6.flag) ? mc6.flag : [];
+        const flags = isUnknownArray(mc6.flag) ? mc6.flag.flatMap((flag) => (typeof flag === "string" ? [flag] : [])) : [];
         return {
             aeid,
             assayEndpoint: aeidMap.get(aeid) ?? `aeid:${aeid}`,
@@ -151,10 +154,10 @@ function extractAc50(r) {
 }
 function extractAc50Raw(r) {
     const mc5 = r.mc5Param;
-    if (mc5 && typeof mc5 === "object") {
-        if (typeof mc5.ac50 === "number")
+    if (mc5 !== null && mc5 !== undefined) {
+        if (mc5.ac50 !== undefined)
             return mc5.ac50;
-        if (typeof mc5.acc === "number")
+        if (mc5.acc !== undefined)
             return mc5.acc;
     }
     return null;
@@ -350,7 +353,7 @@ export async function fetchCtxChemicalDetail(dtxsid, headers) {
     const detailRes = await apiFetchValidated(detailUrl, RawChemicalDetailSchema, { headers });
     if (detailRes.isErr())
         throw new Error(describeApiError(detailRes.error));
-    const d = detailRes.value ?? {};
+    const d = detailRes.value;
     return {
         dtxsid: d.dtxsid ?? dtxsid,
         dtxcid: d.dtxcid ?? "",

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

@@ -11,7 +11,7 @@
  * the SDL gives each modifier and `.optional()` is wrong.
  */
 import { z } from "zod";
-export interface DgidbInteraction {
+export type DgidbInteraction = {
     geneName: string;
     drugName: string;
     drugConceptId?: string;
@@ -28,14 +28,14 @@ export interface DgidbInteraction {
         name: string;
         value: string;
     }[];
-}
-export interface DgidbResult {
+};
+export type DgidbResult = {
     input: string;
     found: boolean;
     interactions: DgidbInteraction[];
     /** Interactions this input had before `limit` trimmed them. */
     totalInteractions: number;
-}
+};
 /** The response envelope. It is exported so that the golden-fixture table drives it. */
 export declare const DgidbResponseSchema: z.ZodObject<{
     data: z.ZodOptional<z.ZodObject<{
@@ -104,13 +104,13 @@ export declare const DgidbResponseSchema: z.ZodObject<{
         message: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>>;
 }, z.core.$strip>;
-export interface DgidbFilters {
+export type DgidbFilters = {
     interactionTypes?: string[];
     sourceDbs?: string[];
     minSources?: number;
     includeAttributes?: boolean;
     limit?: number;
-}
+};
 /**
  * Query DGIdb for interactions of the given genes or drugs.
  *