@cyanheads/protein-mcp-server 0.1.0

package/dist/services/rcsb/types.js.map

@@ -0,0 +1 @@
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package/dist/services/shared/async.d.ts

@@ -0,0 +1,41 @@
+/**
+ * @fileoverview Shared async primitives: bounded submit→poll for the RCSB
+ * alignment and Foldseek services (both expose a job ticket that isn't ready on
+ * the first poll), and a concurrency-capped fan-out for per-ID / per-pair work.
+ * @module services/shared/async
+ */
+import type { Context } from '@cyanheads/mcp-ts-core';
+/** Outcome of a bounded poll: the resolved value, or a "still computing" signal. */
+export type PollOutcome<T> = {
+    status: 'complete';
+    value: T;
+} | {
+    status: 'computing';
+};
+/** One poll attempt result: ready with a value, or not ready yet. */
+export type PollStep<T> = {
+    ready: true;
+    value: T;
+} | {
+    ready: false;
+};
+/**
+ * Poll `step` with backoff until it reports ready or the wall-clock budget is
+ * spent, returning `status: 'computing'` on timeout rather than blocking past the
+ * budget. The agent re-calls to resume — async jobs are modeled as success
+ * variants, not thrown errors.
+ */
+export declare function withAsyncPoll<T>(opts: {
+    step: () => Promise<PollStep<T>>;
+    timeoutMs: number;
+    ctx: Context;
+    intervalMs?: number;
+    maxIntervalMs?: number;
+}): Promise<PollOutcome<T>>;
+/**
+ * Map `items` through `fn` with at most `limit` concurrent calls, preserving
+ * input order. `fn` is expected to handle its own failures (return a result
+ * variant) so one slow/failed unit degrades its row, not the whole call.
+ */
+export declare function mapWithConcurrency<T, R>(items: readonly T[], limit: number, fn: (item: T, index: number) => Promise<R>): Promise<R[]>;
+//# sourceMappingURL=async.d.ts.map

package/dist/services/shared/async.d.ts.map

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package/dist/services/shared/async.js

@@ -0,0 +1,64 @@
+/**
+ * @fileoverview Shared async primitives: bounded submit→poll for the RCSB
+ * alignment and Foldseek services (both expose a job ticket that isn't ready on
+ * the first poll), and a concurrency-capped fan-out for per-ID / per-pair work.
+ * @module services/shared/async
+ */
+/** Sleep for `ms`, resolving early (without rejecting) if the signal aborts. */
+function sleep(ms, signal) {
+    return new Promise((resolve) => {
+        if (signal.aborted)
+            return resolve();
+        const onAbort = () => {
+            clearTimeout(timer);
+            resolve();
+        };
+        const timer = setTimeout(() => {
+            signal.removeEventListener('abort', onAbort);
+            resolve();
+        }, ms);
+        signal.addEventListener('abort', onAbort, { once: true });
+    });
+}
+/**
+ * Poll `step` with backoff until it reports ready or the wall-clock budget is
+ * spent, returning `status: 'computing'` on timeout rather than blocking past the
+ * budget. The agent re-calls to resume — async jobs are modeled as success
+ * variants, not thrown errors.
+ */
+export async function withAsyncPoll(opts) {
+    const start = Date.now();
+    let interval = opts.intervalMs ?? 1000;
+    const maxInterval = opts.maxIntervalMs ?? 2000;
+    while (true) {
+        const step = await opts.step();
+        if (step.ready)
+            return { status: 'complete', value: step.value };
+        const elapsed = Date.now() - start;
+        if (opts.ctx.signal.aborted || elapsed >= opts.timeoutMs)
+            return { status: 'computing' };
+        await sleep(Math.min(interval, opts.timeoutMs - elapsed), opts.ctx.signal);
+        interval = Math.min(interval * 1.5, maxInterval);
+    }
+}
+/**
+ * Map `items` through `fn` with at most `limit` concurrent calls, preserving
+ * input order. `fn` is expected to handle its own failures (return a result
+ * variant) so one slow/failed unit degrades its row, not the whole call.
+ */
+export async function mapWithConcurrency(items, limit, fn) {
+    const results = new Array(items.length);
+    let cursor = 0;
+    const worker = async () => {
+        while (true) {
+            const index = cursor++;
+            if (index >= items.length)
+                return;
+            results[index] = await fn(items[index], index);
+        }
+    };
+    const workers = Array.from({ length: Math.min(Math.max(1, limit), items.length) }, () => worker());
+    await Promise.all(workers);
+    return results;
+}
+//# sourceMappingURL=async.js.map

package/dist/services/shared/async.js.map

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package/dist/services/shared/http.d.ts

@@ -0,0 +1,54 @@
+/**
+ * @fileoverview Shared HTTP layer for the protein data providers. Wraps the
+ * framework's `fetchWithTimeout` + `withRetry` (retry covers the full fetch +
+ * parse pipeline) and centralizes HTML-error-page / empty-body detection so each
+ * service stays thin. The single `Context → RequestContext` cast the framework
+ * utilities expect is isolated here.
+ * @module services/shared/http
+ */
+import type { Context } from '@cyanheads/mcp-ts-core';
+/** Options shared by the JSON/text fetch helpers. */
+export interface FetchOptions {
+    /** Base retry backoff. Default 400ms. */
+    baseDelayMs?: number;
+    /** Request body (pre-serialized JSON string, FormData, etc.). */
+    body?: RequestInit['body'];
+    /** Request headers. */
+    headers?: Record<string, string>;
+    /** Human-readable provider label used in error messages. */
+    label: string;
+    /** Retry attempts after the initial call. Default 3. */
+    maxRetries?: number;
+    /** HTTP method. Default `GET`. */
+    method?: string;
+    /** Operation label for correlated retry logging. */
+    operation: string;
+    /** Per-attempt timeout. Default 30s. */
+    timeoutMs?: number;
+}
+/**
+ * Parse a JSON body, first rejecting HTML error pages and empty responses as
+ * transient `ServiceUnavailable` (so `withRetry` retries them rather than feeding
+ * an HTML page into `JSON.parse`).
+ */
+export declare function parseJson<T>(text: string, label: string): T;
+/** GET/POST JSON with retry over the full fetch + parse pipeline. Throws a status-mapped `McpError` on non-2xx. */
+export declare function fetchJson<T>(url: string, ctx: Context, opts: FetchOptions): Promise<T>;
+/** Fetch raw text (coordinate files, etc.) with retry. Throws a status-mapped `McpError` on non-2xx. */
+export declare function fetchText(url: string, ctx: Context, opts: FetchOptions): Promise<string>;
+/**
+ * Fetch returning the raw `Response` without throwing on non-2xx status, so the
+ * caller can branch on the code (e.g. 3D-Beacons 404 → "no models", an async poll
+ * 404 → "not ready yet"). Retries only network-level failures; HTTP statuses pass
+ * through. Combines `ctx.signal` with a per-attempt timeout.
+ */
+export declare function fetchResponse(url: string, ctx: Context, opts: {
+    method?: string;
+    body?: RequestInit['body'];
+    headers?: Record<string, string>;
+    operation: string;
+    timeoutMs?: number;
+    baseDelayMs?: number;
+    maxRetries?: number;
+}): Promise<Response>;
+//# sourceMappingURL=http.d.ts.map

package/dist/services/shared/http.d.ts.map

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package/dist/services/shared/http.js

@@ -0,0 +1,115 @@
+/**
+ * @fileoverview Shared HTTP layer for the protein data providers. Wraps the
+ * framework's `fetchWithTimeout` + `withRetry` (retry covers the full fetch +
+ * parse pipeline) and centralizes HTML-error-page / empty-body detection so each
+ * service stays thin. The single `Context → RequestContext` cast the framework
+ * utilities expect is isolated here.
+ * @module services/shared/http
+ */
+import { serializationError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
+import { fetchWithTimeout, withRetry } from '@cyanheads/mcp-ts-core/utils';
+const DEFAULT_TIMEOUT_MS = 30_000;
+/**
+ * Identify this client to upstream providers. Node's global `fetch` sends no
+ * User-Agent by default, which some providers' edge WAFs reject outright — the
+ * AlphaFold DB API returns 403 Forbidden on an absent UA. A stable project UA
+ * also lets providers correlate or contact us about heavy traffic.
+ */
+const USER_AGENT = 'protein-mcp-server (+https://github.com/cyanheads/protein-mcp-server)';
+/** Merge the default `User-Agent` under any caller-supplied headers. */
+function withDefaultHeaders(headers) {
+    return { 'User-Agent': USER_AGENT, ...headers };
+}
+/**
+ * The framework HTTP utilities type their context parameter as `RequestContext`;
+ * the handler `Context` is runtime-compatible (the logger strips non-serializable
+ * fields). Cast once here so callers pass `ctx` unchanged.
+ */
+function asRequestContext(ctx) {
+    return ctx;
+}
+/**
+ * Parse a JSON body, first rejecting HTML error pages and empty responses as
+ * transient `ServiceUnavailable` (so `withRetry` retries them rather than feeding
+ * an HTML page into `JSON.parse`).
+ */
+export function parseJson(text, label) {
+    if (/^\s*<(!DOCTYPE\s+html|html[\s>])/i.test(text)) {
+        throw serviceUnavailable(`${label} returned HTML instead of JSON — likely unavailable or rate-limited.`);
+    }
+    if (text.trim().length === 0) {
+        throw serviceUnavailable(`${label} returned an empty response — endpoint may be temporarily unavailable.`);
+    }
+    try {
+        return JSON.parse(text);
+    }
+    catch {
+        throw serializationError(`${label} returned unparseable JSON: ${text.slice(0, 200)}`);
+    }
+}
+/** GET/POST JSON with retry over the full fetch + parse pipeline. Throws a status-mapped `McpError` on non-2xx. */
+export function fetchJson(url, ctx, opts) {
+    const rctx = asRequestContext(ctx);
+    const timeoutMs = opts.timeoutMs ?? DEFAULT_TIMEOUT_MS;
+    return withRetry(async () => {
+        const res = await fetchWithTimeout(url, timeoutMs, rctx, {
+            method: opts.method ?? 'GET',
+            ...(opts.body !== undefined && { body: opts.body }),
+            headers: withDefaultHeaders(opts.headers),
+            signal: ctx.signal,
+        });
+        return parseJson(await res.text(), opts.label);
+    }, {
+        operation: opts.operation,
+        context: rctx,
+        baseDelayMs: opts.baseDelayMs ?? 400,
+        ...(opts.maxRetries !== undefined && { maxRetries: opts.maxRetries }),
+        signal: ctx.signal,
+    });
+}
+/** Fetch raw text (coordinate files, etc.) with retry. Throws a status-mapped `McpError` on non-2xx. */
+export function fetchText(url, ctx, opts) {
+    const rctx = asRequestContext(ctx);
+    const timeoutMs = opts.timeoutMs ?? DEFAULT_TIMEOUT_MS;
+    return withRetry(async () => {
+        const res = await fetchWithTimeout(url, timeoutMs, rctx, {
+            method: opts.method ?? 'GET',
+            ...(opts.body !== undefined && { body: opts.body }),
+            headers: withDefaultHeaders(opts.headers),
+            signal: ctx.signal,
+        });
+        return res.text();
+    }, {
+        operation: opts.operation,
+        context: rctx,
+        baseDelayMs: opts.baseDelayMs ?? 400,
+        ...(opts.maxRetries !== undefined && { maxRetries: opts.maxRetries }),
+        signal: ctx.signal,
+    });
+}
+/**
+ * Fetch returning the raw `Response` without throwing on non-2xx status, so the
+ * caller can branch on the code (e.g. 3D-Beacons 404 → "no models", an async poll
+ * 404 → "not ready yet"). Retries only network-level failures; HTTP statuses pass
+ * through. Combines `ctx.signal` with a per-attempt timeout.
+ */
+export function fetchResponse(url, ctx, opts) {
+    const rctx = asRequestContext(ctx);
+    const timeoutMs = opts.timeoutMs ?? DEFAULT_TIMEOUT_MS;
+    return withRetry(() => {
+        const signal = AbortSignal.any([ctx.signal, AbortSignal.timeout(timeoutMs)]);
+        return fetch(url, {
+            method: opts.method ?? 'GET',
+            ...(opts.body !== undefined && { body: opts.body }),
+            headers: withDefaultHeaders(opts.headers),
+            signal,
+        });
+    }, {
+        operation: opts.operation,
+        context: rctx,
+        baseDelayMs: opts.baseDelayMs ?? 400,
+        maxRetries: opts.maxRetries ?? 2,
+        signal: ctx.signal,
+    });
+}
+//# sourceMappingURL=http.js.map

package/dist/services/shared/http.js.map

@@ -0,0 +1 @@
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package/dist/services/shared/identifiers.d.ts

@@ -0,0 +1,12 @@
+/**
+ * @fileoverview Identifier shape detection for routing between the experimental
+ * (PDB) and predicted (UniProt-keyed) halves of the federation. Pure, no I/O.
+ * @module services/shared/identifiers
+ */
+/** True when `value` is a syntactically valid UniProt accession. */
+export declare function isUniProtAccession(value: string): boolean;
+/** True when `value` is a syntactically valid PDB entry ID. */
+export declare function isPdbId(value: string): boolean;
+/** Extract the PDB entry ID from a polymer-entity ID (`4HHB_1` → `4HHB`). */
+export declare function entryIdOf(identifier: string): string;
+//# sourceMappingURL=identifiers.d.ts.map

package/dist/services/shared/identifiers.d.ts.map

@@ -0,0 +1 @@
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package/dist/services/shared/identifiers.js

@@ -0,0 +1,23 @@
+/**
+ * @fileoverview Identifier shape detection for routing between the experimental
+ * (PDB) and predicted (UniProt-keyed) halves of the federation. Pure, no I/O.
+ * @module services/shared/identifiers
+ */
+/** UniProt accession pattern (6- or 10-character forms). */
+const UNIPROT_RE = /^(?:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2})$/i;
+/** PDB entry ID pattern: 4 alphanumerics, first character a digit (e.g. 4HHB, 1IEP). */
+const PDB_RE = /^[0-9][A-Za-z0-9]{3}$/;
+/** True when `value` is a syntactically valid UniProt accession. */
+export function isUniProtAccession(value) {
+    return UNIPROT_RE.test(value.trim());
+}
+/** True when `value` is a syntactically valid PDB entry ID. */
+export function isPdbId(value) {
+    return PDB_RE.test(value.trim());
+}
+/** Extract the PDB entry ID from a polymer-entity ID (`4HHB_1` → `4HHB`). */
+export function entryIdOf(identifier) {
+    const base = identifier.split(/[_.]/)[0] ?? identifier;
+    return base.toUpperCase();
+}
+//# sourceMappingURL=identifiers.js.map

package/dist/services/shared/identifiers.js.map

@@ -0,0 +1 @@
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package/dist/services/uniprot/uniprot-service.d.ts

@@ -0,0 +1,65 @@
+/**
+ * @fileoverview UniProt service — wraps the UniProt REST API (sequence features,
+ * function, variants) and the InterPro REST API (domain/family memberships across
+ * Pfam, PROSITE, … with GO terms). Backs `protein_get_annotations`. Field
+ * selection trims UniProt payloads to what the requested `include` scope needs.
+ * @module services/uniprot/uniprot-service
+ */
+import type { Context } from '@cyanheads/mcp-ts-core';
+import type { AppConfig } from '@cyanheads/mcp-ts-core/config';
+import type { StorageService } from '@cyanheads/mcp-ts-core/storage';
+import type { ServerConfig } from '../../config/server-config.js';
+/** Which annotation classes to fetch. */
+export type AnnotationInclude = 'features' | 'domains' | 'variants' | 'all';
+/** A positional sequence feature (domain, binding site, PTM, or variant). */
+export interface SequenceFeature {
+    /** `feature` (structural/functional) or `variant`. */
+    category: 'feature' | 'variant';
+    /** Free-text description. */
+    description?: string;
+    /** End residue (1-based). */
+    end?: number;
+    /** Start residue (1-based). */
+    start?: number;
+    /** UniProt feature type (e.g. "Domain", "Binding site", "Natural variant"). */
+    type: string;
+}
+/** Normalized UniProt entry. */
+export interface UniProtEntry {
+    accession: string;
+    features: SequenceFeature[];
+    function?: string;
+    geneNames: string[];
+    organism?: string;
+    proteinName?: string;
+    sequenceLength?: number;
+    taxonId?: number;
+}
+/** A GO term annotation. */
+export interface GoTerm {
+    category?: string;
+    id: string;
+    name: string;
+}
+/** An InterPro domain/family membership for a protein. */
+export interface InterProEntry {
+    accession: string;
+    goTerms: GoTerm[];
+    memberDatabases: string[];
+    name: string;
+    type: string;
+}
+export declare class UniProtService {
+    private readonly uniprotBase;
+    private readonly interproBase;
+    constructor(_config: AppConfig, _storage: StorageService, serverConfig: ServerConfig);
+    /** Fetch a UniProt entry, selecting only the fields the include scope needs. */
+    getEntry(accession: string, include: AnnotationInclude, ctx: Context): Promise<UniProtEntry>;
+    /** Fetch the one-letter amino-acid sequence for a UniProt accession. */
+    getSequence(accession: string, ctx: Context): Promise<string | null>;
+    /** Fetch InterPro domain/family memberships for a UniProt accession. */
+    getInterPro(accession: string, ctx: Context): Promise<InterProEntry[]>;
+}
+export declare function initUniProtService(config: AppConfig, storage: StorageService, serverConfig: ServerConfig): void;
+export declare function getUniProtService(): UniProtService;
+//# sourceMappingURL=uniprot-service.d.ts.map

package/dist/services/uniprot/uniprot-service.d.ts.map

@@ -0,0 +1 @@
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package/dist/services/uniprot/uniprot-service.js

@@ -0,0 +1,146 @@
+/**
+ * @fileoverview UniProt service — wraps the UniProt REST API (sequence features,
+ * function, variants) and the InterPro REST API (domain/family memberships across
+ * Pfam, PROSITE, … with GO terms). Backs `protein_get_annotations`. Field
+ * selection trims UniProt payloads to what the requested `include` scope needs.
+ * @module services/uniprot/uniprot-service
+ */
+import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
+import { fetchJson } from '../shared/http.js';
+const BASE_FIELDS = [
+    'accession',
+    'protein_name',
+    'gene_names',
+    'organism_name',
+    'cc_function',
+    'sequence',
+];
+const FEATURE_FIELDS = [
+    'ft_domain',
+    'ft_binding',
+    'ft_act_site',
+    'ft_site',
+    'ft_mod_res',
+    'ft_carbohyd',
+    'ft_disulfid',
+    'ft_signal',
+    'ft_transmem',
+    'ft_motif',
+    'ft_region',
+];
+const VARIANT_FIELDS = ['ft_variant'];
+export class UniProtService {
+    uniprotBase;
+    interproBase;
+    constructor(_config, _storage, serverConfig) {
+        this.uniprotBase = serverConfig.uniprotBaseUrl;
+        this.interproBase = serverConfig.interproBaseUrl;
+    }
+    /** Fetch a UniProt entry, selecting only the fields the include scope needs. */
+    async getEntry(accession, include, ctx) {
+        const fields = [...BASE_FIELDS];
+        if (include === 'features' || include === 'all')
+            fields.push(...FEATURE_FIELDS);
+        if (include === 'variants' || include === 'all')
+            fields.push(...VARIANT_FIELDS);
+        const url = `${this.uniprotBase}/uniprotkb/${encodeURIComponent(accession.toUpperCase())}?format=json&fields=${fields.join(',')}`;
+        const raw = await fetchJson(url, ctx, {
+            operation: 'UniProtService.getEntry',
+            label: 'UniProt',
+            baseDelayMs: 400,
+        });
+        return normalizeEntry(accession.toUpperCase(), raw);
+    }
+    /** Fetch the one-letter amino-acid sequence for a UniProt accession. */
+    async getSequence(accession, ctx) {
+        const url = `${this.uniprotBase}/uniprotkb/${encodeURIComponent(accession.toUpperCase())}?format=json&fields=sequence`;
+        const raw = await fetchJson(url, ctx, {
+            operation: 'UniProtService.getSequence',
+            label: 'UniProt',
+            baseDelayMs: 400,
+        });
+        return raw.sequence?.value ?? null;
+    }
+    /** Fetch InterPro domain/family memberships for a UniProt accession. */
+    async getInterPro(accession, ctx) {
+        const url = `${this.interproBase}/entry/interpro/protein/UniProt/${encodeURIComponent(accession.toUpperCase())}/`;
+        let raw;
+        try {
+            raw = await fetchJson(url, ctx, {
+                operation: 'UniProtService.getInterPro',
+                label: 'InterPro',
+                baseDelayMs: 400,
+            });
+        }
+        catch (err) {
+            // InterPro returns 404 when no entries match — that's "no domains", not a failure.
+            if (err instanceof McpError && err.code === JsonRpcErrorCode.NotFound)
+                return [];
+            throw err;
+        }
+        return (raw.results ?? [])
+            .map((r) => r.metadata)
+            .filter((m) => m != null && !!m.accession)
+            .map(normalizeInterPro);
+    }
+}
+// ─── Normalizers ──────────────────────────────────────────────────────────────
+function normalizeEntry(accession, raw) {
+    const proteinName = raw.proteinDescription?.recommendedName?.fullName?.value;
+    const geneNames = (raw.genes ?? []).map((g) => g.geneName?.value).filter((n) => !!n);
+    const functionText = raw.comments
+        ?.find((c) => c.commentType === 'FUNCTION')
+        ?.texts?.map((t) => t.value)
+        .filter((v) => !!v)
+        .join(' ');
+    const features = (raw.features ?? []).map(normalizeFeature);
+    return {
+        accession: raw.primaryAccession ?? accession,
+        ...(proteinName ? { proteinName } : {}),
+        geneNames,
+        ...(raw.organism?.scientificName ? { organism: raw.organism.scientificName } : {}),
+        ...(typeof raw.organism?.taxonId === 'number' ? { taxonId: raw.organism.taxonId } : {}),
+        ...(functionText ? { function: functionText } : {}),
+        ...(typeof raw.sequence?.length === 'number' ? { sequenceLength: raw.sequence.length } : {}),
+        features,
+    };
+}
+function normalizeFeature(raw) {
+    const type = raw.type ?? 'Feature';
+    return {
+        category: /variant/i.test(type) ? 'variant' : 'feature',
+        type,
+        ...(raw.description ? { description: raw.description } : {}),
+        ...(typeof raw.location?.start?.value === 'number' ? { start: raw.location.start.value } : {}),
+        ...(typeof raw.location?.end?.value === 'number' ? { end: raw.location.end.value } : {}),
+    };
+}
+function normalizeInterPro(raw) {
+    const memberDatabases = raw.member_databases ? Object.keys(raw.member_databases) : [];
+    const goTerms = (raw.go_terms ?? [])
+        .map((g) => g.identifier && g.name
+        ? {
+            id: g.identifier,
+            name: g.name,
+            ...(g.category?.name ? { category: g.category.name } : {}),
+        }
+        : undefined)
+        .filter((g) => g != null);
+    return {
+        accession: raw.accession,
+        name: raw.name ?? raw.accession ?? '',
+        type: raw.type ?? 'unknown',
+        memberDatabases,
+        goTerms,
+    };
+}
+let _service;
+export function initUniProtService(config, storage, serverConfig) {
+    _service = new UniProtService(config, storage, serverConfig);
+}
+export function getUniProtService() {
+    if (!_service)
+        throw new Error('UniProtService not initialized — call initUniProtService() in setup()');
+    return _service;
+}
+//# sourceMappingURL=uniprot-service.js.map

package/dist/services/uniprot/uniprot-service.js.map

@@ -0,0 +1 @@
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