@cyanheads/interpro-mcp-server 0.1.2 → 0.2.0

package/dist/mcp-server/tools/definitions/interpro-get-protein-domains.tool.js

@@ -8,7 +8,7 @@ import { BUDGET_LABEL, fitWithinBudget, jsonByteLength, RESPONSE_BYTE_BUDGET, }
 import { compareText, continuation, cursorScope, decodePositionCursor, encodePositionCursor, } from '../../../services/interpro/cursors.js';
 import { formatInterpro, normalizeImages } from '../../../services/interpro/format.js';
 import { getInterproService } from '../../../services/interpro/interpro-service.js';
-import { detailSchema, ExtraFeaturesSchema, isAccession, listSchema, MatchSchema, optionalString, ProteinAccessionSchema, ProteinMetadataSchema, } from '../../../services/interpro/schemas.js';
+import { detailSchema, ExtraFeaturesSchema, isAccession, listSchema, MatchSchema, optionalString, ProteinAccessionSchema, ProteinMetadataSchema, ResidueAnnotationsSchema, } from '../../../services/interpro/schemas.js';
 import { UPSTREAM_ERRORS } from '../../../services/interpro/upstream-errors.js';
 const OPERATION = 'interpro_get_protein_domains';
 const PAGE_SIZE = 200;
@@ -21,18 +21,22 @@ const SelectionSchema = z.object({
         .optional()
         .describe('Selected 1-based inclusive residue position.'),
     includeExtraFeatures: z.boolean().describe('Whether extra predicted features were requested.'),
+    includeResidueAnnotations: z
+        .literal(true)
+        .optional()
+        .describe('Present only when residue rules were requested.'),
 });
 const CoverageSchema = z.object({
     totalMatches: z
         .number()
         .int()
         .nonnegative()
-        .describe('Upstream unfiltered total match count; a segment holding only extra features repeats the count the match list reported.'),
+        .describe('Upstream unfiltered total match count; extra-feature-only and residue-rule-only segments repeat the count reported by the match list.'),
     scannedMatches: z
         .number()
         .int()
         .nonnegative()
-        .describe('Match records this segment covered, before residue filtering; across a complete walk the segments sum to totalMatches.'),
+        .describe("Match records this segment covered, before residue filtering; totalMatches is upstream's reported count, and a complete walk can cover a different number."),
     returnedMatches: z
         .number()
         .int()
@@ -50,22 +54,34 @@ const CoverageSchema = z.object({
         .nonnegative()
         .optional()
         .describe('Extra features in this segment; present with extraFeatures.'),
+    totalResidueAnnotations: z
+        .number()
+        .int()
+        .nonnegative()
+        .optional()
+        .describe('Selected residue rules; present only when the residue stage is reached.'),
+    returnedResidueAnnotations: z
+        .number()
+        .int()
+        .nonnegative()
+        .optional()
+        .describe('Whole residue rules returned in this segment.'),
     complete: z
         .boolean()
-        .describe('True only when this call starts without a cursor and returns the whole map: every match and every requested extra feature.'),
+        .describe('True only when this call starts without a cursor and returns every match, requested extra feature, and requested residue rule.'),
     hasMore: z
         .boolean()
-        .describe('Whether another segment remains, holding more matches or requested extra features.'),
+        .describe('Whether another segment remains, holding matches, requested extras, or requested residue rules.'),
     nextCursor: z
         .string()
         .optional()
-        .describe('Opaque cursor resuming at the next whole match or extra feature, for the same protein and selection.'),
+        .describe('Opaque cursor resuming at the next whole match, extra feature, or residue rule for the same protein and selection.'),
 });
 /**
  * Where a continuation resumes: `skip` records into an upstream match page (`page` is that
  * page's upstream cursor, absent for the first page), or `features` selected extra features into
- * the feature list that follows the last match. `after` names the last record an earlier segment
- * covered, so a page or feature list that changed since the cursor was minted is rejected.
+ * the feature list that follows the last match, or `residues` selected rules after the extras.
+ * `after` names the last record an earlier segment covered, so changed lists are rejected.
  */
 const PositionSchema = z.union([
     z
@@ -85,6 +101,14 @@ const PositionSchema = z.union([
     })
         .strict()
         .refine((point) => point.features > 0 === (point.after !== undefined)),
+    z
+        .object({
+        residues: z.number().int().nonnegative(),
+        after: z.string().min(1).optional(),
+        totalMatches: z.number().int().nonnegative(),
+    })
+        .strict()
+        .refine((point) => point.residues > 0 === (point.after !== undefined)),
 ]);
 function contains(locations, position) {
     return locations.some((location) => location.fragments.some((fragment) => fragment.start <= position && position <= fragment.end));
@@ -101,7 +125,7 @@ function byCoordinate(left, right) {
 /** Map signatures to sequence coordinates in budget-bounded segments with explicit coverage. */
 export const interproGetProteinDomains = tool('interpro_get_protein_domains', {
     title: 'Map protein domains',
-    description: 'Retrieve InterPro and member-signature matches on a canonical UniProt protein, preserving every location and discontinuous fragment. Optionally retain matches covering a residue and include extra predicted features. Large maps arrive in segments of whole matches that fit the response budget: the first segment carries the protein metadata, requested extra features follow the last match, and coverage.nextCursor continues until hasMore is false.',
+    description: 'Retrieve InterPro and member-signature matches on a canonical UniProt protein, preserving every location and discontinuous fragment. Optionally select records covering a residue, include extra predicted features, and include functional residue rules with provenance. Budgeted segments hold whole records in order: matches, requested extras, then requested residue rules sorted by key. The first segment carries protein metadata; continue coverage.nextCursor until hasMore is false.',
     annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
     auth: ['tool:interpro_get_protein_domains:read'],
     input: z.object({
@@ -116,7 +140,11 @@ export const interproGetProteinDomains = tool('interpro_get_protein_domains', {
             .boolean()
             .default(false)
             .describe('Include complete extra predicted features, returned after the last match; defaults to false.'),
-        cursor: optionalString(z.string().trim().max(4096)).describe('Opaque coverage.nextCursor with unchanged accession, residuePosition, and includeExtraFeatures.'),
+        includeResidueAnnotations: z
+            .boolean()
+            .default(false)
+            .describe('Include complete functional residue rules after matches and requested extras; defaults to false.'),
+        cursor: optionalString(z.string().trim().max(4096)).describe('Opaque coverage.nextCursor with unchanged accession, residuePosition, includeExtraFeatures, and includeResidueAnnotations.'),
     }),
     output: z.object({
         accession: z.string().describe('Canonical UniProt accession.'),
@@ -125,8 +153,9 @@ export const interproGetProteinDomains = tool('interpro_get_protein_domains', {
             .array(MatchSchema.describe('Complete entry match record.'))
             .describe('Whole selected match records in this segment, sorted by earliest coordinate then accession; a match is never split across segments.'),
         extraFeatures: ExtraFeaturesSchema.optional().describe('Whole selected extra features in this segment, in feature-key order; {} when none are selected. Omitted when not requested or when this segment ends before the features that follow the last match.'),
-        selection: SelectionSchema.describe('Applied residue and extra-feature selection.'),
-        coverage: CoverageSchema.describe('Where this segment sits in the protein map: every match, then requested extra features.'),
+        residueAnnotations: ResidueAnnotationsSchema.optional().describe('Whole selected residue rules sorted by key; {} means the stage was reached with no selected rules. Omitted when unrequested or unreached.'),
+        selection: SelectionSchema.describe('Applied residue, extra-feature, and residue-rule selection.'),
+        coverage: CoverageSchema.describe('Where this segment sits in the protein map: matches, requested extra features, then requested residue rules.'),
         url: z.string().describe('Canonical protein website URL.'),
         sourceUrl: z.string().describe('Official protein API source URL.'),
     }),
@@ -146,9 +175,9 @@ export const interproGetProteinDomains = tool('interpro_get_protein_domains', {
         {
             reason: 'retry_deadline_exceeded',
             code: JsonRpcErrorCode.Timeout,
-            when: 'The shared fifty-second budget expires across protein metadata, match pages, and extra features.',
+            when: 'The shared fifty-second budget expires across metadata, match pages, extra features, and residue rules.',
             retryable: true,
-            recovery: 'Retry interpro_get_protein_domains after waiting; omit extra features when they are not needed.',
+            recovery: 'Retry interpro_get_protein_domains after waiting; omit optional annotations when they are not needed.',
             thrownBy: 'service',
         },
         {
@@ -198,12 +227,15 @@ export const interproGetProteinDomains = tool('interpro_get_protein_domains', {
         const selection = {
             ...(residue !== undefined ? { residuePosition: residue } : {}),
             includeExtraFeatures: input.includeExtraFeatures,
+            ...(input.includeResidueAnnotations ? { includeResidueAnnotations: true } : {}),
         };
         const scope = { accession, ...selection };
         const start = decodePositionCursor(input.cursor, OPERATION, scope, PositionSchema);
         const stale = () => ctx.fail('invalid_cursor', 'Cursor no longer matches the InterPro records it resumes inside.');
         if (start && 'features' in start && !input.includeExtraFeatures)
             throw stale();
+        if (start && 'residues' in start && !input.includeResidueAnnotations)
+            throw stale();
         const resumed = start !== undefined;
         const covers = (locations) => residue === undefined || contains(locations, residue);
         const service = getInterproService();
@@ -214,11 +246,12 @@ export const interproGetProteinDomains = tool('interpro_get_protein_domains', {
         const protein = normalizeImages(detail.data.metadata);
         if (residue !== undefined && residue > protein.length)
             throw ctx.fail('residue_out_of_range', `Residue ${residue} exceeds the ${protein.length}-residue length of ${accession}.`, { accession, proteinLength: protein.length, residuePosition: residue });
-        /** Whole candidate items in walk order: every match, then every selected extra feature. */
+        /** Whole candidate items: matches, selected extra features, then selected residue rules. */
         const items = [];
         let scanned = 0;
-        let totalMatches = start && 'features' in start ? start.totalMatches : 0;
+        let totalMatches = start && !('skip' in start) ? start.totalMatches : 0;
         let totalFeatures;
+        let totalResidueAnnotations;
         /** Where the walk resumes after the last gathered item; undefined once the walk ends. */
         let end;
         const segment = (count) => {
@@ -226,18 +259,24 @@ export const interproGetProteinDomains = tool('interpro_get_protein_domains', {
             const resume = stop ? stop.at : end;
             const matches = [];
             const features = [];
+            const residues = [];
             for (const item of items.slice(0, count))
                 if (item.kind === 'match')
                     matches.push(item.match);
-                else
+                else if (item.kind === 'feature')
                     features.push([item.key, item.feature]);
+                else
+                    residues.push([item.key, item.rule]);
             const featureTotal = totalFeatures;
-            const reachedFeatures = featureTotal !== undefined && (features.length > 0 || resume === undefined);
+            const reachedFeatures = featureTotal !== undefined &&
+                (features.length > 0 || resume === undefined || 'residues' in resume);
+            const reachedResidues = totalResidueAnnotations !== undefined && (residues.length > 0 || resume === undefined);
             return {
                 accession,
                 ...(resumed ? {} : { protein }),
                 matches: matches.toSorted(byCoordinate),
                 ...(reachedFeatures ? { extraFeatures: Object.fromEntries(features) } : {}),
+                ...(reachedResidues ? { residueAnnotations: Object.fromEntries(residues) } : {}),
                 selection,
                 coverage: {
                     totalMatches,
@@ -246,6 +285,9 @@ export const interproGetProteinDomains = tool('interpro_get_protein_domains', {
                     ...(reachedFeatures
                         ? { totalFeatures: featureTotal, returnedFeatures: features.length }
                         : {}),
+                    ...(reachedResidues
+                        ? { totalResidueAnnotations, returnedResidueAnnotations: residues.length }
+                        : {}),
                     complete: !resumed && resume === undefined,
                     hasMore: resume !== undefined,
                     ...(resume ? { nextCursor: encodePositionCursor(OPERATION, scope, resume) } : {}),
@@ -293,7 +335,7 @@ export const interproGetProteinDomains = tool('interpro_get_protein_domains', {
                     break;
             }
         }
-        if (input.includeExtraFeatures && end === undefined) {
+        if (input.includeExtraFeatures && !(start && 'residues' in start) && end === undefined) {
             // Read extras only when the matches fit beside the cursor that would resume at them.
             end = { features: 0, totalMatches };
             if (!overflows()) {
@@ -325,20 +367,53 @@ export const interproGetProteinDomains = tool('interpro_get_protein_domains', {
                 }
             }
         }
+        if (input.includeResidueAnnotations && end === undefined) {
+            end = { residues: 0, totalMatches };
+            if (!overflows()) {
+                end = undefined;
+                const response = await service.request(call, ['protein', 'uniprot', accession], { residues: '' }, ResidueAnnotationsSchema);
+                if (!response.data)
+                    throw ctx.fail('upstream_shape_invalid', 'Residue annotation response is missing.');
+                const selected = Object.entries(normalizeImages(response.data))
+                    .filter(([, rule]) => covers(rule.locations))
+                    .toSorted(([a], [b]) => compareText(a, b));
+                const resumeAt = start && 'residues' in start ? start : undefined;
+                const skip = resumeAt?.residues ?? 0;
+                if (skip > 0 && (skip >= selected.length || selected[skip - 1]?.[0] !== resumeAt?.after))
+                    throw stale();
+                totalResidueAnnotations = selected.length;
+                for (let index = skip; index < selected.length; index++) {
+                    const [key, rule] = selected[index];
+                    items.push({
+                        kind: 'residue',
+                        key,
+                        rule,
+                        scannedBefore: scanned,
+                        at: {
+                            residues: index,
+                            ...(index ? { after: selected[index - 1][0] } : {}),
+                            totalMatches,
+                        },
+                    });
+                }
+            }
+        }
         const { count, output, oversized } = fitWithinBudget(items.length, segment);
         const { coverage } = output;
         const stop = items[count];
         const notices = [];
         if (oversized) {
             const only = items[0];
-            const [named, unnamed, id] = only.kind === 'feature'
-                ? ['Extra feature', 'This extra feature', only.key]
+            const [named, unnamed, id] = only.kind !== 'match'
+                ? only.kind === 'feature'
+                    ? ['Extra feature', 'This extra feature', only.key]
+                    : ['Residue rule', 'This residue rule', only.key]
                 : ['Match', 'This match', only.match.metadata.accession];
             notices.push(`${isAccession(id) ? `${named} ${id}` : unnamed} cannot be split, so this segment holds it alone and exceeds the ${BUDGET_LABEL}.`);
         }
         if (coverage.nextCursor) {
             const reason = stop
-                ? ` and stopped at the ${BUDGET_LABEL} before the next whole ${stop.kind === 'match' ? 'match' : 'extra feature'}`
+                ? ` and stopped at the ${BUDGET_LABEL} before the next whole ${stop.kind === 'match' ? 'match' : stop.kind === 'feature' ? 'extra feature' : 'residue rule'}`
                 : oversized
                     ? ''
                     : ` and reached the ${MAX_PAGES}-page read limit after ${coverage.scannedMatches} match records`;
@@ -346,13 +421,14 @@ export const interproGetProteinDomains = tool('interpro_get_protein_domains', {
                 accession,
                 ...(residue !== undefined ? { residuePosition: residue } : {}),
                 ...(input.includeExtraFeatures ? { includeExtraFeatures: true } : {}),
+                ...(input.includeResidueAnnotations ? { includeResidueAnnotations: true } : {}),
                 cursor: coverage.nextCursor,
             };
             notices.push(`This segment covers part of the protein map${reason}. Continue with interpro_get_protein_domains ${JSON.stringify(nextCall)} before concluding that a residue has no annotation.`);
         }
         else if (resumed)
             notices.push('This is the final resumed segment. Only the combined segments cover the traversal; upstream pagination is not a snapshot.' +
-                (coverage.returnedMatches || 'features' in start
+                (coverage.returnedMatches || !('skip' in start)
                     ? ''
                     : ' No match was selected in this segment.'));
         else if (!coverage.returnedMatches)

package/dist/mcp-server/tools/definitions/interpro-get-protein-domains.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/interpro-get-scan-result.tool.d.ts

@@ -0,0 +1,133 @@
+/**
+ * @fileoverview Read-only status and matches of an InterProScan job started by interpro_scan_sequence.
+ * @module mcp-server/tools/definitions/interpro-get-scan-result.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+export declare const interproGetScanResult: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    jobId: 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: "invalid_cursor";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "The cursor is malformed, belongs to another job, or no longer fits the result.";
+    readonly recovery: "Repeat interpro_get_scan_result with the same jobId and no cursor.";
+    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: "Start a new job by passing the sequence to interpro_scan_sequence again.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "scan_not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "The Job Dispatcher has no such job: it never existed or expired after seven days.";
+    readonly retryable: false;
+    readonly recovery: "Start a new job by passing the sequence to interpro_scan_sequence again.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "retry_deadline_exceeded";
+    readonly code: JsonRpcErrorCode.Timeout;
+    readonly when: "Polling and result reading exhausted the fifty-second call budget.";
+    readonly retryable: true;
+    readonly recovery: "Repeat the same interpro_get_scan_result call; the job keeps running upstream.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_shape_invalid";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "The 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: "The job result 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: "The Job Dispatcher 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: "The Job Dispatcher had a network or server failure.";
+    readonly retryable: true;
+    readonly recovery: "Retry the same interpro_get_scan_result call later; the job keeps running upstream.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_timeout";
+    readonly code: JsonRpcErrorCode.Timeout;
+    readonly when: "A Job Dispatcher request returned HTTP 408/504 or exceeded its attempt deadline.";
+    readonly retryable: true;
+    readonly recovery: "Retry the same interpro_get_scan_result call after waiting a few seconds.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_rate_limited";
+    readonly code: JsonRpcErrorCode.RateLimited;
+    readonly when: "The Job Dispatcher 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-get-scan-result.tool.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/interpro-get-scan-result.tool.js

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+/**
+ * @fileoverview Read-only status and matches of an InterProScan job started by interpro_scan_sequence.
+ * @module mcp-server/tools/definitions/interpro-get-scan-result.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 { JOB_ID_PATTERN, MAX_JOB_ID_CHARS } from '../../../services/sequence-scan/scan-schemas.js';
+import { getSequenceScanService, MAX_WAIT_SECONDS, } from '../../../services/sequence-scan/sequence-scan-service.js';
+export const interproGetScanResult = tool('interpro_get_scan_result', {
+    title: 'Read an InterProScan job',
+    description: 'Check an InterProScan job started by interpro_scan_sequence, waiting up to waitSeconds for it to finish. Returns the matches once finished, otherwise its queued or running status to check again later. Matches are InterProScan records verbatim, 1-based and inclusive, with the InterPro and InterProScan versions that produced them. Jobs and their results expire seven days after submission.',
+    annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
+    auth: ['tool:interpro_get_scan_result:read'],
+    input: z.object({
+        jobId: z
+            .string()
+            .trim()
+            .max(MAX_JOB_ID_CHARS)
+            .regex(JOB_ID_PATTERN, 'Expected an iprscan6 job ID such as iprscan6-R20261028-131532-0930-13189043-p1m.')
+            .describe('jobId returned by interpro_scan_sequence, such as iprscan6-R20261028-131532-0930-13189043-p1m.'),
+        waitSeconds: z
+            .number()
+            .int()
+            .min(0)
+            .max(MAX_WAIT_SECONDS)
+            .default(30)
+            .describe('Seconds to wait for a pending job to finish; 0 checks its status once and returns.'),
+        cursor: optionalString(z.string().trim().max(4096)).describe('Opaque coverage.nextCursor from an earlier result for this same jobId, to read the next segment.'),
+    }),
+    output: ScanOutputSchema,
+    enrichment: ScanEnrichment,
+    errors: [
+        {
+            reason: 'invalid_cursor',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'The cursor is malformed, belongs to another job, or no longer fits the result.',
+            recovery: 'Repeat interpro_get_scan_result with the same jobId and no cursor.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'scan_failed',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'The InterProScan job ended with status ERROR or FAILURE.',
+            retryable: false,
+            recovery: 'Start a new job by passing the sequence to interpro_scan_sequence again.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'scan_not_found',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'The Job Dispatcher has no such job: it never existed or expired after seven days.',
+            retryable: false,
+            recovery: 'Start a new job by passing the sequence to interpro_scan_sequence again.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'retry_deadline_exceeded',
+            code: JsonRpcErrorCode.Timeout,
+            when: 'Polling and result reading exhausted the fifty-second call budget.',
+            retryable: true,
+            recovery: 'Repeat the same interpro_get_scan_result call; the job keeps running upstream.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_shape_invalid',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'The 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: 'The job result 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: 'The Job Dispatcher 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: 'The Job Dispatcher had a network or server failure.',
+            retryable: true,
+            recovery: 'Retry the same interpro_get_scan_result call later; the job keeps running upstream.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_timeout',
+            code: JsonRpcErrorCode.Timeout,
+            when: 'A Job Dispatcher request returned HTTP 408/504 or exceeded its attempt deadline.',
+            retryable: true,
+            recovery: 'Retry the same interpro_get_scan_result call after waiting a few seconds.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_rate_limited',
+            code: JsonRpcErrorCode.RateLimited,
+            when: 'The Job Dispatcher returned HTTP 429.',
+            retryable: true,
+            recovery: 'Wait for retryAfter when supplied, then repeat the same call.',
+            thrownBy: 'service',
+        },
+    ],
+    async handler(input, ctx) {
+        const { jobId } = input;
+        const start = decodeScanCursor(input.cursor, { jobId });
+        const service = getSequenceScanService();
+        const state = await service.result(service.begin(ctx), jobId, input.waitSeconds * 1000);
+        return buildScanOutput(ctx.enrich, { source: 'interproscan', jobId, ...state }, {
+            ...(start ? { start } : {}),
+            continuation: (cursor) => `interpro_get_scan_result ${JSON.stringify({ jobId, cursor })}`,
+        });
+    },
+    format: formatInterpro,
+});
+//# sourceMappingURL=interpro-get-scan-result.tool.js.map

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