@cyanheads/interpro-mcp-server 0.0.0-stage → 0.1.2

package/dist/services/interpro/http-adapter.js

@@ -0,0 +1,134 @@
+/**
+ * @fileoverview Bounded HTTP/1.1 adapter for InterPro's malformed bodyless 204 responses.
+ * @module services/interpro/http-adapter
+ */
+import { request } from 'node:https';
+import { serviceUnavailable, timeout } from '@cyanheads/mcp-ts-core/errors';
+import { API_BASE } from './routing.js';
+/** Maximum decoded response size, shared by native and injected transports. */
+export const MAX_RESPONSE_BYTES = 4 * 1024 * 1024;
+/** Collect one response without following redirects or retaining malformed connections. */
+export const interproHttpFetch = (url, init) => new Promise((resolve, reject) => {
+    const target = new URL(url);
+    if (target.origin !== new URL(API_BASE).origin ||
+        !target.pathname.startsWith('/interpro/api/')) {
+        reject(serviceUnavailable('InterPro request left the fixed API origin.', {
+            reason: 'upstream_rejected',
+            retryable: false,
+        }));
+        return;
+    }
+    const signal = init.signal;
+    signal?.throwIfAborted();
+    let settled = false;
+    let response;
+    const cleanup = () => {
+        clearTimeout(timer);
+        signal?.removeEventListener('abort', abort);
+    };
+    const fail = (error) => {
+        if (settled)
+            return;
+        settled = true;
+        cleanup();
+        response?.destroy();
+        req.destroy();
+        reject(error);
+    };
+    const abort = () => fail(signal?.reason);
+    const timer = setTimeout(() => fail(timeout('InterPro response exceeded its attempt deadline.', {
+        reason: 'upstream_timeout',
+        retryable: true,
+    })), 15_000);
+    const connectionOptions = { ALPNProtocols: ['http/1.1'] };
+    const req = request(target, {
+        ...connectionOptions,
+        method: 'GET',
+        agent: false,
+        headers: { Accept: 'application/json', 'Accept-Encoding': 'identity' },
+    });
+    req.on('error', (cause) => fail(serviceUnavailable('InterPro connection failed.', { reason: 'upstream_unavailable', retryable: true }, { cause })));
+    req.on('close', () => {
+        if (!response)
+            fail(serviceUnavailable('InterPro connection closed before response headers.', {
+                reason: 'upstream_unavailable',
+                retryable: true,
+            }));
+    });
+    req.on('response', (incoming) => {
+        response = incoming;
+        incoming.on('error', (cause) => fail(serviceUnavailable('InterPro response stream failed.', { reason: 'upstream_unavailable', retryable: true }, { cause })));
+        incoming.on('aborted', () => fail(serviceUnavailable('InterPro response ended prematurely.', {
+            reason: 'upstream_unavailable',
+            retryable: true,
+        })));
+        incoming.on('close', () => {
+            if (!incoming.complete)
+                fail(serviceUnavailable('InterPro response closed before completion.', {
+                    reason: 'upstream_unavailable',
+                    retryable: true,
+                }));
+        });
+        const headers = new Headers();
+        for (const [name, value] of Object.entries(incoming.headers))
+            if (value !== undefined)
+                headers.set(name, Array.isArray(value) ? value.join(', ') : value);
+        const status = incoming.statusCode;
+        if (!status) {
+            fail(serviceUnavailable('InterPro response lacks an HTTP status.', {
+                reason: 'upstream_shape_invalid',
+                retryable: false,
+            }));
+            return;
+        }
+        if (status === 204) {
+            settled = true;
+            cleanup();
+            resolve(new Response(null, { status, headers }));
+            incoming.destroy();
+            req.destroy();
+            return;
+        }
+        const encoding = headers.get('content-encoding');
+        if (encoding && encoding.toLowerCase() !== 'identity') {
+            fail(serviceUnavailable('InterPro returned an unexpected content encoding.', {
+                reason: 'upstream_shape_invalid',
+                retryable: false,
+            }));
+            return;
+        }
+        const chunks = [];
+        let bytes = 0;
+        incoming.on('data', (chunk) => {
+            if (settled)
+                return;
+            bytes += chunk.length;
+            if (bytes > MAX_RESPONSE_BYTES) {
+                fail(serviceUnavailable('InterPro response exceeds 4 MiB.', {
+                    reason: 'upstream_response_too_large',
+                    retryable: false,
+                }));
+                return;
+            }
+            chunks.push(chunk);
+        });
+        incoming.on('end', () => {
+            if (settled)
+                return;
+            settled = true;
+            cleanup();
+            try {
+                resolve(new Response(status === 304 ? null : Buffer.concat(chunks), { status, headers }));
+            }
+            catch (cause) {
+                reject(serviceUnavailable('InterPro returned invalid HTTP response metadata.', { reason: 'upstream_shape_invalid', retryable: false }, { cause }));
+            }
+        });
+    });
+    signal?.addEventListener('abort', abort, { once: true });
+    if (signal?.aborted)
+        abort();
+    else
+        req.end();
+});
+//# sourceMappingURL=http-adapter.js.map

package/dist/services/interpro/http-adapter.js.map

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package/dist/services/interpro/interpro-service.d.ts

@@ -0,0 +1,57 @@
+/**
+ * @fileoverview One paced, cancellable InterPro request boundary for every tool workflow.
+ * @module services/interpro/interpro-service
+ */
+import type { Context } from '@cyanheads/mcp-ts-core';
+import { z } from '@cyanheads/mcp-ts-core';
+import { type InterproFetch } from './http-adapter.js';
+/** One deadline shared by every distinct operation of a tool invocation. */
+export interface InterproCall {
+    readonly ctx: Context;
+    readonly deadline: number;
+}
+/** The record a request addresses, reported under `reason` when InterPro has no such record. */
+export interface MissingRecord {
+    readonly accession: string;
+    /** A list scoped to the record: 204 is a valid empty page, so only 404 reports it missing. */
+    readonly list?: boolean;
+    readonly reason: 'entry_not_found' | 'protein_not_found' | 'clan_not_found';
+    readonly sourceDatabase: string;
+}
+/** Domain status handling selected by the tool workflow. */
+export interface RequestOptions {
+    readonly continuation?: boolean;
+    readonly missing?: MissingRecord;
+}
+/** Validated response plus headers needed for release consistency. */
+export interface InterproResponse<T> {
+    readonly data: T | null;
+    readonly headers: Headers;
+    readonly sourceUrl: string;
+}
+/** InterPro service; inject only the network seam, retaining the real domain behavior. */
+export declare class InterproService {
+    private readonly fetch;
+    constructor(fetch?: InterproFetch);
+    /** Start a 50-second call budget, once per handler invocation. */
+    begin(ctx: Context): InterproCall;
+    /** Fetch, classify, parse and validate one fixed-origin operation within a shared call. */
+    request<T extends z.ZodType>(call: InterproCall, segments: readonly string[], query: Readonly<Record<string, string | number | boolean | undefined>>, schema: T, options?: RequestOptions): Promise<InterproResponse<z.output<T>>>;
+    /** Retrieve a coherent current release and its complete database-count object. */
+    release(ctx: Context): Promise<{
+        version: string;
+        date: string;
+        databaseCounts: {
+            [x: string]: z.JSONType;
+            entries: Record<string, z.JSONType>;
+        };
+        sourceUrls: string[];
+    }>;
+}
+/** Initialize the process service in createApp.setup. */
+export declare function initInterproService(fetch?: InterproFetch): void;
+/** Obtain the initialized process service. */
+export declare function getInterproService(): InterproService;
+/** Dispose queued pacing work during application teardown. */
+export declare function disposeInterproService(): void;
+//# sourceMappingURL=interpro-service.d.ts.map

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

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package/dist/services/interpro/interpro-service.js

@@ -0,0 +1,284 @@
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode, McpError, notFound, serviceUnavailable, timeout, validationError, } from '@cyanheads/mcp-ts-core/errors';
+import { createPacer, defaultIsTransient, httpErrorFromResponse, withRetry, } from '@cyanheads/mcp-ts-core/utils';
+import { interproHttpFetch, MAX_RESPONSE_BYTES } from './http-adapter.js';
+import { apiUrl } from './routing.js';
+import { isAccession, JsonObjectSchema, JsonValueSchema } from './schemas.js';
+const pacer = createPacer({
+    name: 'interpro',
+    minStartGapMs: 1000,
+    maxConcurrent: 1,
+    maxQueueDepth: 20,
+});
+/** Upstream fields of a 410 body that are echoed in the withdrawal error. */
+const WITHDRAWAL_FIELDS = new Set([
+    'accession',
+    'source_database',
+    'deletion_date',
+    'short_name',
+    'history',
+]);
+/**
+ * Single-line forms a withdrawal date or short name must match whole before the message names it;
+ * any other upstream value stays in error data only.
+ */
+const WITHDRAWAL_DATE = /^\d{4}-\d{2}-\d{2}(?:T[\d:.]+Z?)?$/;
+const SHORT_NAME = /^[A-Za-z0-9_.:+-]{1,100}$/;
+const RECORD_NOUNS = {
+    entry_not_found: 'entry',
+    clan_not_found: 'set',
+    protein_not_found: 'protein',
+};
+/** Name a record in a caller-facing message, e.g. `entry PF00870 in pfam`. */
+const describeRecord = ({ reason, accession, sourceDatabase }) => `${RECORD_NOUNS[reason]} ${accession} in ${sourceDatabase}`;
+/** InterPro service; inject only the network seam, retaining the real domain behavior. */
+export class InterproService {
+    fetch;
+    constructor(fetch = interproHttpFetch) {
+        this.fetch = fetch;
+    }
+    /** Start a 50-second call budget, once per handler invocation. */
+    begin(ctx) {
+        return { ctx, deadline: performance.now() + 50_000 };
+    }
+    /** Fetch, classify, parse and validate one fixed-origin operation within a shared call. */
+    async request(call, segments, query, schema, options = {}) {
+        call.ctx.signal.throwIfAborted();
+        const remaining = call.deadline - performance.now();
+        if (remaining <= 0)
+            throw timeout('InterPro call exhausted its 50-second budget.', {
+                reason: 'retry_deadline_exceeded',
+                retryable: true,
+                deadlineMs: 50_000,
+            });
+        const sourceUrl = apiUrl(segments, query);
+        return await withRetry(async ({ signal }) => pacer.run(async () => {
+            const attemptMs = Math.min(15_000, call.deadline - performance.now());
+            const controller = new AbortController();
+            const timer = setTimeout(() => controller.abort(timeout('InterPro attempt deadline elapsed.', {
+                reason: 'upstream_timeout',
+                retryable: true,
+            })), Math.max(0, attemptMs));
+            const attemptSignal = AbortSignal.any([signal, controller.signal, call.ctx.signal]);
+            try {
+                const response = await this.fetch(sourceUrl, {
+                    signal: attemptSignal,
+                    headers: { Accept: 'application/json', 'Accept-Encoding': 'identity' },
+                    redirect: 'manual',
+                });
+                attemptSignal.throwIfAborted();
+                if ((response.status === 400 || response.status === 404) && options.continuation)
+                    throw validationError('InterPro rejected the continuation cursor.', {
+                        reason: 'invalid_cursor',
+                        retryable: false,
+                        status: response.status,
+                    });
+                const { missing } = options;
+                if (missing &&
+                    (response.status === 404 || (response.status === 204 && !missing.list)))
+                    throw notFound(`InterPro could not find ${describeRecord(missing)}.`, {
+                        reason: missing.reason,
+                        retryable: false,
+                        status: response.status,
+                        accession: missing.accession,
+                        sourceDatabase: missing.sourceDatabase,
+                    });
+                if (response.status === 204)
+                    return { data: null, sourceUrl, headers: response.headers };
+                if (response.status === 410) {
+                    const body = await readBody(response, attemptSignal);
+                    let withdrawal = {};
+                    try {
+                        const parsed = JsonObjectSchema.parse(JSON.parse(body));
+                        withdrawal = Object.fromEntries(Object.entries(parsed).filter(([key, value]) => WITHDRAWAL_FIELDS.has(key) && JSON.stringify(value).length <= 4096));
+                    }
+                    catch {
+                        /* A withdrawn record need not include valid metadata. */
+                    }
+                    const { accession, deletion_date: deleted, short_name: shortName } = withdrawal;
+                    const subject = missing
+                        ? describeRecord(missing)
+                        : isAccession(accession)
+                            ? `record ${accession}`
+                            : 'the requested record';
+                    const on = typeof deleted === 'string' && WITHDRAWAL_DATE.test(deleted)
+                        ? ` on ${deleted}`
+                        : '';
+                    const named = typeof shortName === 'string' && SHORT_NAME.test(shortName)
+                        ? ` (short name ${shortName})`
+                        : '';
+                    throw notFound(`InterPro reports that ${subject} was withdrawn${on}${named}.`, {
+                        reason: 'entry_withdrawn',
+                        retryable: false,
+                        status: 410,
+                        ...withdrawal,
+                        // The canonical accession the message names wins over upstream's spelling.
+                        ...(missing ? { accession: missing.accession } : {}),
+                    });
+                }
+                if (!response.ok) {
+                    const status = response.status;
+                    const reason = status === 408 || status === 504
+                        ? 'upstream_timeout'
+                        : status === 429
+                            ? 'upstream_rate_limited'
+                            : status >= 500
+                                ? 'upstream_unavailable'
+                                : 'upstream_rejected';
+                    throw await httpErrorFromResponse(response, {
+                        service: 'InterPro',
+                        captureBody: false,
+                        codeOverride: (value) => value < 500 && value !== 408 && value !== 429
+                            ? JsonRpcErrorCode.ServiceUnavailable
+                            : undefined,
+                        data: {
+                            reason,
+                            retryable: (status >= 500 && status !== 501) || status === 408 || status === 429,
+                        },
+                    });
+                }
+                const encoding = response.headers.get('content-encoding');
+                if (encoding && encoding.toLowerCase() !== 'identity')
+                    throw serviceUnavailable('InterPro returned an unexpected content encoding.', {
+                        reason: 'upstream_shape_invalid',
+                        retryable: false,
+                    });
+                const body = await readBody(response, attemptSignal);
+                if (/^\s*<(?:!doctype\s+html|html[\s>])/i.test(body))
+                    throw serviceUnavailable('InterPro returned HTML instead of JSON.', {
+                        reason: 'upstream_unavailable',
+                        retryable: true,
+                    });
+                let json;
+                try {
+                    json = JSON.parse(body);
+                }
+                catch (cause) {
+                    throw serviceUnavailable('InterPro returned malformed JSON.', { reason: 'upstream_shape_invalid', retryable: false }, { cause });
+                }
+                const parsed = schema.safeParse(json);
+                if (!parsed.success)
+                    throw serviceUnavailable('InterPro JSON does not match the required response structure.', { reason: 'upstream_shape_invalid', retryable: false });
+                attemptSignal.throwIfAborted();
+                if (performance.now() > call.deadline)
+                    throw timeout('InterPro call exhausted its total budget.', {
+                        reason: 'retry_deadline_exceeded',
+                        retryable: true,
+                    });
+                return { data: parsed.data, sourceUrl, headers: response.headers };
+            }
+            catch (cause) {
+                if (call.ctx.signal.aborted)
+                    throw call.ctx.signal.reason;
+                if (signal.aborted)
+                    throw signal.reason;
+                if (controller.signal.aborted)
+                    throw controller.signal.reason;
+                if (cause instanceof McpError)
+                    throw cause;
+                throw serviceUnavailable('InterPro network request failed.', { reason: 'upstream_unavailable', retryable: true }, { cause });
+            }
+            finally {
+                clearTimeout(timer);
+            }
+        }, { signal, maxWaitMs: Math.max(0, Math.min(5000, call.deadline - performance.now())) }), {
+            signal: call.ctx.signal,
+            context: call.ctx,
+            operation: 'interpro.request',
+            deadlineMs: remaining,
+            maxRetries: 1,
+            baseDelayMs: 1000,
+            maxDelayMs: 3000,
+            isTransient: defaultIsTransient,
+        });
+    }
+    /** Retrieve a coherent current release and its complete database-count object. */
+    async release(ctx) {
+        const call = this.begin(ctx);
+        const releases = await this.request(call, ['utils', 'release'], {}, z.record(z.string().regex(/^\d+(?:\.\d+)*$/), z.string()));
+        const counts = await this.request(call, ['entry'], {}, z.object({ entries: JsonObjectSchema }).catchall(JsonValueSchema));
+        if (!releases.data || !counts.data || !Object.keys(releases.data).length)
+            throw serviceUnavailable('InterPro release metadata is missing.', {
+                reason: 'upstream_shape_invalid',
+                retryable: false,
+            });
+        const firstVersion = releases.headers.get('interpro-version');
+        const secondVersion = counts.headers.get('interpro-version');
+        if (firstVersion && secondVersion && firstVersion !== secondVersion)
+            throw serviceUnavailable('InterPro release changed between metadata responses.', {
+                reason: 'release_changed',
+                retryable: true,
+            });
+        const version = Object.keys(releases.data).sort((a, b) => {
+            const left = a.split('.').map(Number);
+            const right = b.split('.').map(Number);
+            for (let index = 0; index < Math.max(left.length, right.length); index++) {
+                const difference = (right[index] ?? 0) - (left[index] ?? 0);
+                if (difference)
+                    return difference;
+            }
+            return 0;
+        })[0];
+        if (!version)
+            throw serviceUnavailable('InterPro release map has no version.', {
+                reason: 'upstream_shape_invalid',
+                retryable: false,
+            });
+        return {
+            version,
+            date: releases.data[version],
+            databaseCounts: counts.data,
+            sourceUrls: [releases.sourceUrl, counts.sourceUrl],
+        };
+    }
+}
+async function readBody(response, signal) {
+    if (!response.body)
+        return '';
+    const reader = response.body.getReader();
+    const chunks = [];
+    let bytes = 0;
+    const abort = () => {
+        void reader.cancel(signal.reason).catch(() => { });
+    };
+    signal.addEventListener('abort', abort, { once: true });
+    try {
+        while (true) {
+            signal.throwIfAborted();
+            const { done, value } = await reader.read();
+            signal.throwIfAborted();
+            if (done)
+                break;
+            bytes += value.byteLength;
+            if (bytes > MAX_RESPONSE_BYTES) {
+                await reader.cancel();
+                throw serviceUnavailable('InterPro response exceeds 4 MiB.', {
+                    reason: 'upstream_response_too_large',
+                    retryable: false,
+                });
+            }
+            chunks.push(value);
+        }
+        return Buffer.concat(chunks).toString('utf8');
+    }
+    finally {
+        signal.removeEventListener('abort', abort);
+        reader.releaseLock();
+    }
+}
+let service;
+/** Initialize the process service in createApp.setup. */
+export function initInterproService(fetch = interproHttpFetch) {
+    service = new InterproService(fetch);
+}
+/** Obtain the initialized process service. */
+export function getInterproService() {
+    if (!service)
+        throw new Error('InterPro service is not initialized.');
+    return service;
+}
+/** Dispose queued pacing work during application teardown. */
+export function disposeInterproService() {
+    pacer.dispose();
+}
+//# sourceMappingURL=interpro-service.js.map

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

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package/dist/services/interpro/reference.d.ts

@@ -0,0 +1,31 @@
+/**
+ * @fileoverview Static API vocabulary and common taxonomy examples.
+ * @module services/interpro/reference
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+/** Available reference topics; only release performs network operations. */
+export declare const ReferenceTopicSchema: z.ZodEnum<{
+    accession_patterns: "accession_patterns";
+    databases: "databases";
+    entry_types: "entry_types";
+    release: "release";
+    taxa: "taxa";
+}>;
+/** Applicable reference fields, without fabricated empty annotations. */
+export declare const ReferenceItemSchema: z.ZodObject<{
+    id: z.ZodString;
+    label: z.ZodString;
+    description: z.ZodOptional<z.ZodString>;
+    sourceDatabase: z.ZodOptional<z.ZodString>;
+    accessionPattern: z.ZodOptional<z.ZodString>;
+    example: z.ZodOptional<z.ZodString>;
+    taxonId: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>;
+/** A reference vocabulary row. */
+export type ReferenceItem = z.infer<typeof ReferenceItemSchema>;
+/** Return bounded local reference data without making upstream requests. */
+export declare function staticReference(topic: Exclude<z.infer<typeof ReferenceTopicSchema>, 'release'>): {
+    items: ReferenceItem[];
+    sourceUrls: string[];
+};
+//# sourceMappingURL=reference.d.ts.map

package/dist/services/interpro/reference.d.ts.map

@@ -0,0 +1 @@
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