@cyanheads/interpro-mcp-server 0.1.3 → 0.2.0

package/dist/mcp-server/tools/definitions/interpro-scan-sequence.tool.d.ts

@@ -0,0 +1,168 @@
+/**
+ * @fileoverview Domain matches for a raw protein sequence: precalculated lookup, else InterProScan.
+ * @module mcp-server/tools/definitions/interpro-scan-sequence.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+export declare const interproScanSequence: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    sequence: z.ZodString;
+    waitSeconds: z.ZodDefault<z.ZodNumber>;
+    cursor: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+}, z.core.$strip>, z.ZodObject<{
+    source: z.ZodEnum<{
+        interproscan: "interproscan";
+        precalculated: "precalculated";
+    }>;
+    status: z.ZodEnum<{
+        finished: "finished";
+        queued: "queued";
+        running: "running";
+        submitted: "submitted";
+    }>;
+    jobId: z.ZodOptional<z.ZodString>;
+    md5: z.ZodOptional<z.ZodString>;
+    length: z.ZodOptional<z.ZodNumber>;
+    interproVersion: z.ZodOptional<z.ZodString>;
+    interproscanVersion: z.ZodOptional<z.ZodString>;
+    matches: z.ZodOptional<z.ZodArray<z.ZodObject<{
+        signature: z.ZodObject<{
+            accession: z.ZodString;
+            signatureLibraryRelease: z.ZodObject<{
+                library: z.ZodString;
+                version: z.ZodString;
+            }, z.core.$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.$catchall<z.ZodJSONSchema>>>>;
+    coverage: z.ZodOptional<z.ZodObject<{
+        totalMatches: z.ZodNumber;
+        offset: z.ZodNumber;
+        returnedMatches: z.ZodNumber;
+        hasMore: z.ZodBoolean;
+        nextCursor: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>>;
+    sourceUrl: z.ZodString;
+}, z.core.$strip>, readonly [{
+    readonly reason: "empty_sequence";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "The sequence holds no residue letters.";
+    readonly recovery: "Pass the protein residues as letters, optionally after one FASTA header line.";
+}, {
+    readonly reason: "invalid_residue";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "The sequence holds a character other than a residue letter or whitespace.";
+    readonly recovery: "Remove digits, gap characters, and stop symbols, then repeat with residue letters only.";
+}, {
+    readonly reason: "multiple_sequences";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "The input holds more than one FASTA record.";
+    readonly recovery: "Scan one sequence per call, repeating interpro_scan_sequence for each record.";
+}, {
+    readonly reason: "invalid_cursor";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "The cursor is malformed, belongs to another sequence or result, or the result changed.";
+    readonly recovery: "Repeat interpro_scan_sequence with the same sequence and no cursor.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "scan_not_configured";
+    readonly code: JsonRpcErrorCode.ConfigurationError;
+    readonly when: "The sequence has no precalculated matches and this server cannot submit InterProScan jobs.";
+    readonly recovery: "The server operator must configure InterProScan submission; sequences already in UniParc still return precalculated matches.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "rate_limited";
+    readonly code: JsonRpcErrorCode.RateLimited;
+    readonly when: "The server already holds its maximum of in-flight InterProScan jobs; nothing was submitted.";
+    readonly retryable: true;
+    readonly recovery: "Wait retryAfter seconds, then repeat the same interpro_scan_sequence call.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "scan_rejected";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "The Job Dispatcher rejected the submission with HTTP 400.";
+    readonly retryable: false;
+    readonly recovery: "Check that the input is one protein sequence; if the message names the contact address, the server operator must correct it.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "scan_failed";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "The InterProScan job ended with status ERROR or FAILURE.";
+    readonly retryable: false;
+    readonly recovery: "Repeat interpro_scan_sequence with the same sequence to start a new job.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "scan_not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "The Job Dispatcher no longer holds the job this sequence was waiting on.";
+    readonly retryable: false;
+    readonly recovery: "Repeat interpro_scan_sequence with the same sequence to start a new job.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "retry_deadline_exceeded";
+    readonly code: JsonRpcErrorCode.Timeout;
+    readonly when: "Lookup, submission, polling, and result reading exhausted the fifty-second call budget.";
+    readonly retryable: true;
+    readonly recovery: "Repeat the same call; a job already started is reused, or read it with interpro_get_scan_result using the jobId in the message.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_shape_invalid";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "The Matches API or Job Dispatcher returned a response this server cannot read.";
+    readonly retryable: false;
+    readonly recovery: "Retry the same call later; the upstream response format may have changed.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_response_too_large";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "An upstream response exceeds 4 MiB.";
+    readonly retryable: false;
+    readonly recovery: "Scan a shorter sequence, or split a multi-domain protein into regions and scan each.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_rejected";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "An upstream service returned an unhandled redirect or client rejection.";
+    readonly retryable: false;
+    readonly recovery: "Retry the same call later; the upstream service may be under maintenance.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_unavailable";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "An upstream service had a network or server failure.";
+    readonly retryable: true;
+    readonly recovery: "Retry the same call later; a job already started is reused rather than resubmitted.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_timeout";
+    readonly code: JsonRpcErrorCode.Timeout;
+    readonly when: "An upstream request returned HTTP 408/504 or exceeded its attempt deadline.";
+    readonly retryable: true;
+    readonly recovery: "Retry the same call after waiting; a job already started is reused.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_rate_limited";
+    readonly code: JsonRpcErrorCode.RateLimited;
+    readonly when: "An upstream service returned HTTP 429.";
+    readonly retryable: true;
+    readonly recovery: "Wait for retryAfter when supplied, then repeat the same call.";
+    readonly thrownBy: "service";
+}], {
+    notice: z.ZodOptional<z.ZodString>;
+    totalCount: z.ZodOptional<z.ZodNumber>;
+    truncated: z.ZodOptional<z.ZodBoolean>;
+    shown: z.ZodOptional<z.ZodNumber>;
+}>;
+//# sourceMappingURL=interpro-scan-sequence.tool.d.ts.map

package/dist/mcp-server/tools/definitions/interpro-scan-sequence.tool.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"interpro-scan-sequence.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/interpro-scan-sequence.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmBjE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAyM/B,CAAC"}

package/dist/mcp-server/tools/definitions/interpro-scan-sequence.tool.js

@@ -0,0 +1,187 @@
+/**
+ * @fileoverview Domain matches for a raw protein sequence: precalculated lookup, else InterProScan.
+ * @module mcp-server/tools/definitions/interpro-scan-sequence.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { formatInterpro } from '../../../services/interpro/format.js';
+import { optionalString } from '../../../services/interpro/schemas.js';
+import { buildScanOutput, decodeScanCursor, ScanEnrichment, ScanOutputSchema, } from '../../../services/sequence-scan/scan-output.js';
+import { codePointLabel, MAX_SEQUENCE_CHARS, parseSequence, } from '../../../services/sequence-scan/sequence.js';
+import { getSequenceScanService, MAX_WAIT_SECONDS, } from '../../../services/sequence-scan/sequence-scan-service.js';
+export const interproScanSequence = tool('interpro_scan_sequence', {
+    title: 'Scan a protein sequence',
+    description: 'Find InterPro domain, family, and site matches for one raw protein sequence that has no UniProt accession. Sequences already in UniParc return precalculated matches at once; any other sequence starts one InterProScan 6 job, which commonly runs about ten minutes, so the usual first result is a jobId to read with interpro_get_scan_result. Repeating a sequence whose job is still running returns the same jobId instead of starting another. Matches are InterProScan records verbatim, 1-based and inclusive, each naming its member database and release.',
+    annotations: {
+        readOnlyHint: false,
+        destructiveHint: false,
+        idempotentHint: false,
+        openWorldHint: true,
+    },
+    auth: ['tool:interpro_scan_sequence:write'],
+    input: z.object({
+        sequence: z
+            .string()
+            .max(MAX_SEQUENCE_CHARS)
+            .describe('One protein sequence as residue letters, optionally preceded by a single FASTA header line. Case, spaces, and line breaks are ignored; digits, gaps, and stop symbols (*) are rejected.'),
+        waitSeconds: z
+            .number()
+            .int()
+            .min(0)
+            .max(MAX_WAIT_SECONDS)
+            .default(30)
+            .describe('Seconds to wait for a newly started job to finish before returning its jobId; 0 starts the job and returns at once.'),
+        cursor: optionalString(z.string().trim().max(4096)).describe('Opaque coverage.nextCursor from an earlier call with this same sequence, to read the next segment of precalculated matches.'),
+    }),
+    output: ScanOutputSchema,
+    enrichment: ScanEnrichment,
+    errors: [
+        {
+            reason: 'empty_sequence',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'The sequence holds no residue letters.',
+            recovery: 'Pass the protein residues as letters, optionally after one FASTA header line.',
+        },
+        {
+            reason: 'invalid_residue',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'The sequence holds a character other than a residue letter or whitespace.',
+            recovery: 'Remove digits, gap characters, and stop symbols, then repeat with residue letters only.',
+        },
+        {
+            reason: 'multiple_sequences',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'The input holds more than one FASTA record.',
+            recovery: 'Scan one sequence per call, repeating interpro_scan_sequence for each record.',
+        },
+        {
+            reason: 'invalid_cursor',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'The cursor is malformed, belongs to another sequence or result, or the result changed.',
+            recovery: 'Repeat interpro_scan_sequence with the same sequence and no cursor.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'scan_not_configured',
+            code: JsonRpcErrorCode.ConfigurationError,
+            when: 'The sequence has no precalculated matches and this server cannot submit InterProScan jobs.',
+            recovery: 'The server operator must configure InterProScan submission; sequences already in UniParc still return precalculated matches.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'rate_limited',
+            code: JsonRpcErrorCode.RateLimited,
+            when: 'The server already holds its maximum of in-flight InterProScan jobs; nothing was submitted.',
+            retryable: true,
+            recovery: 'Wait retryAfter seconds, then repeat the same interpro_scan_sequence call.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'scan_rejected',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'The Job Dispatcher rejected the submission with HTTP 400.',
+            retryable: false,
+            recovery: 'Check that the input is one protein sequence; if the message names the contact address, the server operator must correct it.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'scan_failed',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'The InterProScan job ended with status ERROR or FAILURE.',
+            retryable: false,
+            recovery: 'Repeat interpro_scan_sequence with the same sequence to start a new job.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'scan_not_found',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'The Job Dispatcher no longer holds the job this sequence was waiting on.',
+            retryable: false,
+            recovery: 'Repeat interpro_scan_sequence with the same sequence to start a new job.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'retry_deadline_exceeded',
+            code: JsonRpcErrorCode.Timeout,
+            when: 'Lookup, submission, polling, and result reading exhausted the fifty-second call budget.',
+            retryable: true,
+            recovery: 'Repeat the same call; a job already started is reused, or read it with interpro_get_scan_result using the jobId in the message.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_shape_invalid',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'The Matches API or Job Dispatcher returned a response this server cannot read.',
+            retryable: false,
+            recovery: 'Retry the same call later; the upstream response format may have changed.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_response_too_large',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'An upstream response exceeds 4 MiB.',
+            retryable: false,
+            recovery: 'Scan a shorter sequence, or split a multi-domain protein into regions and scan each.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_rejected',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'An upstream service returned an unhandled redirect or client rejection.',
+            retryable: false,
+            recovery: 'Retry the same call later; the upstream service may be under maintenance.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_unavailable',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'An upstream service had a network or server failure.',
+            retryable: true,
+            recovery: 'Retry the same call later; a job already started is reused rather than resubmitted.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_timeout',
+            code: JsonRpcErrorCode.Timeout,
+            when: 'An upstream request returned HTTP 408/504 or exceeded its attempt deadline.',
+            retryable: true,
+            recovery: 'Retry the same call after waiting; a job already started is reused.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_rate_limited',
+            code: JsonRpcErrorCode.RateLimited,
+            when: 'An upstream service returned HTTP 429.',
+            retryable: true,
+            recovery: 'Wait for retryAfter when supplied, then repeat the same call.',
+            thrownBy: 'service',
+        },
+    ],
+    async handler(input, ctx) {
+        const parsed = parseSequence(input.sequence);
+        if (!parsed.ok)
+            switch (parsed.reason) {
+                case 'empty_sequence':
+                    throw ctx.fail('empty_sequence', 'The sequence holds no residue letters.');
+                case 'multiple_sequences':
+                    throw ctx.fail('multiple_sequences', `A second FASTA record starts at character ${parsed.position}; scan one sequence per call.`);
+                case 'invalid_residue':
+                    throw ctx.fail('invalid_residue', `Character ${codePointLabel(parsed.codePoint)} at position ${parsed.position} is not a protein residue letter.`);
+            }
+        const { md5, residues } = parsed;
+        const start = decodeScanCursor(input.cursor, { md5 });
+        const service = getSequenceScanService();
+        const outcome = await service.scan(service.begin(ctx), { md5, residues }, input.waitSeconds * 1000, start !== undefined);
+        return buildScanOutput(ctx.enrich, outcome, {
+            md5,
+            length: residues.length,
+            ...(start ? { start } : {}),
+            // The sequence is not echoed (titin is 34 kB), so the precalculated call is named, not printed.
+            continuation: (cursor) => outcome.source === 'precalculated'
+                ? 'interpro_scan_sequence, passing the same sequence and cursor set to coverage.nextCursor,'
+                : `interpro_get_scan_result ${JSON.stringify({ jobId: outcome.jobId, cursor })}`,
+        });
+    },
+    format: formatInterpro,
+});
+//# sourceMappingURL=interpro-scan-sequence.tool.js.map

package/dist/mcp-server/tools/definitions/interpro-scan-sequence.tool.js.map

@@ -0,0 +1 @@
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package/dist/services/interpro/http-adapter.d.ts

@@ -1,11 +1,20 @@
 /**
- * @fileoverview Bounded HTTP/1.1 adapter for InterPro's malformed bodyless 204 responses.
+ * @fileoverview Bounded HTTP/1.1 adapter for InterPro's malformed bodyless 204 responses, also
+ * carrying the Matches API and Job Dispatcher requests on the same fixed origin.
  * @module services/interpro/http-adapter
  */
+import { type McpError } from '@cyanheads/mcp-ts-core/errors';
 /** Maximum decoded response size, shared by native and injected transports. */
 export declare const MAX_RESPONSE_BYTES: number;
 /** Fetch-compatible injection seam; callers supply the composed request signal. */
 export type InterproFetch = (url: string, init: RequestInit) => Promise<Response>;
-/** Collect one response without following redirects or retaining malformed connections. */
+/**
+ * Classify a non-OK upstream response: 5xx (except 501), 408, and 429 are retryable; any other
+ * client status is reported as a non-retryable service failure, not a caller error.
+ */
+export declare function upstreamStatusError(response: Response, service: string): Promise<McpError>;
+/** A transport whose whole-response backstop is `attemptMs`; callers bound attempts more tightly. */
+export declare const createInterproHttpFetch: (attemptMs: number) => InterproFetch;
+/** The InterPro API transport: small JSON pages, so 15 seconds bounds each whole response. */
 export declare const interproHttpFetch: InterproFetch;
 //# sourceMappingURL=http-adapter.d.ts.map

package/dist/services/interpro/http-adapter.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"http-adapter.d.ts","sourceRoot":"","sources":["../../../src/services/interpro/http-adapter.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAKH,OAAO,EAEL,KAAK,QAAQ,EAGd,MAAM,+BAA+B,CAAC;AAIvC,+EAA+E;AAC/E,eAAO,MAAM,kBAAkB,QAAkB,CAAC;AAClD,mFAAmF;AACnF,MAAM,MAAM,aAAa,GAAG,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,KAAK,OAAO,CAAC,QAAQ,CAAC,CAAC;AAiMlF;;;GAGG;AACH,wBAAsB,mBAAmB,CAAC,QAAQ,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAsBhG;AAED,qGAAqG;AACrG,eAAO,MAAM,uBAAuB,cACtB,MAAM,KAAG,aAEU,CAAC;AAElC,8FAA8F;AAC9F,eAAO,MAAM,iBAAiB,EAAE,aAA+C,CAAC"}

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

@@ -1,17 +1,31 @@
 /**
- * @fileoverview Bounded HTTP/1.1 adapter for InterPro's malformed bodyless 204 responses.
+ * @fileoverview Bounded HTTP/1.1 adapter for InterPro's malformed bodyless 204 responses, also
+ * carrying the Matches API and Job Dispatcher requests on the same fixed origin.
  * @module services/interpro/http-adapter
  */
 import { request } from 'node:https';
-import { serviceUnavailable, timeout } from '@cyanheads/mcp-ts-core/errors';
+import { JsonRpcErrorCode, serviceUnavailable, timeout, } from '@cyanheads/mcp-ts-core/errors';
+import { httpErrorFromResponse } from '@cyanheads/mcp-ts-core/utils';
 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) => {
+/**
+ * The documented path prefixes on the fixed origin: the InterPro API, the InterPro Matches API,
+ * and the Job Dispatcher's InterProScan 6 service. The URL parser resolves dot segments first.
+ */
+const ALLOWED_PATH_PREFIXES = [
+    '/interpro/api/',
+    '/interpro/matches/api/',
+    '/Tools/services/rest/iprscan6/',
+];
+/**
+ * Collect one response without following redirects or retaining malformed connections, failing
+ * as `upstream_timeout` when the whole response outlasts `attemptMs`.
+ */
+const collect = (url, init, attemptMs) => new Promise((resolve, reject) => {
     const target = new URL(url);
     if (target.origin !== new URL(API_BASE).origin ||
-        !target.pathname.startsWith('/interpro/api/')) {
+        !ALLOWED_PATH_PREFIXES.some((prefix) => target.pathname.startsWith(prefix))) {
         reject(serviceUnavailable('InterPro request left the fixed API origin.', {
             reason: 'upstream_rejected',
             retryable: false,
@@ -39,13 +53,26 @@ export const interproHttpFetch = (url, init) => new Promise((resolve, reject) =>
     const timer = setTimeout(() => fail(timeout('InterPro response exceeded its attempt deadline.', {
         reason: 'upstream_timeout',
         retryable: true,
-    })), 15_000);
+    })), attemptMs);
     const connectionOptions = { ALPNProtocols: ['http/1.1'] };
+    const body = typeof init.body === 'string' ? init.body : undefined;
+    const requestHeaders = new Headers(init.headers);
+    const accept = requestHeaders.get('accept') ?? 'application/json';
+    const contentType = requestHeaders.get('content-type');
     const req = request(target, {
         ...connectionOptions,
-        method: 'GET',
+        method: body === undefined ? 'GET' : 'POST',
         agent: false,
-        headers: { Accept: 'application/json', 'Accept-Encoding': 'identity' },
+        headers: {
+            Accept: accept,
+            'Accept-Encoding': 'identity',
+            ...(body === undefined
+                ? {}
+                : {
+                    'Content-Type': contentType ?? 'application/json',
+                    'Content-Length': String(Buffer.byteLength(body, 'utf8')),
+                }),
+        },
     });
     req.on('error', (cause) => fail(serviceUnavailable('InterPro connection failed.', { reason: 'upstream_unavailable', retryable: true }, { cause })));
     req.on('close', () => {
@@ -128,7 +155,38 @@ export const interproHttpFetch = (url, init) => new Promise((resolve, reject) =>
     signal?.addEventListener('abort', abort, { once: true });
     if (signal?.aborted)
         abort();
-    else
+    else if (body === undefined)
         req.end();
+    else
+        req.end(body);
 });
+/**
+ * Classify a non-OK upstream response: 5xx (except 501), 408, and 429 are retryable; any other
+ * client status is reported as a non-retryable service failure, not a caller error.
+ */
+export async function upstreamStatusError(response, service) {
+    const status = response.status;
+    const reason = status === 408 || status === 504
+        ? 'upstream_timeout'
+        : status === 429
+            ? 'upstream_rate_limited'
+            : status >= 500
+                ? 'upstream_unavailable'
+                : 'upstream_rejected';
+    return await httpErrorFromResponse(response, {
+        service,
+        captureBody: false,
+        codeOverride: (value) => value < 500 && value !== 408 && value !== 429
+            ? JsonRpcErrorCode.ServiceUnavailable
+            : undefined,
+        data: {
+            reason,
+            retryable: (status >= 500 && status !== 501) || status === 408 || status === 429,
+        },
+    });
+}
+/** A transport whose whole-response backstop is `attemptMs`; callers bound attempts more tightly. */
+export const createInterproHttpFetch = (attemptMs) => (url, init) => collect(url, init, attemptMs);
+/** The InterPro API transport: small JSON pages, so 15 seconds bounds each whole response. */
+export const interproHttpFetch = createInterproHttpFetch(15_000);
 //# sourceMappingURL=http-adapter.js.map

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

@@ -1 +1 @@
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package/dist/services/interpro/interpro-service.d.ts

@@ -15,7 +15,7 @@ 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 reason: 'entry_not_found' | 'protein_not_found' | 'clan_not_found' | 'structure_not_found';
     readonly sourceDatabase: string;
 }
 /** Domain status handling selected by the tool workflow. */

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

@@ -1 +1 @@
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package/dist/services/interpro/interpro-service.js

@@ -1,7 +1,7 @@
 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 { McpError, notFound, serviceUnavailable, timeout, validationError, } from '@cyanheads/mcp-ts-core/errors';
+import { createPacer, defaultIsTransient, withRetry } from '@cyanheads/mcp-ts-core/utils';
+import { interproHttpFetch, MAX_RESPONSE_BYTES, upstreamStatusError, } from './http-adapter.js';
 import { apiUrl } from './routing.js';
 import { isAccession, JsonObjectSchema, JsonValueSchema } from './schemas.js';
 const pacer = createPacer({
@@ -28,6 +28,7 @@ const RECORD_NOUNS = {
     entry_not_found: 'entry',
     clan_not_found: 'set',
     protein_not_found: 'protein',
+    structure_not_found: 'structure',
 };
 /** 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}`;
@@ -116,27 +117,8 @@ export class InterproService {
                         ...(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,
-                        },
-                    });
-                }
+                if (!response.ok)
+                    throw await upstreamStatusError(response, 'InterPro');
                 const encoding = response.headers.get('content-encoding');
                 if (encoding && encoding.toLowerCase() !== 'identity')
                     throw serviceUnavailable('InterPro returned an unexpected content encoding.', {