@inflexa-ai/harness 0.45.1 → 0.46.2

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`.

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

@@ -8,7 +8,9 @@
  * key to omit.
  */
 import { z } from "zod";
-import { apiFetch, apiFetchValidated, parseTSV } from "./api-utils.js";
+import { apiFetchText, apiFetchValidated, parseTSV } from "./api-utils.js";
+import { collapseWhitespace } from "../../lib/text.js";
+import { stripHtmlTags } from "./html-text.js";
 const KEGG_BASE = "https://rest.kegg.jp";
 // Both `reactome.org/ContentService` and `release.reactome.org/ContentService`
 // answer 200 on each path that this file calls. The two hosts serve different
@@ -17,16 +19,7 @@ const KEGG_BASE = "https://rest.kegg.jp";
 // links to stay on the primary host.
 const REACTOME_BASE = "https://release.reactome.org/ContentService";
 export function stripHtmlAndCollapseWs(s) {
-    // 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 = s;
-    let prev;
-    do {
-        prev = out;
-        out = out.replace(/<[^>]+>/g, "");
-    } while (out !== prev);
-    return out.replace(/\s+/g, " ").trim();
+    return collapseWhitespace(stripHtmlTags(s));
 }
 const ORGANISM_MAP = {
     hsa: "Homo sapiens",
@@ -60,7 +53,7 @@ export const ReactomeParticipantEntitiesSchema = z.array(z.object({
     refEntities: z.array(z.object({ schemaClass: z.string().optional(), identifier: z.string().optional() })).optional(),
 }));
 export async function searchKegg(query, organism, maxResults, includeGenes) {
-    const searchRes = await apiFetch(`${KEGG_BASE}/find/pathway/${encodeURIComponent(query)}`, { parseAs: "text" });
+    const searchRes = await apiFetchText(`${KEGG_BASE}/find/pathway/${encodeURIComponent(query)}`);
     if (searchRes.isErr())
         return [];
     const rows = parseTSV(searchRes.value);
@@ -75,7 +68,7 @@ export async function searchKegg(query, organism, maxResults, includeGenes) {
     });
     if (includeGenes) {
         for (const pw of pathways) {
-            const geneRes = await apiFetch(`${KEGG_BASE}/link/${organism}/${pw.id}`, { parseAs: "text" });
+            const geneRes = await apiFetchText(`${KEGG_BASE}/link/${organism}/${pw.id}`);
             if (geneRes.isOk()) {
                 const geneRows = parseTSV(geneRes.value);
                 pw.genes = geneRows.map((r) => (r[1] ?? "").replace(`${organism}:`, ""));
@@ -125,13 +118,13 @@ export function parseKeggPathwayLinks(rows) {
  * organism, thus it replaces one `get/{id}` call for each membership.
  */
 export async function keggPathwaysForGene(geneSymbol, organism, maxResults) {
-    const geneRes = await apiFetch(`${KEGG_BASE}/find/${organism}/${encodeURIComponent(geneSymbol)}`, { parseAs: "text" });
+    const geneRes = await apiFetchText(`${KEGG_BASE}/find/${organism}/${encodeURIComponent(geneSymbol)}`);
     if (geneRes.isErr())
         return [];
     const geneId = selectKeggGeneId(parseTSV(geneRes.value), geneSymbol);
     if (!geneId)
         return [];
-    const linkRes = await apiFetch(`${KEGG_BASE}/link/pathway/${encodeURIComponent(geneId)}`, { parseAs: "text" });
+    const linkRes = await apiFetchText(`${KEGG_BASE}/link/pathway/${encodeURIComponent(geneId)}`);
     if (linkRes.isErr())
         return [];
     const pathwayIds = parseKeggPathwayLinks(parseTSV(linkRes.value)).slice(0, maxResults);
@@ -148,7 +141,7 @@ export async function keggPathwaysForGene(geneSymbol, organism, maxResults) {
 /** The pathway vocabulary of one organism, keyed by the pathway identifier. */
 async function keggPathwayNames(organism) {
     const names = new Map();
-    const res = await apiFetch(`${KEGG_BASE}/list/pathway/${encodeURIComponent(organism)}`, { parseAs: "text" });
+    const res = await apiFetchText(`${KEGG_BASE}/list/pathway/${encodeURIComponent(organism)}`);
     if (res.isErr())
         return names;
     for (const cols of parseTSV(res.value)) {
@@ -217,16 +210,19 @@ export async function searchPathways(query, options = {}) {
     return results.flat();
 }
 /** A Reactome stable identifier, for example `R-HSA-109581`. */
+// oxlint-disable-next-line eslint-js/no-restricted-syntax -- the Reactome stable-id grammar: R-, three letters, digits, and an optional dotted subnumber.
 const REACTOME_ID_RE = /^R-[A-Z]{3}-\d+(\.\d+)?$/;
 /** A KEGG pathway identifier, for example `hsa04010` or `map04010`. */
+// oxlint-disable-next-line eslint-js/no-restricted-syntax -- the KEGG pathway-id grammar: three or four lowercase organism letters plus five digits.
 const KEGG_ID_RE = /^[a-z]{3,4}\d{5}$/;
 /** Read one field out of a KEGG flat-file record. */
 function keggField(record, field) {
+    // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the field name is a caller literal ("NAME", "DESCRIPTION"); the anchored multiline form reads the KEGG flat-file grammar.
     const match = new RegExp(`^${field}\\s+(.*)$`, "m").exec(record);
     return match?.[1]?.trim() || null;
 }
 async function getKeggPathway(id) {
-    const res = await apiFetch(`${KEGG_BASE}/get/${encodeURIComponent(id)}`, { parseAs: "text" });
+    const res = await apiFetchText(`${KEGG_BASE}/get/${encodeURIComponent(id)}`);
     if (res.isErr())
         return null;
     const record = res.value;
@@ -238,7 +234,7 @@ async function getKeggPathway(id) {
         id,
         name,
         source: "kegg",
-        ...(description ? { description } : {}),
+        description: description ?? undefined,
         url: `https://www.kegg.jp/pathway/${id}`,
     };
 }
@@ -255,7 +251,7 @@ async function getReactomePathway(id) {
         id: stId,
         name: stripHtmlAndCollapseWs(entry.displayName ?? ""),
         source: "reactome",
-        ...(description ? { description: stripHtmlAndCollapseWs(description) } : {}),
+        description: description === undefined ? undefined : stripHtmlAndCollapseWs(description),
         url: `https://reactome.org/content/detail/${stId}`,
     };
 }

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

@@ -45,11 +45,11 @@ export declare const PharmgkbResponseSchema: z.ZodObject<{
  * phenotype, guideline source and summary live on other PharmGKB resources, so
  * they are absent here rather than present-and-null.
  */
-export interface PharmgkbAnnotation {
+export type PharmgkbAnnotation = {
     gene: string;
     drug: string;
     levelOfEvidence: string;
-}
+};
 export declare function searchPharmgkb(query: string, searchType: "gene" | "drug", limit?: number): Promise<{
     annotations: PharmgkbAnnotation[];
     totalFound: number;

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

@@ -38,7 +38,7 @@ export async function searchPharmgkb(query, searchType, limit = 20) {
             return { annotations: [], totalFound: 0 };
         throw new Error(describeApiError(res.error));
     }
-    const data = res.value?.data ?? [];
+    const data = res.value.data ?? [];
     const annotations = data.slice(0, limit).map((ann) => ({
         gene: ann.location?.genes?.map((g) => g.symbol).join(", ") ?? query,
         drug: ann.relatedChemicals?.map((c) => c.name).join(", ") ?? "",

package/dist/tools/lib/protein-family-modality.d.ts

@@ -2,12 +2,12 @@
  * Protein-family → preferred modality lookup, used by §2.2 Tractability
  * fallback when Open Targets has no tractability assessment for the target.
  */
-export interface ModalityFallback {
+export type ModalityFallback = {
     family: string | null;
     preferred_modality: string;
     rationale: string;
     source: "family-match" | "default";
-}
+};
 /**
  * Infer a preferred modality from a free-text protein-family description
  * (typically the UniProt family/keyword). Returns the dataset default when

package/dist/tools/lib/protein-family-modality.js

@@ -4,8 +4,6 @@
  */
 import familyMappingData from "../../data/protein-family-modality.json" with { type: "json" };
 import { normalizeProteinFamily } from "./protein-family-normalize.js";
-// The JSON import yields an untyped/structurally-wide value; cast to the declared
-// shape, which the bundled data file is authored to satisfy.
 const dataset = familyMappingData;
 function loadDataset() {
     return dataset;

package/dist/tools/lib/protein-family-normalize.js

@@ -11,19 +11,26 @@ const FAMILIES = [
     {
         canonical: "g protein-coupled receptor",
         patterns: [
+            // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the hyphen-variant spellings of the GPCR name, matched as whole words.
             /\bg[-\s]?protein[-\s]?coupled\s+receptor\b/i,
+            // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the GPCR abbreviation as a whole word.
             /\bgpcr\b/i,
+            // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the seven-transmembrane spelling of the family name.
             /\b7tm\s+receptor\b/i,
+            // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the rhodopsin-like subfamily spelling.
             /\brhodopsin-like\s+receptor\b/i,
+            // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the secretin-like subfamily spelling.
             /\bsecretin-like\s+receptor\b/i,
         ],
     },
     {
         canonical: "serine/threonine-protein kinase",
+        // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the hyphen-variant spellings of the serine/threonine kinase name.
         patterns: [/\bserine\/threonine[-\s]?protein\s+kinase\b/i],
     },
     {
         canonical: "tyrosine-protein kinase",
+        // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the hyphen-variant spellings of the tyrosine kinase name.
         patterns: [/\btyrosine[-\s]?protein\s+kinase\b/i],
     },
     // Extend as additional hyphen-style mismatches surface. The default branch

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

@@ -13,14 +13,14 @@
  * carries `.optional()`, not `.nullable()`.
  */
 import { z } from "zod";
-export interface PubChemCompoundProperties {
+export type PubChemCompoundProperties = {
     cid: number;
     molecularWeight: number | null;
     inchiKey: string | null;
     canonicalSmiles: string | null;
     hBondDonorCount: number | null;
     hBondAcceptorCount: number | null;
-}
+};
 export declare const PubChemPropertyResponseSchema: z.ZodObject<{
     PropertyTable: z.ZodOptional<z.ZodObject<{
         Properties: z.ZodOptional<z.ZodArray<z.ZodObject<{

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

@@ -100,6 +100,7 @@ export async function getCompoundPropertiesByInChIKey(inchiKey) {
         return null;
     return getCompoundPropertiesByCID(cid);
 }
+// oxlint-disable-next-line eslint-js/no-restricted-syntax -- the amide-bond motif C(=O)N read out of a SMILES string; the literal atoms are the chemistry.
 const AMIDE_BOND_RE = /C\(=O\)N/g;
 /**
  * Heuristic molecule-type classifier driven by PubChem properties.

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

@@ -102,11 +102,11 @@ export declare const PubChemPropertyResponseSchema: z.ZodObject<{
         }>>>>;
     }, z.core.$strip>>;
 }, z.core.$strip>;
-export interface PubChemCrossRef {
+export type PubChemCrossRef = {
     /** The registry that the identifier pattern names, or `null` when no pattern matches. */
     source: string | null;
     id: string;
-}
+};
 export declare const PubChemXrefResponseSchema: z.ZodObject<{
     InformationList: z.ZodOptional<z.ZodObject<{
         Information: z.ZodOptional<z.ZodArray<z.ZodObject<{
@@ -117,13 +117,13 @@ export declare const PubChemXrefResponseSchema: z.ZodObject<{
 }, z.core.$strip>;
 /** The registry of one identifier, or `null` when no pattern matches it. */
 export declare function classifyRegistryId(id: string): string | null;
-export interface PubChemAssay {
+export type PubChemAssay = {
     aid: number;
     assayName: string | null;
     targetName: string | null;
     activityOutcome: string | null;
     activityValue: number | null;
-}
+};
 export declare const PugAssaySummarySchema: z.ZodObject<{
     Table: z.ZodOptional<z.ZodObject<{
         Columns: z.ZodOptional<z.ZodObject<{

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

@@ -95,18 +95,26 @@ export const PubChemXrefResponseSchema = z.object({
  * A loose pattern runs last, thus a specific registry claims its own id first.
  */
 const REGISTRY_PATTERNS = [
+    // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the ChEMBL id format: the CHEMBL prefix plus digits.
     ["ChEMBL", /^CHEMBL\d+$/],
+    // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the ChEBI id format: the CHEBI: prefix plus digits.
     ["ChEBI", /^CHEBI:\d+$/],
+    // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the DrugBank id format: the DB prefix plus five digits.
     ["DrugBank", /^DB\d{5}$/],
+    // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the KEGG id format: one C or D compound letter plus five digits.
     ["KEGG", /^[CD]\d{5}$/],
+    // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the HMDB id format: the HMDB prefix plus digits.
     ["HMDB", /^HMDB\d+$/],
+    // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the CAS registry format: two to seven digits, a dash pair, and one check digit.
     ["CAS", /^\d{2,7}-\d{2}-\d$/],
     // A PDB id is four characters that start with a digit. The lookahead demands a
     // letter as well, thus a plain registry number does not read as a structure.
+    // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the PDB id format: a digit, then three alphanumerics, with the lookahead that demands a letter among them.
     ["PDB", /^[1-9](?=.*[A-Za-z])[0-9A-Za-z]{3}$/],
     // A UNII is ten alphanumeric characters, and the lookahead demands a letter
     // among them. A plain ten-digit registry number, such as `0000050782`, matches
     // the pattern without it, and the row then names the wrong registry.
+    // oxlint-disable-next-line eslint-js/no-restricted-syntax -- the UNII format: ten uppercase alphanumerics, with the lookahead that demands a letter among them.
     ["UNII", /^(?=.*[A-Z])[A-Z0-9]{10}$/],
 ];
 /** The registry of one identifier, or `null` when no pattern matches it. */