@inflexa-ai/harness 0.45.0 → 0.46.0

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.
  *

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

@@ -84,7 +84,7 @@ function mapInteraction(raw, perspective, inputSide, includeAttributes) {
     const pmids = (raw.publications ?? []).map((p) => (p.pmid != null ? String(p.pmid) : "")).filter(Boolean);
     const types = (raw.interactionTypes ?? []).map((t) => ({
         type: t.type ?? "",
-        ...(t.directionality ? { directionality: t.directionality } : {}),
+        directionality: t.directionality ?? undefined,
     }));
     const geneName = perspective === "gene" ? (inputSide.geneName ?? "") : (raw.gene?.name ?? "");
     const drugName = perspective === "drug" ? (inputSide.drugName ?? "") : (raw.drug?.name ?? "");
@@ -92,21 +92,19 @@ function mapInteraction(raw, perspective, inputSide, includeAttributes) {
     return {
         geneName,
         drugName,
-        ...(drugConceptId ? { drugConceptId } : {}),
+        drugConceptId,
         interactionTypes: types,
-        ...(raw.interactionScore != null ? { interactionScore: raw.interactionScore } : {}),
+        interactionScore: raw.interactionScore ?? undefined,
         sourceCount: sources.length,
         sources,
         publicationCount: pmids.length,
         pmids: pmids.slice(0, MAX_PMIDS),
-        ...(includeAttributes
-            ? {
-                attributes: (raw.interactionAttributes ?? []).slice(0, MAX_ATTRIBUTES).map((a) => ({
-                    name: a.name ?? "",
-                    value: (a.value ?? "").slice(0, MAX_ATTRIBUTE_CHARS),
-                })),
-            }
-            : {}),
+        attributes: includeAttributes
+            ? (raw.interactionAttributes ?? []).slice(0, MAX_ATTRIBUTES).map((a) => ({
+                name: a.name ?? "",
+                value: (a.value ?? "").slice(0, MAX_ATTRIBUTE_CHARS),
+            }))
+            : undefined,
     };
 }
 function applyFilters(interactions, filters) {
@@ -144,7 +142,7 @@ export async function searchDgidb(inputs, searchType, filters = {}, onPartialErr
     if (res.isErr())
         throw new Error(describeApiError(res.error));
     const body = res.value;
-    if (!body || !body.data)
+    if (!body.data)
         throw new Error("DGIdb returned no data");
     if (body.errors?.length)
         onPartialErrors?.(body.errors.slice(0, 3));

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

@@ -122,16 +122,16 @@ export type DisgenetSearchType = "gene" | "disease";
  */
 export declare const DISGENET_SOURCES: readonly ["ALL", "BIOBANK", "CHEMBL", "CLINICALTRIALS", "CLINGEN", "CLINPGX", "CLINVAR", "CURATED", "FINNGEN", "GENCC", "GWASCAT", "HPO", "INFERRED", "MGD_HUMAN", "MGD_MOUSE", "MODELS", "ORPHANET", "PHEWASCAT", "PSYGENET", "RGD_HUMAN", "RGD_RAT", "TEXTMINING_HUMAN", "TEXTMINING_MODELS", "UKBIOBANK", "UNIPROT"];
 export type DisgenetSource = (typeof DISGENET_SOURCES)[number];
-export interface DisgenetSearchOptions {
+export type DisgenetSearchOptions = {
     minScore?: number;
     source?: DisgenetSource;
     limit?: number;
-}
+};
 /** The result of one GDA query: the records of the first page, and the count of the whole query. */
-export interface DisgenetSearchResult {
+export type DisgenetSearchResult = {
     records: Gda[];
     totalFound: number;
-}
+};
 /**
  * Gene-disease associations for a gene symbol or for a disease.
  *

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

@@ -13,7 +13,7 @@
  * `.optional()`.
  */
 import { z } from "zod";
-export interface EmaReferral {
+export type EmaReferral = {
     category: string;
     referralName: string;
     inn: string;
@@ -33,7 +33,7 @@ export interface EmaReferral {
     firstPublishedDate: string;
     lastUpdatedDate: string;
     referralUrl: string;
-}
+};
 /** The catalogue file. It is exported so that the golden-fixture table drives it. */
 export declare const ReferralFileSchema: z.ZodObject<{
     meta: z.ZodOptional<z.ZodObject<{

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

@@ -7,7 +7,7 @@
  * an explicit `null`. Thus a maybe-absent field carries `.optional()`, not
  * `.nullable()`.
  */
-export interface GeneInfo {
+export type GeneInfo = {
     symbol: string;
     id: string;
     displayName: string;
@@ -18,10 +18,10 @@ export interface GeneInfo {
     strand: number;
     assemblyName: string;
     seqRegionName: string;
-}
-export interface LookupOptions {
+};
+export type LookupOptions = {
     species?: string;
-}
+};
 /**
  * Look up genes by symbol. Gene-level only: `RawGeneSchema`/`mapGene` model the
  * gene record itself, so there is no transcript or exon detail to ask for.

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

@@ -48,15 +48,16 @@ function mapGene(symbol, raw) {
  */
 export async function lookupGenes(symbols, options = {}) {
     const species = options.species ?? "homo_sapiens";
-    if (symbols.length === 1) {
-        const result = await apiFetchValidated(`${ENSEMBL_BASE}/lookup/symbol/${species}/${symbols[0]}`, RawGeneSchema, { headers: HEADERS });
+    const [singleSymbol] = symbols;
+    if (symbols.length === 1 && singleSymbol !== undefined) {
+        const result = await apiFetchValidated(`${ENSEMBL_BASE}/lookup/symbol/${species}/${singleSymbol}`, RawGeneSchema, { headers: HEADERS });
         if (result.isErr()) {
             if (result.error.type === "http_status" && result.error.status === 400) {
-                return { genes: [], notFound: [symbols[0]] };
+                return { genes: [], notFound: [singleSymbol] };
             }
             throw new Error(describeApiError(result.error));
         }
-        return { genes: [mapGene(symbols[0], result.value)], notFound: [] };
+        return { genes: [mapGene(singleSymbol, result.value)], notFound: [] };
     }
     const result = await apiFetchValidated(`${ENSEMBL_BASE}/lookup/symbol/${species}`, z.record(z.string(), RawGeneSchema), {
         method: "POST",

package/dist/tools/lib/gwas-catalog-client.d.ts

@@ -11,7 +11,7 @@
  * only when the projection that the request named excludes it.
  */
 import { z } from "zod";
-export interface GwasAssociation {
+export type GwasAssociation = {
     rsId: string;
     pValue: number;
     pValueMantissa: number;
@@ -25,7 +25,7 @@ export interface GwasAssociation {
     studyAccession: string;
     pubmedId: string;
     sampleSize: string;
-}
+};
 export type GwasSearchType = "gene" | "trait" | "variant" | "study";
 declare const RawGwasAssociationSchema: z.ZodObject<{
     _snpRsId: z.ZodOptional<z.ZodString>;
@@ -113,10 +113,10 @@ export declare const GwasSnpSearchResponseSchema: z.ZodObject<{
     }, z.core.$strip>>;
 }, z.core.$strip>;
 export declare function mapAssociation(a: RawGwasAssociation): GwasAssociation;
-export interface GwasSearchOptions {
+export type GwasSearchOptions = {
     pValueThreshold?: number;
     limit?: number;
-}
+};
 export declare function searchGwasCatalog(query: string, searchType: GwasSearchType, options?: GwasSearchOptions): Promise<{
     totalFound: number;
     associations: GwasAssociation[];

package/dist/tools/lib/gwas-catalog-client.js

@@ -72,26 +72,26 @@ export const GwasSnpSearchResponseSchema = z.object({
 });
 export function mapAssociation(a) {
     const loci = a.loci ?? [];
-    const riskAlleles = loci.flatMap((l) => l.strongestRiskAlleles?.map((ra) => String(ra.riskAlleleName ?? "")) ?? []);
-    const genes = loci.flatMap((l) => l.authorReportedGenes?.map((g) => String(g.geneName ?? "")) ?? []);
-    const traits = (a.efoTraits ?? []).map((t) => String(t.trait ?? ""));
+    const riskAlleles = loci.flatMap((l) => l.strongestRiskAlleles?.map((ra) => ra.riskAlleleName ?? "") ?? []);
+    const genes = loci.flatMap((l) => l.authorReportedGenes?.map((g) => g.geneName ?? "") ?? []);
+    const traits = (a.efoTraits ?? []).map((t) => t.trait ?? "");
     const study = a.study ?? {};
     const pMantissa = a.pvalueMantissa ?? 0;
     const pExponent = a.pvalueExponent ?? 0;
     return {
-        rsId: String(a._snpRsId ?? riskAlleles[0]?.split("-")[0] ?? ""),
+        rsId: a._snpRsId ?? riskAlleles[0]?.split("-")[0] ?? "",
         pValue: pMantissa * Math.pow(10, pExponent),
         pValueMantissa: pMantissa,
         pValueExponent: pExponent,
         riskAllele: riskAlleles.join(", "),
-        riskFrequency: String(a.riskFrequency ?? ""),
-        orBeta: (a.orPerCopyNum ?? a.betaNum ?? null),
-        ci: String(a.range ?? ""),
+        riskFrequency: a.riskFrequency ?? "",
+        orBeta: a.orPerCopyNum ?? a.betaNum ?? null,
+        ci: a.range ?? "",
         trait: traits.join("; "),
         mappedGenes: [...new Set(genes)],
-        studyAccession: String(study.accessionId ?? ""),
-        pubmedId: String(study.publicationInfo?.pubmedId ?? ""),
-        sampleSize: String(study.initialSampleSize ?? ""),
+        studyAccession: study.accessionId ?? "",
+        pubmedId: study.publicationInfo?.pubmedId ?? "",
+        sampleSize: study.initialSampleSize ?? "",
     };
 }
 /** Max SNPs whose associations the 'gene' path walks; each is one request. */
@@ -104,15 +104,15 @@ export async function searchGwasCatalog(query, searchType, options = {}) {
         const snpRes = await apiFetchValidated(url, GwasSnpSearchResponseSchema, { headers: GWAS_HEADERS });
         if (snpRes.isErr())
             throw new Error(describeApiError(snpRes.error));
-        const snps = snpRes.value?._embedded?.singleNucleotidePolymorphisms ?? [];
+        const snps = snpRes.value._embedded?.singleNucleotidePolymorphisms ?? [];
         const allAssocs = [];
         for (const snp of snps.slice(0, Math.min(limit, GENE_PATH_MAX_SNPS))) {
-            const assocLink = snp?._links?.associations?.href;
+            const assocLink = snp._links?.associations?.href;
             if (!assocLink)
                 continue;
             const aRes = await apiFetchValidated(assocLink, GwasEmbeddedSchema, { headers: GWAS_HEADERS });
             if (aRes.isOk()) {
-                for (const a of aRes.value?._embedded?.associations ?? []) {
+                for (const a of aRes.value._embedded?.associations ?? []) {
                     a._snpRsId = snp.rsId;
                     allAssocs.push(a);
                 }
@@ -143,10 +143,10 @@ export async function searchGwasCatalog(query, searchType, options = {}) {
         });
         if (traitRes.isErr())
             throw new Error(describeApiError(traitRes.error));
-        const traitUri = (traitRes.value?._embedded?.efoTraits ?? [])[0]?._links?.self?.href;
+        const traitUri = (traitRes.value._embedded?.efoTraits ?? [])[0]?._links?.self?.href;
         if (!traitUri)
             return { totalFound: 0, associations: [] };
-        associationsUrl = `${GWAS_BASE}/efoTraits/${traitUri.split("/").pop()}/associations?size=${limit}`;
+        associationsUrl = `${GWAS_BASE}/efoTraits/${String(traitUri.split("/").pop())}/associations?size=${limit}`;
     }
     const res = await apiFetchValidated(associationsUrl, GwasEmbeddedSchema, { headers: GWAS_HEADERS });
     if (res.isErr()) {
@@ -156,8 +156,8 @@ export async function searchGwasCatalog(query, searchType, options = {}) {
             return { totalFound: 0, associations: [] };
         throw new Error(describeApiError(res.error));
     }
-    const rawAssocs = res.value?._embedded?.associations ?? [];
-    const totalFound = res.value?.page?.totalElements ?? rawAssocs.length;
+    const rawAssocs = res.value._embedded?.associations ?? [];
+    const totalFound = res.value.page?.totalElements ?? rawAssocs.length;
     const filtered = rawAssocs.filter((a) => (a.pvalueMantissa ?? 1) * Math.pow(10, a.pvalueExponent ?? 0) <= pValueThreshold).slice(0, limit);
     return { totalFound, associations: filtered.map(mapAssociation) };
 }

package/dist/tools/lib/html-text.d.ts

@@ -0,0 +1,6 @@
+/**
+ * Strip each `<...>` run to its first closing bracket. One pass already
+ * reaches the fixpoint: a span's interior holds no `>`, so a removal cannot
+ * form a new `<...>` pair.
+ */
+export declare function stripHtmlTags(text: string): string;

package/dist/tools/lib/html-text.js

@@ -0,0 +1,9 @@
+/**
+ * Strip each `<...>` run to its first closing bracket. One pass already
+ * reaches the fixpoint: a span's interior holds no `>`, so a removal cannot
+ * form a new `<...>` pair.
+ */
+export function stripHtmlTags(text) {
+    // oxlint-disable-next-line eslint-js/no-restricted-syntax -- an HTML tag run to the first closing bracket; a quoted `>` inside an attribute is deliberately not seen.
+    return text.replace(/<[^>]+>/g, "");
+}

package/dist/tools/lib/identifier-resolver.d.ts

@@ -18,7 +18,7 @@
  */
 import { z } from "zod";
 import type { Logger } from "../../lib/logger.js";
-export interface ResolvedTarget {
+export type ResolvedTarget = {
     /** Canonical id used as the entity-resolution anchor — preferred order: HGNC, then Ensembl. */
     canonicalId: string;
     /** What ontology produced the canonical id ("hgnc" or "ensembl"). */
@@ -48,7 +48,7 @@ export interface ResolvedTarget {
         ensembl: boolean;
         chembl: boolean;
     };
-}
+};
 export declare const HgncResponseSchema: z.ZodObject<{
     response: z.ZodOptional<z.ZodObject<{
         docs: z.ZodOptional<z.ZodArray<z.ZodObject<{
@@ -69,7 +69,7 @@ export declare const HgncResponseSchema: z.ZodObject<{
  * @throws when the input cannot be mapped to any human gene/protein.
  */
 export declare function resolveTarget(input: string, logger?: Logger): Promise<ResolvedTarget>;
-export interface AutocompleteCandidate {
+export type AutocompleteCandidate = {
     /** Approved HGNC symbol when known, otherwise the input symbol. */
     symbol: string;
     /** Full gene/protein name. */
@@ -79,7 +79,7 @@ export interface AutocompleteCandidate {
     uniprotId: string | null;
     /** Sorted synonyms across HGNC + UniProt. */
     synonyms: string[];
-}
+};
 /**
  * Resolve a single gene-symbol query for the autocomplete UI by fanning
  * out HGNC + UniProt + Ensembl in parallel and merging into one canonical

package/dist/tools/lib/identifier-resolver.js

@@ -26,9 +26,13 @@ const HGNC_BASE = "https://rest.genenames.org/fetch";
 const UNIPROT_BASE = "https://rest.uniprot.org/uniprotkb/search";
 const HGNC_HEADERS = { Accept: "application/json" };
 const UNIPROT_HEADERS = { Accept: "application/json" };
+// oxlint-disable-next-line eslint-js/no-restricted-syntax -- Ensembl gene ids are ENSG plus 11 digits; the fixed shape is the identifier rule.
 const ENSG_RE = /^ENSG\d{11}$/;
+// oxlint-disable-next-line eslint-js/no-restricted-syntax -- the UniProt accession shape with its optional isoform suffix (-<n>).
 const UNIPROT_RE = /^[A-Z][0-9][A-Z0-9]{3}[0-9](-\d+)?$/;
+// oxlint-disable-next-line eslint-js/no-restricted-syntax -- ChEMBL ids carry the fixed CHEMBL<n> shape.
 const CHEMBL_RE = /^CHEMBL\d+$/;
+// oxlint-disable-next-line eslint-js/no-restricted-syntax -- HGNC ids are the HGNC: prefix plus digits.
 const HGNC_RE = /^HGNC:\d+$/;
 // HGNC search payload, validated at the fetch boundary. Every field is optional
 // because the API omits absent values; each read below is optional-chained /
@@ -166,7 +170,7 @@ export async function resolveTarget(input, logger) {
         }
     }
     else if (seedHgncId) {
-        hgncDoc = await fetchHgncBy("hgnc_id", seedHgncId.replace(/^HGNC:/, ""));
+        hgncDoc = await fetchHgncBy("hgnc_id", seedHgncId.startsWith("HGNC:") ? seedHgncId.slice("HGNC:".length) : seedHgncId);
     }
     else if (seedEnsemblId) {
         hgncDoc = await fetchHgncBy("ensembl_gene_id", seedEnsemblId);
@@ -230,9 +234,9 @@ export async function resolveTarget(input, logger) {
     }
     const synonyms = new Set();
     for (const s of hgncDoc?.alias_symbol ?? [])
-        synonyms.add(String(s));
+        synonyms.add(s);
     for (const s of hgncDoc?.prev_symbol ?? [])
-        synonyms.add(String(s));
+        synonyms.add(s);
     for (const g of uniprotDoc?.genes ?? []) {
         for (const syn of g.synonyms ?? []) {
             if (syn.value)

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

@@ -8,27 +8,27 @@
  * sends an explicit `null`. Thus a maybe-absent field carries `.optional()`,
  * not `.nullable()`.
  */
-export interface MpTerm {
+export type MpTerm = {
     id: string;
     term: string;
     bestPValue: number | null;
-}
-export interface PhenotypeProfile {
+};
+export type PhenotypeProfile = {
     mpTerms: MpTerm[];
     organSystems: string[];
     sexDimorphic: boolean;
     phenotypeCount: number;
-}
-export interface ViabilityCall {
+};
+export type ViabilityCall = {
     zygosity: string;
     parameterStableId: string;
     mpTerm: {
         id: string;
         name: string;
     } | null;
-}
+};
 export type ViabilityCategory = "lethal_pre_weaning" | "subviable" | "viable" | null;
-export interface KoPhenotypeProfile {
+export type KoPhenotypeProfile = {
     geneSymbol: string;
     mouseMarkerSymbol: string | null;
     mgiAccessionId: string | null;
@@ -40,7 +40,7 @@ export interface KoPhenotypeProfile {
     phenotypeCount: number;
     phenotypeDocsTotal: number;
     phenotypesTruncated: boolean;
-}
+};
 export declare function parsePhenotypeResponse(raw: unknown): PhenotypeProfile;
 export declare function buildViabilityCalls(docsB: unknown, docsC: unknown): ViabilityCall[];
 export declare function derivedViability(calls: ViabilityCall[]): ViabilityCategory;