@inflexa-ai/harness 0.45.0 → 0.46.0

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.
  *

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

@@ -9,11 +9,11 @@
  * not `.nullable()`.
  */
 import { z } from "zod";
-export interface AdverseEventCount {
+export type AdverseEventCount = {
     reaction: string;
     count: number;
-}
-export interface DrugLabelAction {
+};
+export type DrugLabelAction = {
     applicationNumber: string | null;
     brandName: string | null;
     genericName: string | null;
@@ -23,8 +23,8 @@ export interface DrugLabelAction {
     warningsAndCautions: string | null;
     hasRems: boolean;
     sourceUrl: string;
-}
-export interface SeriousnessProfile {
+};
+export type SeriousnessProfile = {
     totalReports: number;
     fatalCount: number;
     hospitalizationCount: number;
@@ -32,7 +32,7 @@ export interface SeriousnessProfile {
     disablingCount: number;
     congenitalAnomalyCount: number;
     otherSeriousCount: number;
-}
+};
 /** Top adverse-reaction terms by count for a generic drug name. */
 export declare function getFaersByDrug(drugName: string, options?: {
     limit?: number;
@@ -49,29 +49,29 @@ export declare function getFaersByDrug(drugName: string, options?: {
 export declare function getFaersSeriousness(drugName: string): Promise<SeriousnessProfile | null>;
 export declare const OpenFdaLabelResponseSchema: z.ZodObject<{
     results: z.ZodOptional<z.ZodArray<z.ZodPipe<z.ZodObject<{
-        set_id: z.ZodOptional<z.ZodUnknown>;
+        set_id: z.ZodOptional<z.ZodJSONSchema>;
         openfda: z.ZodOptional<z.ZodObject<{
-            application_number: z.ZodOptional<z.ZodUnknown>;
-            brand_name: z.ZodOptional<z.ZodUnknown>;
-            generic_name: z.ZodOptional<z.ZodUnknown>;
+            application_number: z.ZodOptional<z.ZodJSONSchema>;
+            brand_name: z.ZodOptional<z.ZodJSONSchema>;
+            generic_name: z.ZodOptional<z.ZodJSONSchema>;
         }, z.core.$strip>>;
-        effective_time: z.ZodOptional<z.ZodUnknown>;
-        boxed_warning: z.ZodOptional<z.ZodUnknown>;
-        warnings_and_cautions: z.ZodOptional<z.ZodUnknown>;
-        warnings: z.ZodOptional<z.ZodUnknown>;
+        effective_time: z.ZodOptional<z.ZodJSONSchema>;
+        boxed_warning: z.ZodOptional<z.ZodJSONSchema>;
+        warnings_and_cautions: z.ZodOptional<z.ZodJSONSchema>;
+        warnings: z.ZodOptional<z.ZodJSONSchema>;
         spl_medguide: z.ZodOptional<z.ZodArray<z.ZodString>>;
         patient_medication_information: z.ZodOptional<z.ZodArray<z.ZodString>>;
     }, z.core.$strip>, z.ZodTransform<DrugLabelAction, {
-        set_id?: unknown;
+        set_id?: z.JSONType | undefined;
         openfda?: {
-            application_number?: unknown;
-            brand_name?: unknown;
-            generic_name?: unknown;
+            application_number?: z.JSONType | undefined;
+            brand_name?: z.JSONType | undefined;
+            generic_name?: z.JSONType | undefined;
         } | undefined;
-        effective_time?: unknown;
-        boxed_warning?: unknown;
-        warnings_and_cautions?: unknown;
-        warnings?: unknown;
+        effective_time?: z.JSONType | undefined;
+        boxed_warning?: z.JSONType | undefined;
+        warnings_and_cautions?: z.JSONType | undefined;
+        warnings?: z.JSONType | undefined;
         spl_medguide?: string[] | undefined;
         patient_medication_information?: string[] | undefined;
     }>>>>;

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

@@ -9,6 +9,7 @@
  * not `.nullable()`.
  */
 import { z } from "zod";
+import { isUnknownArray } from "../../lib/unknown-array.js";
 import { apiFetchValidated, describeApiError } from "./api-utils.js";
 import { OPENFDA_BASE, OPENFDA_LABEL_BASE } from "./openfda-config.js";
 // FAERS count/meta wire shapes, validated at the fetch boundary. Every field is
@@ -22,9 +23,9 @@ const FaersMetaResponseSchema = z.object({
 });
 /** openFDA drug-label metadata block (`openfda`) — all fields free-form JSON. */
 const OpenFdaLabelMetaSchema = z.object({
-    application_number: z.unknown().optional(),
-    brand_name: z.unknown().optional(),
-    generic_name: z.unknown().optional(),
+    application_number: z.json().optional(),
+    brand_name: z.json().optional(),
+    generic_name: z.json().optional(),
 });
 /**
  * A single openFDA structured-product-label record (raw wire shape).
@@ -34,12 +35,12 @@ const OpenFdaLabelMetaSchema = z.object({
  * provider types both as an array of string.
  */
 const OpenFdaLabelSchema = z.object({
-    set_id: z.unknown().optional(),
+    set_id: z.json().optional(),
     openfda: OpenFdaLabelMetaSchema.optional(),
-    effective_time: z.unknown().optional(),
-    boxed_warning: z.unknown().optional(),
-    warnings_and_cautions: z.unknown().optional(),
-    warnings: z.unknown().optional(),
+    effective_time: z.json().optional(),
+    boxed_warning: z.json().optional(),
+    warnings_and_cautions: z.json().optional(),
+    warnings: z.json().optional(),
     spl_medguide: z.array(z.string()).optional(),
     patient_medication_information: z.array(z.string()).optional(),
 });
@@ -49,7 +50,7 @@ const OpenFdaLabelSchema = z.object({
  * unescaped `"` past the quote escaping and break out of the phrase.
  */
 function escapeQueryPhrase(value) {
-    return value.replace(/\\/g, "\\\\").replace(/"/g, '\\"');
+    return value.replaceAll("\\", "\\\\").replaceAll('"', '\\"');
 }
 /**
  * A boolean operator is separated by a space, never by a literal `+`. The whole
@@ -76,13 +77,13 @@ export async function getFaersByDrug(drugName, options = {}) {
             return { totalReports: 0, adverseEvents: [] };
         throw new Error(describeApiError(res.error));
     }
-    const adverseEvents = (res.value?.results ?? []).map((r) => ({
+    const adverseEvents = (res.value.results ?? []).map((r) => ({
         reaction: r.term ?? "Unknown",
         count: r.count ?? 0,
     }));
     const totalUrl = `${OPENFDA_BASE}?search=${encodeURIComponent(search)}&limit=1`;
     const totalRes = await apiFetchValidated(totalUrl, FaersMetaResponseSchema);
-    const totalReports = totalRes.isOk() ? totalRes.value?.meta?.results?.total : undefined;
+    const totalReports = totalRes.isOk() ? totalRes.value.meta?.results?.total : undefined;
     return { totalReports, adverseEvents };
 }
 /**
@@ -100,7 +101,7 @@ export async function getFaersSeriousness(drugName) {
             return null;
         throw new Error(describeApiError(totalRes.error));
     }
-    const totalReports = totalRes.value?.meta?.results?.total ?? 0;
+    const totalReports = totalRes.value.meta?.results?.total ?? 0;
     if (totalReports === 0) {
         return {
             totalReports: 0,
@@ -118,7 +119,7 @@ export async function getFaersSeriousness(drugName) {
         const res = await apiFetchValidated(url, FaersMetaResponseSchema);
         if (res.isErr())
             return 0;
-        return res.value?.meta?.results?.total ?? 0;
+        return res.value.meta?.results?.total ?? 0;
     }
     const [fatal, hosp, lifeT, dis, cong, other] = await Promise.all([
         countWith("seriousnessdeath"),
@@ -139,7 +140,7 @@ export async function getFaersSeriousness(drugName) {
     };
 }
 function firstString(value) {
-    if (Array.isArray(value)) {
+    if (isUnknownArray(value)) {
         const first = value.find((v) => typeof v === "string" && v.trim());
         return typeof first === "string" ? first : null;
     }
@@ -149,7 +150,7 @@ function firstString(value) {
 }
 function joinSection(value) {
     if (Array.isArray(value)) {
-        const parts = value.filter((v) => typeof v === "string" && v.trim().length > 0);
+        const parts = value.flatMap((v) => (typeof v === "string" && v.trim().length > 0 ? [v] : []));
         if (parts.length === 0)
             return null;
         return parts.join("\n\n");
@@ -164,30 +165,30 @@ function joinSection(value) {
  * keyed by application number when only that is available.
  */
 function buildLabelSourceUrl(label) {
-    const setId = typeof label?.set_id === "string" ? label.set_id : null;
+    const setId = typeof label.set_id === "string" ? label.set_id : null;
     if (setId)
         return `https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=${setId}`;
-    const appNum = firstString(label?.openfda?.application_number);
+    const appNum = firstString(label.openfda?.application_number);
     if (appNum) {
         return `https://www.accessdata.fda.gov/scripts/cder/daf/index.cfm?event=overview.process&ApplNo=${encodeURIComponent(appNum)}`;
     }
     return "https://www.accessdata.fda.gov/scripts/cder/daf/";
 }
 function mapLabel(raw) {
-    const openfda = raw?.openfda ?? {};
+    const openfda = raw.openfda ?? {};
     // The label reference carries no REMS field, thus the signal is the word
     // itself in one of the three sections that a REMS program writes to. The
     // presence of a medication guide alone is not the signal: many labels with no
     // REMS carry one, and a presence test would report a REMS that does not exist.
-    const remsTextCandidates = [raw?.boxed_warning, raw?.spl_medguide, raw?.patient_medication_information];
+    const remsTextCandidates = [raw.boxed_warning, raw.spl_medguide, raw.patient_medication_information];
     const hasRems = remsTextCandidates.some((v) => joinSection(v)?.toLowerCase().includes("rems") ?? false);
     return {
         applicationNumber: firstString(openfda.application_number),
         brandName: firstString(openfda.brand_name),
         genericName: firstString(openfda.generic_name),
-        effectiveTime: typeof raw?.effective_time === "string" ? raw.effective_time : null,
-        boxedWarning: joinSection(raw?.boxed_warning),
-        warningsAndCautions: joinSection(raw?.warnings_and_cautions) ?? joinSection(raw?.warnings),
+        effectiveTime: typeof raw.effective_time === "string" ? raw.effective_time : null,
+        boxedWarning: joinSection(raw.boxed_warning),
+        warningsAndCautions: joinSection(raw.warnings_and_cautions) ?? joinSection(raw.warnings),
         hasRems,
         sourceUrl: buildLabelSourceUrl(raw),
     };

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

@@ -8,7 +8,7 @@
  * thus the SDL gives each modifier and `.optional()` is wrong.
  */
 import { z } from "zod";
-export interface Association {
+export type Association = {
     diseaseId: string;
     diseaseName: string;
     targetId?: string;
@@ -21,42 +21,42 @@ export interface Association {
     animalModelScore: number | null;
     somaticMutationScore: number | null;
     literaturePmids: string[];
-}
+};
 /**
  * The positive tractability buckets of each modality, by their Open Targets label
  * ('Approved Drug', 'Structure with Ligand', 'UniProt loc high conf', …). An empty
  * list means no positive bucket. `null` means Open Targets gives no row for the modality.
  */
-export interface TargetTractability {
+export type TargetTractability = {
     smallMolecule: string[] | null;
     antibody: string[] | null;
     otherModalities: string[] | null;
-}
-export interface TargetInfo {
+};
+export type TargetInfo = {
     ensemblId: string;
     approvedSymbol: string;
     approvedName: string;
     tractability: TargetTractability | null;
     associations: Association[];
-}
-export interface SafetyLiability {
+};
+export type SafetyLiability = {
     event: string;
     biosamples: string[];
     effects: string | null;
     source: string;
-}
+};
 /**
  * One disease or trait that Open Targets holds, as the free-text resolver
  * returns it. The `id` is the identifier that `searchDiseaseAssociations`
  * accepts. Open Targets keys a disease on the EFO ontology, which imports
  * MONDO, Orphanet and HP, thus an id can read `EFO_…`, `MONDO_…` or `HP_…`.
  */
-export interface DiseaseCandidate {
+export type DiseaseCandidate = {
     id: string;
     name: string;
     description: string | null;
-}
-export interface BaselineExpressionEntry {
+};
+export type BaselineExpressionEntry = {
     tissueId: string;
     tissueLabel: string;
     organSystem: string | null;
@@ -74,7 +74,7 @@ export interface BaselineExpressionEntry {
     protein: {
         level: number | null;
     } | null;
-}
+};
 export declare const TargetAssociationsDataSchema: z.ZodObject<{
     target: z.ZodOptional<z.ZodNullable<z.ZodObject<{
         id: z.ZodString;

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

@@ -10,7 +10,7 @@
 import { z } from "zod";
 export declare function stripHtmlAndCollapseWs(s: string): string;
 export type PathwaySource = "kegg" | "reactome";
-export interface Pathway {
+export type Pathway = {
     id: string;
     name: string;
     source: PathwaySource;
@@ -18,7 +18,7 @@ export interface Pathway {
     genes?: string[];
     entity_uniprots?: string[];
     url?: string;
-}
+};
 export declare const ReactomeSearchResponseSchema: z.ZodObject<{
     results: z.ZodOptional<z.ZodArray<z.ZodObject<{
         entries: z.ZodOptional<z.ZodArray<z.ZodObject<{
@@ -38,12 +38,12 @@ export declare const ReactomeParticipantEntitiesSchema: z.ZodArray<z.ZodObject<{
         identifier: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>>;
 }, z.core.$strip>>;
-export interface PathwaySearchOptions {
+export type PathwaySearchOptions = {
     source?: "kegg" | "reactome" | "both";
     organism?: string;
     includeGenes?: boolean;
     maxResults?: number;
-}
+};
 export declare function searchKegg(query: string, organism: string, maxResults: number, includeGenes: boolean): Promise<Pathway[]>;
 /**
  * Read the KEGG gene identifier of a symbol, for example `hsa:7157` for `TP53`.