@inflexa-ai/harness 0.45.1 → 0.46.2

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;

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

@@ -9,6 +9,9 @@
  * not `.nullable()`.
  */
 import { z } from "zod";
+import { isUnknownArray } from "../../lib/unknown-array.js";
+import { presentGet } from "../../lib/present.js";
+import { parseUnknownRecord } from "../../lib/unknown-containers.js";
 import { apiFetchValidated, describeApiError, isUnexpectedApiError } from "./api-utils.js";
 const IMPC_BASE = "https://www.ebi.ac.uk/mi/impc/solr";
 const PHENOTYPE_ROW_CAP = 500;
@@ -40,14 +43,14 @@ const ORGAN_SYSTEM_MAP = {
     "embryo phenotype": "growth",
 };
 // A single IMPC Solr document — fields vary by core; all optional. `top_level_mp_term_name`
-// and `sex` are `z.unknown()` because the code reads them defensively (`Array.isArray`,
+// and `sex` ride as JSON values: the code reads them defensively (`Array.isArray`,
 // `typeof === "string"`) rather than trusting a wire type.
 const ImpcSolrDocSchema = z.object({
     mp_term_id: z.string().optional(),
     mp_term_name: z.string().optional(),
     p_value: z.number().optional(),
-    top_level_mp_term_name: z.unknown().optional(),
-    sex: z.unknown().optional(),
+    top_level_mp_term_name: z.json().optional(),
+    sex: z.json().optional(),
     parameter_stable_id: z.string().optional(),
     parameter_name: z.string().optional(),
     marker_symbol: z.string().optional(),
@@ -57,14 +60,21 @@ const ImpcSolrDocSchema = z.object({
 const ImpcSolrResponseSchema = z.object({
     response: z.object({ docs: z.array(ImpcSolrDocSchema).optional(), numFound: z.number().optional() }).optional(),
 });
+import { hasWhitespace } from "../../lib/text.js";
 function escapeSolrValue(value) {
-    return value.replace(/([+\-&|!(){}[\]^"~*?:\\/\s])/g, "\\$1");
+    const specials = '+-&|!(){}[]^"~*?:\\/';
+    let out = "";
+    for (const char of value) {
+        if (specials.includes(char) || hasWhitespace(char))
+            out += "\\" + char;
+        else
+            out += char;
+    }
+    return out;
 }
 export function parsePhenotypeResponse(raw) {
-    // `raw` is the untyped IMPC Solr response; we reach `.response.docs` defensively
-    // (optional-chained, defaulted to []) and treat each doc's fields as optional below.
-    const docs = raw?.response?.docs ?? [];
-    if (!Array.isArray(docs) || docs.length === 0) {
+    const docs = solrDocsOf(raw);
+    if (docs.length === 0) {
         return { mpTerms: [], organSystems: [], sexDimorphic: false, phenotypeCount: 0 };
     }
     const byMp = new Map();
@@ -72,13 +82,13 @@ export function parsePhenotypeResponse(raw) {
     const mpToSexes = new Map();
     const allSexes = new Set();
     for (const doc of docs) {
-        const mpId = doc.mp_term_id;
+        const mpId = readString(doc, "mp_term_id");
         if (!mpId)
             continue;
         const newP = typeof doc.p_value === "number" && Number.isFinite(doc.p_value) ? doc.p_value : null;
         const existing = byMp.get(mpId);
         if (!existing) {
-            byMp.set(mpId, { id: mpId, term: doc.mp_term_name ?? "", bestPValue: newP });
+            byMp.set(mpId, { id: mpId, term: readString(doc, "mp_term_name") ?? "", bestPValue: newP });
         }
         else if (newP !== null && (existing.bestPValue === null || newP < existing.bestPValue)) {
             existing.bestPValue = newP;
@@ -97,7 +107,7 @@ export function parsePhenotypeResponse(raw) {
             allSexes.add(sex);
             if (!mpToSexes.has(mpId))
                 mpToSexes.set(mpId, new Set());
-            mpToSexes.get(mpId).add(sex);
+            presentGet(mpToSexes, mpId, "the sex set of the phenotype").add(sex);
         }
     }
     const mpTerms = [...byMp.values()].sort((a, b) => {
@@ -110,33 +120,34 @@ export function parsePhenotypeResponse(raw) {
     const sexDimorphic = bothSexesTested && [...mpToSexes.values()].some((sexes) => (sexes.has("male") && !sexes.has("female")) || (sexes.has("female") && !sexes.has("male")));
     return { mpTerms, organSystems, sexDimorphic, phenotypeCount: byMp.size };
 }
+function readString(record, key) {
+    const value = record[key];
+    return typeof value === "string" ? value : undefined;
+}
+/** The `.response.docs` of a Solr envelope, each doc as the record its fields are read off; a non-record doc is skipped. */
+function solrDocsOf(raw) {
+    const docs = parseUnknownRecord(parseUnknownRecord(raw)?.response)?.docs;
+    if (!isUnknownArray(docs))
+        return [];
+    return docs.flatMap((doc) => {
+        const record = parseUnknownRecord(doc);
+        return record === undefined ? [] : [record];
+    });
+}
 export function buildViabilityCalls(docsB, docsC) {
-    // `docsB`/`docsC` are untyped IMPC Solr responses; the `.response.docs` reach is
-    // optional-chained + defaulted, so a shape mismatch degrades to an empty result.
-    const bDocs = docsB?.response?.docs ?? [];
-    const cDocs = docsC?.response?.docs ?? [];
     const seen = new Set();
     const out = [];
-    for (const d of bDocs) {
-        const pid = d.parameter_stable_id;
-        if (!pid || seen.has(pid))
-            continue;
-        seen.add(pid);
-        out.push({
-            zygosity: d.parameter_name ?? "",
-            parameterStableId: pid,
-            mpTerm: d.mp_term_id && d.mp_term_name ? { id: d.mp_term_id, name: d.mp_term_name } : null,
-        });
-    }
-    for (const d of cDocs) {
-        const pid = d.parameter_stable_id;
+    for (const d of [...solrDocsOf(docsB), ...solrDocsOf(docsC)]) {
+        const pid = readString(d, "parameter_stable_id");
         if (!pid || seen.has(pid))
             continue;
         seen.add(pid);
+        const mpId = readString(d, "mp_term_id");
+        const mpName = readString(d, "mp_term_name");
         out.push({
-            zygosity: d.parameter_name ?? "",
+            zygosity: readString(d, "parameter_name") ?? "",
             parameterStableId: pid,
-            mpTerm: null,
+            mpTerm: mpId && mpName ? { id: mpId, name: mpName } : null,
         });
     }
     return out;
@@ -159,15 +170,15 @@ async function resolveImpcGene(humanSymbol) {
             throw new Error(describeApiError(res.error));
         return null;
     }
-    const docs = res.value?.response?.docs ?? [];
+    const docs = res.value.response?.docs ?? [];
     if (!Array.isArray(docs) || docs.length === 0)
         return null;
     const doc = docs[0];
-    if (!doc.marker_symbol || !doc.mgi_accession_id)
+    if (doc === undefined || !doc.marker_symbol || !doc.mgi_accession_id)
         return null;
     return {
-        mouseMarkerSymbol: String(doc.marker_symbol),
-        mgiAccessionId: String(doc.mgi_accession_id),
+        mouseMarkerSymbol: doc.marker_symbol,
+        mgiAccessionId: doc.mgi_accession_id,
     };
 }
 async function fetchPhenotypes(mouseSym) {
@@ -179,7 +190,7 @@ async function fetchPhenotypes(mouseSym) {
             throw new Error(describeApiError(res.error));
         return { raw: { response: { docs: [] } }, numFound: 0 };
     }
-    const numFound = Number(res.value?.response?.numFound ?? 0);
+    const numFound = res.value.response?.numFound ?? 0;
     return { raw: res.value, numFound };
 }
 async function fetchAssignedViability(mouseSym) {

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

@@ -19,14 +19,14 @@ export declare const IupharTargetSchema: z.ZodObject<{
     subunitType: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>;
 export type IupharTarget = z.infer<typeof IupharTargetSchema>;
-export interface IupharHeterodimer {
+export type IupharHeterodimer = {
     /** Complex target record (e.g., the AMY1 receptor). */
     complex: IupharTarget;
     /** All subunits of the complex, including the primary protein and accessory(ies). */
     subunits: IupharTarget[];
     /** Accessory-protein subunits only (type === "AccessoryProtein"). */
     accessories: IupharTarget[];
-}
+};
 export declare function findTargetByGeneSymbol(geneSymbol: string): Promise<IupharTarget | null>;
 export declare function findTargetByUniprot(accession: string): Promise<IupharTarget | null>;
 /**

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

@@ -9,6 +9,8 @@
  */
 import { z } from "zod";
 import { createNoopLogger } from "../../lib/console-logger.js";
+import { presentAt } from "../../lib/present.js";
+import { stripHtmlTags } from "./html-text.js";
 import { apiFetchValidated, describeApiError, isUnexpectedApiError } from "./api-utils.js";
 import { IUPHAR_BASE, IUPHAR_HEADERS as HEADERS } from "./iuphar-config.js";
 // Validated at the fetch boundary. GtoPdb serves the target record in three
@@ -36,19 +38,8 @@ export const IupharTargetSchema = z.object({
     complexIds: z.array(z.number()).optional(),
     subunitType: z.string().optional(),
 });
+// oxlint-disable-next-line eslint-js/no-restricted-syntax -- the issued UniProt accession shape is the identifier rule of the target records.
 const UNIPROT_ACCESSION_RE = /^[A-Z][0-9][A-Z0-9]{3}[0-9]$/;
-function stripHtml(name) {
-    // Strip tags to a fixpoint: a single pass can leave a `<…>` behind when
-    // removing an inner tag lets the surrounding angle brackets form a new one,
-    // so repeat until the string stops changing.
-    let out = name;
-    let prev;
-    do {
-        prev = out;
-        out = out.replace(/<[^>]+>/g, "");
-    } while (out !== prev);
-    return out;
-}
 function notFound(error) {
     return error.type === "http_status" && (error.status === 404 || error.status === 204);
 }
@@ -123,9 +114,9 @@ export async function getFamilyHeterodimers(uniprotOrGeneSymbol) {
         const batch = complexes.slice(i, i + concurrency);
         const subunitLists = await Promise.all(batch.map((c) => getSubunits(c.targetId)));
         for (let j = 0; j < batch.length; j++) {
-            const complex = batch[j];
-            const subunits = subunitLists[j];
-            const cleanedSubunits = subunits.map((s) => ({ ...s, name: stripHtml(s.name) }));
+            const complex = presentAt(batch, j, "the complex of the batch");
+            const subunits = presentAt(subunitLists, j, "the subunits of the complex");
+            const cleanedSubunits = subunits.map((s) => ({ ...s, name: stripHtmlTags(s.name) }));
             // Only a shape B row reaches this filter, because `getSubunits`
             // calls `/targets/{id}/subunits`. Shape B is the one shape that
             // names the kind of a target as `AccessoryProtein`, and the
@@ -134,7 +125,7 @@ export async function getFamilyHeterodimers(uniprotOrGeneSymbol) {
             // row or a single-target row would match nothing.
             const accessories = cleanedSubunits.filter((s) => (s.type ?? "").toLowerCase() === "accessoryprotein");
             results.push({
-                complex: { ...complex, name: stripHtml(complex.name) },
+                complex: { ...complex, name: stripHtmlTags(complex.name) },
                 subunits: cleanedSubunits,
                 accessories,
             });

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

@@ -17,7 +17,7 @@
  * field carries `.nullish()` exactly.
  */
 /** A curated human phenotype attributed to variation in the gene. */
-export interface MonarchPhenotypeAssociation {
+export type MonarchPhenotypeAssociation = {
     /** HPO term id, e.g. `HP:0001392`. */
     readonly hpoId: string;
     readonly label: string;
@@ -30,12 +30,12 @@ export interface MonarchPhenotypeAssociation {
     /** Share of affected individuals showing the phenotype, when annotated. */
     readonly frequencyPercent: number | null;
     readonly primaryKnowledgeSource: string | null;
-}
-export interface MonarchGeneProfile {
+};
+export type MonarchGeneProfile = {
     /** The curie the gene was queried by, e.g. `HGNC:1097`. */
     readonly geneCurie: string;
     readonly phenotypes: MonarchPhenotypeAssociation[];
-}
+};
 /**
  * Curated human phenotype associations for one gene.
  *