@cyanheads/interpro-mcp-server 0.1.3 → 0.2.0

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

@@ -0,0 +1,174 @@
+/**
+ * @fileoverview Output schema and budget-bounded segments of whole match records shared by the
+ * scan and scan-result tools, with cursors scoped to the sequence MD5 or the job ID.
+ * @module services/sequence-scan/scan-output
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { validationError } from '@cyanheads/mcp-ts-core/errors';
+import { BUDGET_LABEL, fitWithinBudget } from '../interpro/budget.js';
+import { compareText, decodePositionCursor, encodePositionCursor, } from '../interpro/cursors.js';
+import { ScanMatchSchema } from './scan-schemas.js';
+const PRECALCULATED_OPERATION = 'interpro_scan_sequence.precalculated';
+const JOB_OPERATION = 'interpro_get_scan_result.job';
+const PositionSchema = z
+    .object({ offset: z.number().int().positive(), total: z.number().int().positive() })
+    .strict();
+/** Output fields both tools return. */
+export const ScanOutputSchema = z.object({
+    source: z
+        .enum(['precalculated', 'interproscan'])
+        .describe('Which path produced the result: precalculated matches from the InterPro Matches API, or an InterProScan 6 job run through the EBI Job Dispatcher.'),
+    status: z
+        .enum(['finished', 'queued', 'running', 'submitted'])
+        .describe('finished: matches are present. queued or running: the job is pending; read it later with interpro_get_scan_result. submitted: accepted in this call and not yet polled.'),
+    jobId: z
+        .string()
+        .optional()
+        .describe('InterProScan job ID on the interproscan path; results stay retrievable for seven days.'),
+    md5: z
+        .string()
+        .optional()
+        .describe('Uppercase hex MD5 of the uppercased residues, the UniParc sequence digest.'),
+    length: z.number().int().optional().describe('Sequence length in residues.'),
+    interproVersion: z
+        .string()
+        .optional()
+        .describe('InterPro release of a finished InterProScan job.'),
+    interproscanVersion: z.string().optional().describe('InterProScan version of a finished job.'),
+    matches: z
+        .array(ScanMatchSchema)
+        .optional()
+        .describe('Whole match records in this segment when finished, sorted by earliest location start then signature accession; coordinates are 1-based and inclusive. Each record keeps its own source and signatureLibraryRelease.'),
+    coverage: z
+        .object({
+        totalMatches: z.number().int().describe('Match records in the complete result.'),
+        offset: z.number().int().describe('Match records that precede this segment.'),
+        returnedMatches: z.number().int().describe('Match records in this segment.'),
+        hasMore: z.boolean().describe('Whether another segment remains.'),
+        nextCursor: z
+            .string()
+            .optional()
+            .describe('Opaque cursor for the next segment; pass it unchanged to the tool the notice names.'),
+    })
+        .optional()
+        .describe('Where this segment sits in the complete match list; present when finished.'),
+    sourceUrl: z.string().describe('Upstream endpoint that supplied this result.'),
+});
+/** Enrichment fields both tools declare. */
+export const ScanEnrichment = {
+    notice: z.string().optional().describe('Job, continuation, or empty-result guidance.'),
+    totalCount: z.number().optional().describe('Match records in the complete result.'),
+    truncated: z.boolean().optional().describe('More segments remain.'),
+    shown: z.number().int().optional().describe('Match records in this segment.'),
+};
+const cursorTarget = (state, md5) => state.source === 'precalculated'
+    ? { operation: PRECALCULATED_OPERATION, scope: { md5 } }
+    : { operation: JOB_OPERATION, scope: { jobId: state.jobId } };
+/** Decode a continuation for the given target before any upstream request. */
+export function decodeScanCursor(cursor, target) {
+    return 'md5' in target
+        ? decodePositionCursor(cursor, PRECALCULATED_OPERATION, { md5: target.md5 }, PositionSchema)
+        : decodePositionCursor(cursor, JOB_OPERATION, { jobId: target.jobId }, PositionSchema);
+}
+function minStart(match) {
+    let start = Number.POSITIVE_INFINITY;
+    for (const location of match.locations)
+        start = Math.min(start, location.start);
+    return start;
+}
+/** Deterministic order, so a cursor offset names the same record on every read. */
+function sortMatches(matches) {
+    return matches
+        .map((match) => ({ match, start: minStart(match), json: JSON.stringify(match) }))
+        .sort((a, b) => a.start - b.start ||
+        compareText(a.match.signature.accession, b.match.signature.accession) ||
+        compareText(a.match.source, b.match.source) ||
+        compareText(a.json, b.json))
+        .map(({ match }) => match);
+}
+/**
+ * Build one segment of a finished result, or the pending output, and the notices that go with
+ * it. `continuation` names the call that reads the next segment, as the agent should make it.
+ */
+export function buildScanOutput(enrich, state, options) {
+    const base = {
+        source: state.source,
+        ...(state.source === 'interproscan' ? { jobId: state.jobId } : {}),
+    };
+    if (state.source === 'interproscan' && state.status !== 'FINISHED') {
+        const status = state.status === 'submitted' ? 'submitted' : state.status === 'QUEUED' ? 'queued' : 'running';
+        enrich.notice(`InterProScan job ${state.jobId} is ${status}; de novo scans commonly take about ten minutes. Call interpro_get_scan_result ${JSON.stringify({ jobId: state.jobId })} to wait for it. Results stay retrievable for seven days.`);
+        return {
+            ...base,
+            status,
+            ...(options.md5 ? { md5: options.md5 } : {}),
+            ...(options.length ? { length: options.length } : {}),
+            sourceUrl: state.sourceUrl,
+        };
+    }
+    const finished = state.source === 'precalculated'
+        ? { matches: state.matches, md5: options.md5, length: options.length }
+        : {
+            matches: state.result.matches,
+            md5: state.result.md5,
+            length: state.result.length,
+            interproVersion: state.result.interproVersion,
+            interproscanVersion: state.result.interproscanVersion,
+        };
+    const all = sortMatches(finished.matches);
+    const total = all.length;
+    const offset = options.start?.offset ?? 0;
+    if (options.start && (options.start.total !== total || offset >= total))
+        throw validationError('Cursor no longer matches this result; restart without cursor.', {
+            reason: 'invalid_cursor',
+            retryable: false,
+        });
+    const { operation, scope } = cursorTarget(state, finished.md5);
+    const remaining = total - offset;
+    const segment = (count) => {
+        const end = offset + count;
+        return {
+            ...base,
+            status: 'finished',
+            ...(finished.md5 ? { md5: finished.md5 } : {}),
+            ...(finished.length ? { length: finished.length } : {}),
+            ...('interproVersion' in finished
+                ? {
+                    interproVersion: finished.interproVersion,
+                    interproscanVersion: finished.interproscanVersion,
+                }
+                : {}),
+            matches: all.slice(offset, end),
+            coverage: {
+                totalMatches: total,
+                offset,
+                returnedMatches: count,
+                hasMore: end < total,
+                ...(end < total
+                    ? { nextCursor: encodePositionCursor(operation, scope, { offset: end, total }) }
+                    : {}),
+            },
+            sourceUrl: state.sourceUrl,
+        };
+    };
+    const { count, output, oversized } = remaining
+        ? fitWithinBudget(remaining, segment)
+        : { count: 0, output: segment(0), oversized: false };
+    const notices = [];
+    if (oversized)
+        notices.push(`Match ${all[offset]?.signature.accession} cannot be split, so this segment holds it alone and exceeds the ${BUDGET_LABEL}.`);
+    const next = output.coverage?.nextCursor;
+    if (next) {
+        notices.push(`This segment holds matches ${offset + 1}–${offset + count} of ${total} and stopped at the ${BUDGET_LABEL}. Continue with ${options.continuation(next)} before concluding a region has no match.`);
+        enrich.truncated({ shown: count });
+    }
+    else if (!total)
+        notices.push(state.source === 'precalculated'
+            ? 'The InterPro Matches API holds a precalculated result for this sequence with no signature matches.'
+            : 'InterProScan finished and reported no signature matches for this sequence.');
+    enrich.total(total);
+    if (notices.length)
+        enrich.notice(notices.join(' '));
+    return output;
+}
+//# sourceMappingURL=scan-output.js.map

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

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

@@ -0,0 +1,112 @@
+/**
+ * @fileoverview Wire and output schemas for InterProScan match records, Matches API lookups, and
+ * Job Dispatcher iprscan6 jobs. Match records pass through verbatim, unknown fields included.
+ * @module services/sequence-scan/scan-schemas
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+/**
+ * Job Dispatcher iprscan6 job identifier, e.g. `iprscan6-R20261028-131532-0930-13189043-p1m`:
+ * submission channel letter and date, time, two numeric fields, then a short host suffix. The
+ * channel letter and suffix are kept open beyond the observed `R` and `p1m`.
+ */
+export declare const JOB_ID_PATTERN: RegExp;
+/** Longest job identifier the pattern admits, so the input bound and the grammar agree. */
+export declare const MAX_JOB_ID_CHARS = 64;
+/** Job Dispatcher `status` vocabulary; NOT_FOUND arrives as HTTP 200 for unknown and expired IDs. */
+export declare const JobStatusSchema: z.ZodEnum<{
+    ERROR: "ERROR";
+    FAILURE: "FAILURE";
+    FINISHED: "FINISHED";
+    NOT_FOUND: "NOT_FOUND";
+    QUEUED: "QUEUED";
+    RUNNING: "RUNNING";
+}>;
+export type JobStatus = z.infer<typeof JobStatusSchema>;
+/** One InterProScan match record, the shape the Matches API and iprscan6 JSON share. */
+export declare const ScanMatchSchema: z.ZodObject<{
+    signature: z.ZodObject<{
+        accession: z.ZodString;
+        signatureLibraryRelease: z.ZodObject<{
+            library: z.ZodString;
+            version: z.ZodString;
+        }, z.core.$catchall<z.ZodJSONSchema>>;
+        entry: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+            accession: z.ZodString;
+        }, z.core.$catchall<z.ZodJSONSchema>>>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>;
+    'model-ac': z.ZodNullable<z.ZodString>;
+    source: z.ZodString;
+    locations: z.ZodArray<z.ZodObject<{
+        start: z.ZodNumber;
+        end: z.ZodNumber;
+        'location-fragments': z.ZodArray<z.ZodObject<{
+            start: z.ZodNumber;
+            end: z.ZodNumber;
+            'dc-status': z.ZodString;
+        }, z.core.$catchall<z.ZodJSONSchema>>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>;
+}, z.core.$catchall<z.ZodJSONSchema>>;
+export type ScanMatch = z.infer<typeof ScanMatchSchema>;
+/** `POST /interpro/matches/api/matches` response for one MD5. */
+export declare const MatchesLookupSchema: z.ZodObject<{
+    results: z.ZodArray<z.ZodObject<{
+        md5: z.ZodString;
+        found: z.ZodBoolean;
+        matches: z.ZodArray<z.ZodObject<{
+            signature: z.ZodObject<{
+                accession: z.ZodString;
+                signatureLibraryRelease: z.ZodObject<{
+                    library: z.ZodString;
+                    version: z.ZodString;
+                }, z.core.$catchall<z.ZodJSONSchema>>;
+                entry: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+                    accession: z.ZodString;
+                }, z.core.$catchall<z.ZodJSONSchema>>>>;
+            }, z.core.$catchall<z.ZodJSONSchema>>;
+            'model-ac': z.ZodNullable<z.ZodString>;
+            source: z.ZodString;
+            locations: z.ZodArray<z.ZodObject<{
+                start: z.ZodNumber;
+                end: z.ZodNumber;
+                'location-fragments': z.ZodArray<z.ZodObject<{
+                    start: z.ZodNumber;
+                    end: z.ZodNumber;
+                    'dc-status': z.ZodString;
+                }, z.core.$catchall<z.ZodJSONSchema>>>;
+            }, z.core.$catchall<z.ZodJSONSchema>>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>>;
+    }, z.core.$strip>>;
+}, z.core.$strip>;
+/** `result/{jobId}/json` body for a single-sequence iprscan6 job. */
+export declare const ScanResultSchema: z.ZodObject<{
+    'interproscan-version': z.ZodString;
+    'interpro-version': z.ZodString;
+    results: z.ZodArray<z.ZodObject<{
+        md5: z.ZodString;
+        sequence: z.ZodString;
+        matches: z.ZodArray<z.ZodObject<{
+            signature: z.ZodObject<{
+                accession: z.ZodString;
+                signatureLibraryRelease: z.ZodObject<{
+                    library: z.ZodString;
+                    version: z.ZodString;
+                }, z.core.$catchall<z.ZodJSONSchema>>;
+                entry: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+                    accession: z.ZodString;
+                }, z.core.$catchall<z.ZodJSONSchema>>>>;
+            }, z.core.$catchall<z.ZodJSONSchema>>;
+            'model-ac': z.ZodNullable<z.ZodString>;
+            source: z.ZodString;
+            locations: z.ZodArray<z.ZodObject<{
+                start: z.ZodNumber;
+                end: z.ZodNumber;
+                'location-fragments': z.ZodArray<z.ZodObject<{
+                    start: z.ZodNumber;
+                    end: z.ZodNumber;
+                    'dc-status': z.ZodString;
+                }, z.core.$catchall<z.ZodJSONSchema>>>;
+            }, z.core.$catchall<z.ZodJSONSchema>>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>;
+}, z.core.$strip>;
+//# sourceMappingURL=scan-schemas.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/services/sequence-scan/scan-schemas.js

@@ -0,0 +1,97 @@
+/**
+ * @fileoverview Wire and output schemas for InterProScan match records, Matches API lookups, and
+ * Job Dispatcher iprscan6 jobs. Match records pass through verbatim, unknown fields included.
+ * @module services/sequence-scan/scan-schemas
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonValueSchema } from '../interpro/schemas.js';
+/**
+ * Job Dispatcher iprscan6 job identifier, e.g. `iprscan6-R20261028-131532-0930-13189043-p1m`:
+ * submission channel letter and date, time, two numeric fields, then a short host suffix. The
+ * channel letter and suffix are kept open beyond the observed `R` and `p1m`.
+ */
+export const JOB_ID_PATTERN = /^iprscan6-[A-Z]\d{8}-\d{6}-\d{4}-\d{1,12}-[a-z0-9]{1,8}$/;
+/** Longest job identifier the pattern admits, so the input bound and the grammar agree. */
+export const MAX_JOB_ID_CHARS = 64;
+/** Job Dispatcher `status` vocabulary; NOT_FOUND arrives as HTTP 200 for unknown and expired IDs. */
+export const JobStatusSchema = z.enum([
+    'QUEUED',
+    'RUNNING',
+    'FINISHED',
+    'ERROR',
+    'FAILURE',
+    'NOT_FOUND',
+]);
+const ScanFragmentSchema = z
+    .object({
+    start: z.number().int().positive().describe('Inclusive 1-based start residue.'),
+    end: z.number().int().positive().describe('Inclusive 1-based end residue.'),
+    'dc-status': z
+        .string()
+        .describe('Discontinuity status, such as CONTINUOUS, N_TERMINAL_DISC, or C_TERMINAL_DISC.'),
+})
+    .catchall(JsonValueSchema)
+    .describe('One continuous piece of a possibly discontinuous match location.');
+const ScanLocationSchema = z
+    .object({
+    start: z.number().int().positive().describe('Inclusive 1-based start residue.'),
+    end: z.number().int().positive().describe('Inclusive 1-based end residue.'),
+    'location-fragments': z
+        .array(ScanFragmentSchema)
+        .min(1)
+        .describe('Nonempty fragments of this location.'),
+})
+    .catchall(JsonValueSchema)
+    .describe('One match location with every upstream field, such as scores, e-values, HMM bounds, envelope, sites, and alignments.');
+/** One InterProScan match record, the shape the Matches API and iprscan6 JSON share. */
+export const ScanMatchSchema = z
+    .object({
+    signature: z
+        .object({
+        accession: z.string().describe('Member-database signature accession, such as PF13499.'),
+        signatureLibraryRelease: z
+            .object({
+            library: z
+                .string()
+                .describe('Member database name exactly as the source spells it, such as Pfam.'),
+            version: z.string().describe('Member database release that produced this match.'),
+        })
+            .catchall(JsonValueSchema)
+            .describe('Library and release of this signature.'),
+        entry: z
+            .object({
+            accession: z.string().describe('Integrated InterPro entry accession.'),
+        })
+            .catchall(JsonValueSchema)
+            .nullable()
+            .optional()
+            .describe('InterPro entry the signature is integrated into; null when unintegrated.'),
+    })
+        .catchall(JsonValueSchema)
+        .describe('Matched signature, including name, description, and type when supplied.'),
+    'model-ac': z.string().nullable().describe('Model accession within the signature.'),
+    source: z
+        .string()
+        .describe('Method that produced the match, such as Pfam or InterPro-N, exactly as the source spells it.'),
+    locations: z.array(ScanLocationSchema).describe('Match locations on the sequence.'),
+})
+    .catchall(JsonValueSchema)
+    .describe('One InterProScan match record, verbatim.');
+const Md5Schema = z.string().regex(/^[0-9a-fA-F]{32}$/);
+/** `POST /interpro/matches/api/matches` response for one MD5. */
+export const MatchesLookupSchema = z.object({
+    results: z
+        .array(z.object({ md5: Md5Schema, found: z.boolean(), matches: z.array(ScanMatchSchema) }))
+        .length(1),
+});
+/** `result/{jobId}/json` body for a single-sequence iprscan6 job. */
+export const ScanResultSchema = z.object({
+    'interproscan-version': z.string(),
+    'interpro-version': z.string(),
+    results: z
+        .array(z
+        .object({ md5: Md5Schema, sequence: z.string(), matches: z.array(ScanMatchSchema) })
+        .catchall(JsonValueSchema))
+        .length(1),
+});
+//# sourceMappingURL=scan-schemas.js.map

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

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

@@ -0,0 +1,119 @@
+/**
+ * @fileoverview Sequence scanning: precalculated lookup in the InterPro Matches API, then
+ * submission to the EBI Job Dispatcher iprscan6 service with a bounded, cancellable wait. The
+ * process-wide in-flight cap and the per-MD5 submission dedupe live on the service instance.
+ * @module services/sequence-scan/sequence-scan-service
+ */
+import type { Context } from '@cyanheads/mcp-ts-core';
+import { type InterproFetch } from '../interpro/http-adapter.js';
+import { type ScanMatch } from './scan-schemas.js';
+/** One budget per tool call, below the 60-second default MCP client request timeout. */
+export declare const CALL_BUDGET_MS = 50000;
+/** Minimum spacing between `status` polls of one job within a call. */
+export declare const POLL_INTERVAL_MS = 5000;
+/** Longest wait window a call can use: the budget less the result reserve. */
+export declare const MAX_WAIT_SECONDS: number;
+/** Job Dispatcher fair use asks for at most 30 jobs in flight per user; one address is one user. */
+export declare const MAX_IN_FLIGHT = 25;
+/** A tracked job nobody observed finishing frees its slot after this long (runs take ~10 min). */
+export declare const IN_FLIGHT_TTL_MS: number;
+export declare const MATCHES_URL = "https://www.ebi.ac.uk/interpro/matches/api/matches";
+export declare const JOB_DISPATCHER_BASE = "https://www.ebi.ac.uk/Tools/services/rest/iprscan6/";
+/** A tool invocation's single deadline, measured on the `performance` clock. */
+export interface ScanCall {
+    readonly ctx: Context;
+    readonly deadline: number;
+    readonly started: number;
+}
+/** Everything a finished iprscan6 job returns that the tools surface. */
+export interface JobResult {
+    readonly interproscanVersion: string;
+    readonly interproVersion: string;
+    readonly length: number;
+    readonly matches: ScanMatch[];
+    readonly md5: string;
+}
+/** Where a job stands when a call's wait window closes. */
+export type JobState = {
+    readonly status: 'submitted' | 'QUEUED' | 'RUNNING';
+} | {
+    readonly status: 'FINISHED';
+    readonly result: JobResult;
+};
+/** What one scan call produced. */
+export type ScanOutcome = {
+    readonly source: 'precalculated';
+    readonly matches: ScanMatch[];
+    readonly sourceUrl: string;
+} | ({
+    readonly source: 'interproscan';
+    readonly jobId: string;
+    readonly sourceUrl: string;
+} & JobState);
+/** Lookup, submission, polling, and result reads for one configured submission address. */
+export declare class SequenceScanService {
+    private readonly email;
+    private readonly fetch;
+    private readonly inFlight;
+    constructor(email: string | undefined, fetch?: InterproFetch);
+    /** Start the call's single deadline. */
+    begin(ctx: Context): ScanCall;
+    /**
+     * 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.
+     */
+    scan(call: ScanCall, sequence: {
+        readonly md5: string;
+        readonly residues: string;
+    }, waitMs: number, lookupOnly?: boolean): Promise<ScanOutcome>;
+    /** Read a job's state, waiting up to `waitMs` for it to finish; polls at least once. */
+    result(call: ScanCall, jobId: string, waitMs: number): Promise<JobState & {
+        sourceUrl: string;
+    }>;
+    private jobUrl;
+    /** Name the in-flight job in any failure after submission, so the caller keeps its handle. */
+    private withJob;
+    /** Precalculated matches, or undefined when UniParc holds no result for the MD5. */
+    private lookup;
+    /** Expire tracked jobs nobody saw finish, so the map stays bounded without a timer. */
+    private sweep;
+    /** Free the slot of a job observed in a terminal state. */
+    private release;
+    /**
+     * 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.
+     */
+    private submit;
+    /**
+     * Await a shared submission. A caller leaving early detaches only itself; the request is
+     * aborted when the last waiting caller leaves before it settles.
+     */
+    private join;
+    /** One `run` request, never retried: a lost response may still have created a job. */
+    private run;
+    /**
+     * The `<description>` of a Job Dispatcher XML error, single-line, bounded, and with the
+     * configured address replaced, since rejections can echo submitted fields.
+     */
+    private describeRejection;
+    /**
+     * 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.
+     */
+    private awaitJob;
+    private status;
+    private read;
+    /**
+     * 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.
+     */
+    private send;
+}
+/** Initialize the process service in createApp.setup with the configured submission address. */
+export declare function initSequenceScanService(email: string | undefined, fetch?: InterproFetch): void;
+/** Obtain the initialized process service. */
+export declare function getSequenceScanService(): SequenceScanService;
+//# sourceMappingURL=sequence-scan-service.d.ts.map

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

@@ -0,0 +1 @@
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