@cyanheads/interpro-mcp-server 0.1.3 → 0.2.0

package/dist/services/sequence-scan/sequence-scan-service.js

@@ -0,0 +1,453 @@
+import { configurationError, McpError, notFound, rateLimited, serviceUnavailable, timeout, validationError, } from '@cyanheads/mcp-ts-core/errors';
+import { withRetry } from '@cyanheads/mcp-ts-core/utils';
+import { createInterproHttpFetch, MAX_RESPONSE_BYTES, upstreamStatusError, } from '../interpro/http-adapter.js';
+import { JOB_ID_PATTERN, JobStatusSchema, MAX_JOB_ID_CHARS, MatchesLookupSchema, ScanResultSchema, } from './scan-schemas.js';
+/** One budget per tool call, below the 60-second default MCP client request timeout. */
+export const CALL_BUDGET_MS = 50_000;
+/**
+ * Most one attempt of each request may take, further bounded by what remains of the call budget.
+ * Bodies get the longest bound: EBI throughput varies, and a 0.7 MB lookup or a 1.5 MB result
+ * has taken 13-15 seconds, where a retry would only restart the same download.
+ */
+const ATTEMPT_MS = { status: 15_000, run: 20_000, body: 40_000 };
+/** Minimum spacing between `status` polls of one job within a call. */
+export const POLL_INTERVAL_MS = 5_000;
+/** Call budget kept back from polling so a FINISHED job's result can still be read. */
+const RESULT_RESERVE_MS = 15_000;
+/** Longest wait window a call can use: the budget less the result reserve. */
+export const MAX_WAIT_SECONDS = (CALL_BUDGET_MS - RESULT_RESERVE_MS) / 1000;
+/** Job Dispatcher fair use asks for at most 30 jobs in flight per user; one address is one user. */
+export const MAX_IN_FLIGHT = 25;
+/** A tracked job nobody observed finishing frees its slot after this long (runs take ~10 min). */
+export const IN_FLIGHT_TTL_MS = 20 * 60_000;
+export const MATCHES_URL = 'https://www.ebi.ac.uk/interpro/matches/api/matches';
+export const JOB_DISPATCHER_BASE = 'https://www.ebi.ac.uk/Tools/services/rest/iprscan6/';
+const now = () => performance.now();
+const deadlineError = () => timeout('InterProScan call exhausted its 50-second budget.', {
+    reason: 'retry_deadline_exceeded',
+    retryable: true,
+    deadlineMs: CALL_BUDGET_MS,
+});
+/**
+ * Resolve with `promise`, or reject with the caller's abort reason or the call's deadline error,
+ * whichever comes first. Uses the global timer so fake timers drive it in tests.
+ */
+function bounded(promise, signal, deadline) {
+    signal.throwIfAborted();
+    return new Promise((resolve, reject) => {
+        const done = () => {
+            clearTimeout(timer);
+            signal.removeEventListener('abort', abort);
+        };
+        const abort = () => {
+            done();
+            reject(signal.reason);
+        };
+        const timer = setTimeout(() => {
+            done();
+            reject(deadlineError());
+        }, Math.max(0, deadline - now()));
+        signal.addEventListener('abort', abort, { once: true });
+        promise.then((value) => {
+            done();
+            resolve(value);
+        }, (error) => {
+            done();
+            reject(error);
+        });
+    });
+}
+/** Wait `ms`, rejecting at once with the caller's reason when the signal aborts. */
+function delay(ms, signal) {
+    signal.throwIfAborted();
+    return new Promise((resolve, reject) => {
+        const abort = () => {
+            clearTimeout(timer);
+            reject(signal.reason);
+        };
+        const timer = setTimeout(() => {
+            signal.removeEventListener('abort', abort);
+            resolve();
+        }, Math.max(0, ms));
+        signal.addEventListener('abort', abort, { once: true });
+    });
+}
+async function readText(response, signal) {
+    if (!response.body)
+        return '';
+    const reader = response.body.getReader();
+    const chunks = [];
+    let bytes = 0;
+    try {
+        while (true) {
+            signal.throwIfAborted();
+            const { done, value } = await reader.read();
+            if (done)
+                break;
+            bytes += value.byteLength;
+            if (bytes > MAX_RESPONSE_BYTES) {
+                await reader.cancel();
+                throw serviceUnavailable('InterProScan response exceeds 4 MiB.', {
+                    reason: 'upstream_response_too_large',
+                    retryable: false,
+                });
+            }
+            chunks.push(value);
+        }
+        return Buffer.concat(chunks).toString('utf8');
+    }
+    finally {
+        reader.releaseLock();
+    }
+}
+function parseJson(body) {
+    try {
+        return JSON.parse(body);
+    }
+    catch (cause) {
+        throw serviceUnavailable('InterProScan service returned malformed JSON.', { reason: 'upstream_shape_invalid', retryable: false }, { cause });
+    }
+}
+const shapeInvalid = (what) => serviceUnavailable(`${what} does not match the required response structure.`, {
+    reason: 'upstream_shape_invalid',
+    retryable: false,
+});
+/** The native transport, its backstop no tighter than the per-operation attempt bounds. */
+const scanHttpFetch = createInterproHttpFetch(CALL_BUDGET_MS);
+/** Lookup, submission, polling, and result reads for one configured submission address. */
+export class SequenceScanService {
+    email;
+    fetch;
+    inFlight = new Map();
+    constructor(email, fetch = scanHttpFetch) {
+        this.email = email;
+        this.fetch = fetch;
+    }
+    /** Start the call's single deadline. */
+    begin(ctx) {
+        const started = now();
+        return { ctx, started, deadline: started + CALL_BUDGET_MS };
+    }
+    /**
+     * Look the MD5 up in the Matches API; on a miss, submit (or join the submission already in
+     * flight for this MD5) and wait up to `waitMs`. `lookupOnly` resumes a precalculated walk and
+     * never submits.
+     */
+    async scan(call, sequence, waitMs, lookupOnly = false) {
+        const hit = await this.lookup(call, sequence.md5);
+        if (hit)
+            return { source: 'precalculated', matches: hit, sourceUrl: MATCHES_URL };
+        if (lookupOnly)
+            throw validationError('The precalculated result this cursor continues is no longer available.', { reason: 'invalid_cursor', retryable: false });
+        const { jobId, submittedAt } = await this.submit(call, sequence);
+        const state = await this.withJob(jobId, () => this.awaitJob(call, jobId, submittedAt === undefined ? now() : submittedAt + POLL_INTERVAL_MS, waitMs));
+        if (state.status === 'FINISHED' && state.result.md5 !== sequence.md5)
+            throw shapeInvalid('InterProScan result for a different sequence');
+        return { source: 'interproscan', jobId, sourceUrl: this.jobUrl(jobId, state.status), ...state };
+    }
+    /** Read a job's state, waiting up to `waitMs` for it to finish; polls at least once. */
+    async result(call, jobId, waitMs) {
+        const state = await this.awaitJob(call, jobId, call.started, waitMs);
+        return { ...state, sourceUrl: this.jobUrl(jobId, state.status) };
+    }
+    jobUrl(jobId, status) {
+        return status === 'FINISHED'
+            ? `${JOB_DISPATCHER_BASE}result/${jobId}/json`
+            : `${JOB_DISPATCHER_BASE}status/${jobId}`;
+    }
+    /** Name the in-flight job in any failure after submission, so the caller keeps its handle. */
+    async withJob(jobId, work) {
+        try {
+            return await work();
+        }
+        catch (cause) {
+            if (!(cause instanceof McpError) || cause.data?.jobId)
+                throw cause;
+            throw new McpError(cause.code, `${cause.message} InterProScan job ${jobId} was submitted; read it with interpro_get_scan_result.`, { ...cause.data, jobId }, { cause });
+        }
+    }
+    /** Precalculated matches, or undefined when UniParc holds no result for the MD5. */
+    async lookup(call, md5) {
+        const parsed = await this.send(call, call.ctx.signal, 'interpro.matches.lookup', MATCHES_URL, {
+            method: 'POST',
+            body: JSON.stringify({ md5: [md5] }),
+            headers: { Accept: 'application/json', 'Content-Type': 'application/json' },
+        }, 'body', async (response, signal) => {
+            if (!response.ok)
+                throw await upstreamStatusError(response, 'InterPro Matches API');
+            const result = MatchesLookupSchema.safeParse(parseJson(await readText(response, signal)));
+            if (!result.success)
+                throw shapeInvalid('InterPro Matches API JSON');
+            return result.data;
+        });
+        const [entry] = parsed.results;
+        if (entry?.md5.toUpperCase() !== md5)
+            throw shapeInvalid('InterPro Matches API result');
+        return entry.found ? entry.matches : undefined;
+    }
+    /** Expire tracked jobs nobody saw finish, so the map stays bounded without a timer. */
+    sweep() {
+        const cutoff = now() - IN_FLIGHT_TTL_MS;
+        for (const [md5, slot] of this.inFlight)
+            if (slot.kind === 'job' && slot.since < cutoff)
+                this.inFlight.delete(md5);
+    }
+    /** Free the slot of a job observed in a terminal state. */
+    release(jobId) {
+        for (const [md5, slot] of this.inFlight)
+            if (slot.kind === 'job' && slot.jobId === jobId)
+                this.inFlight.delete(md5);
+    }
+    /**
+     * The job for this MD5: one already tracked, one being submitted by another call, or a new
+     * submission. `submittedAt` is set only when this call's own `run` (or one it joined) made it.
+     */
+    async submit(call, sequence) {
+        this.sweep();
+        const existing = this.inFlight.get(sequence.md5);
+        if (existing?.kind === 'job')
+            return { jobId: existing.jobId };
+        if (existing)
+            return { jobId: await this.join(existing, call), submittedAt: existing.since };
+        const { email } = this;
+        if (!email)
+            throw configurationError('This sequence has no precalculated matches, and this server is not configured to submit InterProScan jobs.', { reason: 'scan_not_configured', retryable: false });
+        if (this.inFlight.size >= MAX_IN_FLIGHT) {
+            const frees = Math.min(...[...this.inFlight.values()].map((slot) => slot.kind === 'job' ? slot.since + IN_FLIGHT_TTL_MS : slot.since + ATTEMPT_MS.run));
+            throw rateLimited(`This server already has ${MAX_IN_FLIGHT} InterProScan jobs in flight, the most it keeps under the Job Dispatcher fair-use limit.`, {
+                reason: 'rate_limited',
+                retryable: true,
+                retryAfter: Math.max(1, Math.ceil((frees - now()) / 1000)),
+            });
+        }
+        const slot = {
+            kind: 'submitting',
+            md5: sequence.md5,
+            since: now(),
+            controller: new AbortController(),
+            outcome: Promise.resolve({ ok: false, error: undefined }),
+            waiters: 0,
+            settled: false,
+        };
+        this.inFlight.set(sequence.md5, slot);
+        slot.outcome = (async () => {
+            try {
+                const jobId = await this.run(call, slot.controller.signal, email, sequence);
+                const current = this.inFlight.get(sequence.md5);
+                if (current === slot || current === undefined)
+                    this.inFlight.set(sequence.md5, { kind: 'job', since: now(), jobId });
+                return { ok: true, value: jobId };
+            }
+            catch (error) {
+                if (this.inFlight.get(sequence.md5) === slot)
+                    this.inFlight.delete(sequence.md5);
+                return { ok: false, error };
+            }
+            finally {
+                slot.settled = true;
+            }
+        })();
+        return { jobId: await this.join(slot, call), submittedAt: slot.since };
+    }
+    /**
+     * Await a shared submission. A caller leaving early detaches only itself; the request is
+     * aborted when the last waiting caller leaves before it settles.
+     */
+    async join(slot, call) {
+        slot.waiters++;
+        try {
+            const outcome = await bounded(slot.outcome, call.ctx.signal, call.deadline);
+            if (!outcome.ok)
+                throw outcome.error;
+            return outcome.value;
+        }
+        finally {
+            slot.waiters--;
+            if (!slot.waiters && !slot.settled) {
+                // Abandoned: a later call for this MD5 must start afresh, not inherit this abort.
+                if (this.inFlight.get(slot.md5) === slot)
+                    this.inFlight.delete(slot.md5);
+                slot.controller.abort(call.ctx.signal.aborted ? call.ctx.signal.reason : deadlineError());
+            }
+        }
+    }
+    /** One `run` request, never retried: a lost response may still have created a job. */
+    async run(call, signal, email, sequence) {
+        const body = new URLSearchParams({
+            email,
+            sequence: `>query\n${sequence.residues}`,
+            stype: 'p',
+            goterms: 'false',
+            pathways: 'false',
+        }).toString();
+        const jobId = await this.send(call, signal, 'interpro.scan.run', `${JOB_DISPATCHER_BASE}run`, {
+            method: 'POST',
+            body,
+            headers: { Accept: 'text/plain', 'Content-Type': 'application/x-www-form-urlencoded' },
+        }, 'run', async (response, attemptSignal) => {
+            const text = await readText(response, attemptSignal);
+            if (response.status === 400) {
+                const description = this.describeRejection(text);
+                throw serviceUnavailable(`Job Dispatcher rejected the InterProScan submission${description ? `: ${description}` : '.'}`, { reason: 'scan_rejected', retryable: false, status: 400 });
+            }
+            if (!response.ok)
+                throw await upstreamStatusError(response, 'Job Dispatcher');
+            const id = text.trim();
+            if (id.length > MAX_JOB_ID_CHARS || !JOB_ID_PATTERN.test(id))
+                throw shapeInvalid('Job Dispatcher job ID');
+            return id;
+        });
+        call.ctx.log.info('InterProScan job submitted', { md5: sequence.md5, jobId });
+        return jobId;
+    }
+    /**
+     * The `<description>` of a Job Dispatcher XML error, single-line, bounded, and with the
+     * configured address replaced, since rejections can echo submitted fields.
+     */
+    describeRejection(xml) {
+        const match = /<description>([^<]{1,500})<\/description>/.exec(xml.slice(0, 4096));
+        if (!match?.[1])
+            return undefined;
+        let text = match[1].replace(/[\p{Cc}\s]+/gu, ' ').trim();
+        if (this.email)
+            text = text.replace(new RegExp(this.email.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'), 'gi'), '[address]');
+        return text.slice(0, 300) || undefined;
+    }
+    /**
+     * Poll `status` from `firstPollAt`, at most every five seconds, until a terminal status or
+     * the window closes, then read the result of a FINISHED job. The window is `waitMs` from the
+     * call's start, capped so the result read keeps its reserve of the deadline.
+     */
+    async awaitJob(call, jobId, firstPollAt, waitMs) {
+        const windowEnd = Math.min(call.started + waitMs, call.deadline - RESULT_RESERVE_MS);
+        let status;
+        for (let next = firstPollAt; next <= windowEnd; next = now() + POLL_INTERVAL_MS) {
+            await delay(next - now(), call.ctx.signal);
+            status = await this.status(call, jobId);
+            if (status !== 'QUEUED' && status !== 'RUNNING')
+                break;
+        }
+        switch (status) {
+            case undefined:
+                return { status: 'submitted' };
+            case 'QUEUED':
+            case 'RUNNING':
+                return { status };
+            case 'FINISHED': {
+                // Released only once read, so a retried scan after a failed read rejoins this job.
+                const result = await this.read(call, jobId);
+                this.release(jobId);
+                return { status, result };
+            }
+            case 'NOT_FOUND':
+                this.release(jobId);
+                throw notFound(`Job Dispatcher has no InterProScan job ${jobId}; it never existed or expired after seven days.`, { reason: 'scan_not_found', retryable: false, jobId });
+            default:
+                this.release(jobId);
+                throw serviceUnavailable(`InterProScan job ${jobId} ended with status ${status}.`, {
+                    reason: 'scan_failed',
+                    retryable: false,
+                    jobId,
+                    status,
+                });
+        }
+    }
+    async status(call, jobId) {
+        return await this.send(call, call.ctx.signal, 'interpro.scan.status', `${JOB_DISPATCHER_BASE}status/${jobId}`, { headers: { Accept: 'text/plain' } }, 'status', async (response, signal) => {
+            if (!response.ok)
+                throw await upstreamStatusError(response, 'Job Dispatcher');
+            const parsed = JobStatusSchema.safeParse((await readText(response, signal)).trim());
+            if (!parsed.success)
+                throw shapeInvalid('Job Dispatcher status');
+            return parsed.data;
+        });
+    }
+    async read(call, jobId) {
+        return await this.send(call, call.ctx.signal, 'interpro.scan.result', `${JOB_DISPATCHER_BASE}result/${jobId}/json`, { headers: { Accept: 'application/json' } }, 'body', async (response, signal) => {
+            if (response.status === 400 || response.status === 404) {
+                this.release(jobId);
+                throw notFound(`Job Dispatcher has no result for InterProScan job ${jobId}.`, {
+                    reason: 'scan_not_found',
+                    retryable: false,
+                    jobId,
+                });
+            }
+            if (!response.ok)
+                throw await upstreamStatusError(response, 'Job Dispatcher');
+            const parsed = ScanResultSchema.safeParse(parseJson(await readText(response, signal)));
+            if (!parsed.success)
+                throw shapeInvalid('InterProScan result JSON');
+            const [result] = parsed.data.results;
+            return {
+                md5: result.md5.toUpperCase(),
+                length: result.sequence.length,
+                interproVersion: parsed.data['interpro-version'],
+                interproscanVersion: parsed.data['interproscan-version'],
+                matches: result.matches,
+            };
+        });
+    }
+    /**
+     * One fixed-origin request under the call deadline. Each attempt is bounded by the smaller of
+     * the operation's attempt bound and what remains. Reads get one more attempt on a transient
+     * failure; a `run` never does.
+     */
+    async send(call, signal, operation, url, init, kind, read) {
+        signal.throwIfAborted();
+        const remaining = call.deadline - now();
+        if (remaining <= 0)
+            throw deadlineError();
+        return await withRetry(async ({ signal: retrySignal }) => {
+            const controller = new AbortController();
+            const timer = setTimeout(() => controller.abort(timeout('InterProScan attempt deadline elapsed.', {
+                reason: 'upstream_timeout',
+                retryable: true,
+            })), Math.max(0, Math.min(ATTEMPT_MS[kind], call.deadline - now())));
+            const attemptSignal = AbortSignal.any([retrySignal, controller.signal, signal]);
+            try {
+                const response = await this.fetch(url, {
+                    ...init,
+                    signal: attemptSignal,
+                    redirect: 'manual',
+                });
+                const value = await read(response, attemptSignal);
+                attemptSignal.throwIfAborted();
+                return value;
+            }
+            catch (cause) {
+                if (signal.aborted)
+                    throw signal.reason;
+                if (retrySignal.aborted)
+                    throw retrySignal.reason;
+                if (controller.signal.aborted)
+                    throw controller.signal.reason;
+                if (cause instanceof McpError)
+                    throw cause;
+                throw serviceUnavailable('InterProScan network request failed.', { reason: 'upstream_unavailable', retryable: true }, { cause });
+            }
+            finally {
+                clearTimeout(timer);
+            }
+        }, {
+            signal,
+            context: call.ctx,
+            operation,
+            deadlineMs: remaining,
+            maxRetries: kind === 'run' ? 0 : 1,
+            baseDelayMs: 1000,
+            maxDelayMs: 3000,
+        });
+    }
+}
+let service;
+/** Initialize the process service in createApp.setup with the configured submission address. */
+export function initSequenceScanService(email, fetch = scanHttpFetch) {
+    service = new SequenceScanService(email, fetch);
+}
+/** Obtain the initialized process service. */
+export function getSequenceScanService() {
+    if (!service)
+        throw new Error('Sequence scan service is not initialized.');
+    return service;
+}
+//# sourceMappingURL=sequence-scan-service.js.map

package/dist/services/sequence-scan/sequence-scan-service.js.map

@@ -0,0 +1 @@
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package/dist/services/sequence-scan/sequence.d.ts

@@ -0,0 +1,32 @@
+/** Most characters one sequence argument may hold, FASTA header and line breaks included. */
+export declare const MAX_SEQUENCE_CHARS = 100000;
+/** A parsed sequence, or the reason it cannot be scanned. */
+export type ParsedSequence = {
+    readonly ok: true;
+    readonly residues: string;
+    readonly md5: string;
+} | {
+    readonly ok: false;
+    readonly reason: 'empty_sequence';
+} | {
+    readonly ok: false;
+    readonly reason: 'multiple_sequences';
+    readonly position: number;
+} | {
+    readonly ok: false;
+    readonly reason: 'invalid_residue';
+    readonly position: number;
+    readonly codePoint: number;
+};
+/**
+ * Read one protein sequence: an optional byte-order mark as the very first character, optional
+ * leading whitespace, an optional single FASTA header line, then IUPAC residue letters (all 26,
+ * case-insensitive) separated by any spaces, tabs, or line breaks. A `>` past the header starts a
+ * second record; a byte-order mark anywhere else is an invalid residue. Each character is visited
+ * once, so the cost is linear in the input. Positions are 1-based character offsets into the
+ * argument, the skipped mark included.
+ */
+export declare function parseSequence(text: string): ParsedSequence;
+/** A code point as `U+XXXX`, so an invalid character is named without echoing it. */
+export declare const codePointLabel: (codePoint: number) => string;
+//# sourceMappingURL=sequence.d.ts.map

package/dist/services/sequence-scan/sequence.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"sequence.d.ts","sourceRoot":"","sources":["../../../src/services/sequence-scan/sequence.ts"],"names":[],"mappings":"AAMA,6FAA6F;AAC7F,eAAO,MAAM,kBAAkB,SAAU,CAAC;AAE1C,6DAA6D;AAC7D,MAAM,MAAM,cAAc,GACtB;IAAE,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC;IAAC,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC;IAAC,QAAQ,CAAC,GAAG,EAAE,MAAM,CAAA;CAAE,GACtE;IAAE,QAAQ,CAAC,EAAE,EAAE,KAAK,CAAC;IAAC,QAAQ,CAAC,MAAM,EAAE,gBAAgB,CAAA;CAAE,GACzD;IAAE,QAAQ,CAAC,EAAE,EAAE,KAAK,CAAC;IAAC,QAAQ,CAAC,MAAM,EAAE,oBAAoB,CAAC;IAAC,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,GACxF;IACE,QAAQ,CAAC,EAAE,EAAE,KAAK,CAAC;IACnB,QAAQ,CAAC,MAAM,EAAE,iBAAiB,CAAC;IACnC,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC;IAC1B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;CAC5B,CAAC;AAWN;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,cAAc,CA8B1D;AAED,qFAAqF;AACrF,eAAO,MAAM,cAAc,cAAe,MAAM,WACc,CAAC"}

package/dist/services/sequence-scan/sequence.js

@@ -0,0 +1,63 @@
+/**
+ * @fileoverview One-pass protein sequence parsing and the UniParc-compatible MD5 digest.
+ * @module services/sequence-scan/sequence
+ */
+import { createHash } from 'node:crypto';
+/** Most characters one sequence argument may hold, FASTA header and line breaks included. */
+export const MAX_SEQUENCE_CHARS = 100_000;
+const CR = 0x0d;
+const LF = 0x0a;
+const GT = 0x3e;
+/** U+FEFF, the byte-order mark a text file saved as UTF-8 with BOM opens with. */
+const BOM = 0xfeff;
+const isWhitespace = (code) => code === 0x20 || code === 0x09 || code === CR || code === LF;
+const isUpper = (code) => code >= 0x41 && code <= 0x5a;
+const isLower = (code) => code >= 0x61 && code <= 0x7a;
+/**
+ * Read one protein sequence: an optional byte-order mark as the very first character, optional
+ * leading whitespace, an optional single FASTA header line, then IUPAC residue letters (all 26,
+ * case-insensitive) separated by any spaces, tabs, or line breaks. A `>` past the header starts a
+ * second record; a byte-order mark anywhere else is an invalid residue. Each character is visited
+ * once, so the cost is linear in the input. Positions are 1-based character offsets into the
+ * argument, the skipped mark included.
+ */
+export function parseSequence(text) {
+    const residues = new Uint8Array(text.length);
+    let count = 0;
+    let index = text.charCodeAt(0) === BOM ? 1 : 0;
+    while (index < text.length && isWhitespace(text.charCodeAt(index)))
+        index++;
+    if (text.charCodeAt(index) === GT) {
+        while (index < text.length && text.charCodeAt(index) !== LF && text.charCodeAt(index) !== CR)
+            index++;
+    }
+    for (; index < text.length; index++) {
+        const code = text.charCodeAt(index);
+        if (isUpper(code))
+            residues[count++] = code;
+        else if (isLower(code))
+            residues[count++] = code - 0x20;
+        else if (isWhitespace(code))
+            continue;
+        else if (code === GT)
+            return { ok: false, reason: 'multiple_sequences', position: index + 1 };
+        else
+            return {
+                ok: false,
+                reason: 'invalid_residue',
+                position: index + 1,
+                codePoint: text.codePointAt(index) ?? code,
+            };
+    }
+    if (!count)
+        return { ok: false, reason: 'empty_sequence' };
+    const bytes = residues.subarray(0, count);
+    return {
+        ok: true,
+        residues: Buffer.from(bytes).toString('latin1'),
+        md5: createHash('md5').update(bytes).digest('hex').toUpperCase(),
+    };
+}
+/** A code point as `U+XXXX`, so an invalid character is named without echoing it. */
+export const codePointLabel = (codePoint) => `U+${codePoint.toString(16).toUpperCase().padStart(4, '0')}`;
+//# sourceMappingURL=sequence.js.map

package/dist/services/sequence-scan/sequence.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"sequence.js","sourceRoot":"","sources":["../../../src/services/sequence-scan/sequence.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AAEzC,6FAA6F;AAC7F,MAAM,CAAC,MAAM,kBAAkB,GAAG,OAAO,CAAC;AAc1C,MAAM,EAAE,GAAG,IAAI,CAAC;AAChB,MAAM,EAAE,GAAG,IAAI,CAAC;AAChB,MAAM,EAAE,GAAG,IAAI,CAAC;AAChB,kFAAkF;AAClF,MAAM,GAAG,GAAG,MAAM,CAAC;AACnB,MAAM,YAAY,GAAG,CAAC,IAAY,EAAE,EAAE,CAAC,IAAI,KAAK,IAAI,IAAI,IAAI,KAAK,IAAI,IAAI,IAAI,KAAK,EAAE,IAAI,IAAI,KAAK,EAAE,CAAC;AACpG,MAAM,OAAO,GAAG,CAAC,IAAY,EAAE,EAAE,CAAC,IAAI,IAAI,IAAI,IAAI,IAAI,IAAI,IAAI,CAAC;AAC/D,MAAM,OAAO,GAAG,CAAC,IAAY,EAAE,EAAE,CAAC,IAAI,IAAI,IAAI,IAAI,IAAI,IAAI,IAAI,CAAC;AAE/D;;;;;;;GAOG;AACH,MAAM,UAAU,aAAa,CAAC,IAAY;IACxC,MAAM,QAAQ,GAAG,IAAI,UAAU,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IAC7C,IAAI,KAAK,GAAG,CAAC,CAAC;IACd,IAAI,KAAK,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC/C,OAAO,KAAK,GAAG,IAAI,CAAC,MAAM,IAAI,YAAY,CAAC,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;QAAE,KAAK,EAAE,CAAC;IAC5E,IAAI,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,KAAK,EAAE,EAAE,CAAC;QAClC,OAAO,KAAK,GAAG,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,KAAK,EAAE,IAAI,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,KAAK,EAAE;YAC1F,KAAK,EAAE,CAAC;IACZ,CAAC;IACD,OAAO,KAAK,GAAG,IAAI,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE,CAAC;QACpC,MAAM,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;QACpC,IAAI,OAAO,CAAC,IAAI,CAAC;YAAE,QAAQ,CAAC,KAAK,EAAE,CAAC,GAAG,IAAI,CAAC;aACvC,IAAI,OAAO,CAAC,IAAI,CAAC;YAAE,QAAQ,CAAC,KAAK,EAAE,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC;aACnD,IAAI,YAAY,CAAC,IAAI,CAAC;YAAE,SAAS;aACjC,IAAI,IAAI,KAAK,EAAE;YAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE,oBAAoB,EAAE,QAAQ,EAAE,KAAK,GAAG,CAAC,EAAE,CAAC;;YAE5F,OAAO;gBACL,EAAE,EAAE,KAAK;gBACT,MAAM,EAAE,iBAAiB;gBACzB,QAAQ,EAAE,KAAK,GAAG,CAAC;gBACnB,SAAS,EAAE,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,IAAI,IAAI;aAC3C,CAAC;IACN,CAAC;IACD,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE,gBAAgB,EAAE,CAAC;IAC3D,MAAM,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC;IAC1C,OAAO;QACL,EAAE,EAAE,IAAI;QACR,QAAQ,EAAE,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,QAAQ,CAAC,QAAQ,CAAC;QAC/C,GAAG,EAAE,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,WAAW,EAAE;KACjE,CAAC;AACJ,CAAC;AAED,qFAAqF;AACrF,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,SAAiB,EAAE,EAAE,CAClD,KAAK,SAAS,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,CAAC"}

package/package.json

@@ -1,8 +1,8 @@
 {
   "name": "@cyanheads/interpro-mcp-server",
-  "version": "0.1.3",
+  "version": "0.2.0",
   "mcpName": "io.github.cyanheads/interpro-mcp-server",
-  "description": "Search InterPro entries, map protein domains and functional sites, and find proteins by domain via MCP. STDIO or Streamable HTTP.",
+  "description": "Search InterPro entries, map domains and functional sites onto UniProt proteins and PDB structures, find proteins by domain, and scan raw protein sequences via MCP. STDIO or Streamable HTTP.",
   "author": "Casey Hand <casey@caseyjhand.com> (https://caseyjhand.com)",
   "homepage": "https://github.com/cyanheads/interpro-mcp-server#readme",
   "bugs": {
@@ -33,7 +33,8 @@
     "CLAUDE.md",
     "AGENTS.md",
     "Dockerfile",
-    "server.json"
+    "server.json",
+    "skills/"
   ],
   "scripts": {
     "build": "bun run scripts/build.ts",
@@ -70,6 +71,8 @@
     "interpro",
     "pfam",
     "protein-domains",
+    "pdb",
+    "interproscan",
     "bioinformatics"
   ],
   "repository": {
@@ -86,20 +89,20 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.13.16",
+    "@cyanheads/mcp-ts-core": "^0.13.18",
     "htmlparser2": "^12.0.0",
     "pino-pretty": "^13.2.0",
     "zod": "^4.6.7"
   },
   "devDependencies": {
-    "@biomejs/biome": "2.6.2",
+    "@biomejs/biome": "2.6.3",
     "@socketsecurity/bun-security-scanner": "^1.1.3",
     "@types/node": "26.6.5",
     "@vitest/coverage-istanbul": "5.0.5",
     "depcheck": "^1.4.7",
     "fast-check": "^4.10.2",
-    "ignore": "^7.0.13",
-    "tsc-alias": "^1.9.8",
+    "ignore": "^7.0.14",
+    "tsc-alias": "^1.9.9",
     "typescript": "^7.0.2",
     "vitest": "^5.0.5"
   }