npm - @cyanheads/interpro-mcp-server - Versions diffs - 0.1.3 → 0.2.0 - Mend

@cyanheads/interpro-mcp-server 0.1.3 → 0.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (71) hide show

package/dist/mcp-server/tools/definitions/interpro-find-proteins-by-domain.tool.js CHANGED Viewed

@@ -26,7 +26,16 @@ const QuerySchema = z.object({
         .string()
         .optional()
         .describe('Applied lowercase Pfam architecture grouping identifier.'),
+    proteomeId: z.string().optional().describe('Applied uppercase UniProt proteome accession.'),
 });
+const ProteomesSchema = z
+    .array(z
+    .object({
+    accession: z.string().describe('Proteome accession as upstream writes it, lowercase.'),
+})
+    .catchall(JsonValueSchema)
+    .describe('Complete proteome record.'))
+    .describe('Complete records of the selected proteome, preserved verbatim.');
 const ProteinResultSchema = z
     .object({
     metadata: ProteinMetadataSchema.describe('Complete sparse protein summary.'),
@@ -63,26 +72,27 @@ const ProteinResultSchema = z
 })
     .catchall(JsonValueSchema)
     .describe('Complete protein discovery record.');
+const ProteomeResultSchema = ProteinResultSchema.extend({ proteomes: ProteomesSchema }).describe('Complete proteome-filtered protein discovery record.');
 const ArchitectureResultSchema = ProteinResultSchema.extend({
     entries: ProteinResultSchema.shape.entries.optional(),
     taxa: ProteinResultSchema.shape.taxa.optional(),
+    proteomes: ProteomesSchema.optional(),
 });
+const Availability = z.enum(['available', 'unavailable']);
+const availability = (details) => details === undefined ? 'unavailable' : 'available';
 const ArchitectureOutputSchema = ArchitectureResultSchema.extend({
     detailAvailability: z
         .object({
-        entries: z
-            .enum(['available', 'unavailable'])
-            .describe('Whether upstream supplied entry records.'),
-        taxa: z
-            .enum(['available', 'unavailable'])
-            .describe('Whether upstream supplied taxon records.'),
+        entries: Availability.describe('Whether upstream supplied entry records.'),
+        taxa: Availability.describe('Whether upstream supplied taxon records.'),
+        proteomes: Availability.optional().describe('Whether upstream supplied proteome records; present only when proteomeId is set.'),
     })
         .describe('Absent details are unavailable, rather than biologically empty.'),
 }).describe('Complete architecture-filtered protein record with explicit detail availability.');
 /** Discover proteins without fetching per-protein metadata. */
 export const interproFindProteinsByDomain = tool('interpro_find_proteins_by_domain', {
     title: 'Find proteins by domain',
-    description: 'Find UniProt proteins carrying an InterPro or member signature. Defaults to reviewed human proteins; reviewedOnly=false includes all review statuses in the chosen taxon. Optional isFragment filters fragment annotations; false does not prove sequence completeness. architectureId intersects the provider Pfam grouping with these selections, without implying functional equivalence; metadata-only hits disclose unavailable entry and taxon details without per-protein requests.',
+    description: 'Find UniProt proteins carrying an InterPro or member signature. Defaults to reviewed human proteins; reviewedOnly=false includes all review statuses in the chosen taxon. Optional isFragment filters fragment annotations; false does not prove sequence completeness. architectureId intersects the provider Pfam grouping with these selections, without implying functional equivalence; metadata-only hits disclose unavailable entry and taxon details without per-protein requests. proteomeId intersects one UniProt proteome, such as protein.proteome from interpro_get_protein_domains, with every selection including taxonId.',
     annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
     auth: ['tool:interpro_find_proteins_by_domain:read'],
     input: z.object({
@@ -107,20 +117,26 @@ export const interproFindProteinsByDomain = tool('interpro_find_proteins_by_doma
             .trim()
             .regex(/^[a-fA-F0-9]{40}$/)
             .toLowerCase()).describe('Optional 40-character hexadecimal Pfam architecture grouping ID from protein.ida_accession; grouping does not establish functional equivalence.'),
+        proteomeId: optionalString(z
+            .string()
+            .trim()
+            .max(11)
+            .regex(/^[Uu][Pp][0-9]{9}$/)
+            .toUpperCase()).describe('Optional UniProt proteome accession, UP followed by 9 digits, such as protein.proteome from interpro_get_protein_domains. taxonId still applies, including its 9606 default: set taxonId to the mapped protein.source_organism.taxId or an ancestor, or no proteins match.'),
         limit: z
             .number()
             .int()
             .min(1)
             .default(20)
             .describe('Positive integer page size; values above 50 are clamped to 50 with a notice; defaults to 20.'),
-        cursor: optionalString(z.string().trim().max(4096)).describe('Opaque nextCursor with unchanged target, taxonId, reviewedOnly, isFragment, and architectureId selection; limit may change.'),
+        cursor: optionalString(z.string().trim().max(4096)).describe('Opaque nextCursor with unchanged target, taxonId, reviewedOnly, isFragment, architectureId, and proteomeId selection; limit may change.'),
     }),
     output: z.object({
         query: QuerySchema.describe('Applied canonical target and selection, including defaults.'),
         proteins: z
             .array(z
-            .union([ProteinResultSchema, ArchitectureOutputSchema])
-            .describe('Ordinary protein details or an architecture-filtered record with detail availability.'))
+            .union([ProteinResultSchema, ProteomeResultSchema, ArchitectureOutputSchema])
+            .describe('Ordinary protein details, with proteome records when proteomeId is set, or an architecture-filtered record with detail availability.'))
             .describe('Complete upstream protein records; architecture mode discloses unavailable details.'),
         page: PageSchema.describe('Page coverage and continuation.'),
         sourceUrl: z.string().describe('Official API source URL.'),
@@ -193,6 +209,7 @@ export const interproFindProteinsByDomain = tool('interpro_find_proteins_by_doma
             reviewedOnly: input.reviewedOnly,
             ...(input.isFragment !== undefined ? { isFragment: input.isFragment } : {}),
             ...(input.architectureId !== undefined ? { architectureId: input.architectureId } : {}),
+            ...(input.proteomeId !== undefined ? { proteomeId: input.proteomeId } : {}),
         };
         const cursor = decodeCursor(input.cursor, 'interpro_find_proteins_by_domain', query);
         const service = getInterproService();
@@ -207,11 +224,16 @@ export const interproFindProteinsByDomain = tool('interpro_find_proteins_by_doma
                     fields.ida_id === input.architectureId);
             }, 'A supplied architecture identifier must match the requested grouping.').transform((row) => Object.assign({}, row, {
                 detailAvailability: {
-                    entries: row.entries === undefined ? 'unavailable' : 'available',
-                    taxa: row.taxa === undefined ? 'unavailable' : 'available',
+                    entries: availability(row.entries),
+                    taxa: availability(row.taxa),
+                    ...(input.proteomeId !== undefined
+                        ? { proteomes: availability(row.proteomes) }
+                        : {}),
                 },
             }))
-            : ProteinResultSchema;
+            : input.proteomeId
+                ? ProteomeResultSchema
+                : ProteinResultSchema;
         const response = await service.request(service.begin(ctx), [
             'protein',
             query.reviewedOnly ? 'reviewed' : 'uniprot',
@@ -221,6 +243,7 @@ export const interproFindProteinsByDomain = tool('interpro_find_proteins_by_doma
             'taxonomy',
             'uniprot',
             query.taxonId,
+            ...(query.proteomeId ? ['proteome', 'uniprot', query.proteomeId] : []),
         ], {
             page_size: limit,
             cursor,
@@ -250,7 +273,7 @@ export const interproFindProteinsByDomain = tool('interpro_find_proteins_by_doma
         ctx.enrich.total(page.total);
         ctx.enrich.echo(JSON.stringify(query));
         if (!proteins.length)
-            notices.push(`No proteins matched the applied entry and selection. Retry interpro_find_proteins_by_domain with reviewedOnly=false or another taxonId${input.isFragment !== undefined ? ', or omit isFragment to include both fragment annotation groups' : ''}; use interpro_get_entry to verify the accession.`);
+            notices.push(`No proteins matched the applied entry and selection. Retry interpro_find_proteins_by_domain with reviewedOnly=false or another taxonId${input.isFragment !== undefined ? ', or omit isFragment to include both fragment annotation groups' : ''}; use interpro_get_entry to verify the accession.${query.proteomeId ? ` taxonId ${query.taxonId} still applies with proteomeId ${query.proteomeId}: set taxonId to protein.source_organism.taxId from interpro_get_protein_domains for a protein in that proteome, or an ancestor taxon, and confirm proteomeId against its protein.proteome.` : ''}`);
         if (next) {
             notices.push(pageGuidance('interpro_find_proteins_by_domain', 'proteins', limit, MAX_LIMIT));
             ctx.enrich.truncated({ shown: proteins.length, cap: limit, guidance: notices.join(' ') });

package/dist/mcp-server/tools/definitions/interpro-find-proteins-by-domain.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/interpro-get-protein-domains.tool.d.ts CHANGED Viewed

@@ -24,6 +24,7 @@ export declare const interproGetProteinDomains: import("@cyanheads/mcp-ts-core")
             scientificName: z.ZodString;
             fullName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
         }, z.core.$catchall<z.ZodJSONSchema>>>;
+        proteome: z.ZodOptional<z.ZodNullable<z.ZodString>>;
     }, z.core.$catchall<z.ZodJSONSchema>>>;
     matches: z.ZodArray<z.ZodObject<{
         metadata: z.ZodObject<{

package/dist/mcp-server/tools/definitions/interpro-get-protein-domains.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"interpro-get-protein-domains.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/interpro-get-protein-domains.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmLjE,gGAAgG;AAChG,eAAO,MAAM,yBAAyB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EAoYpC,CAAC"}
1	+ {"version":3,"file":"interpro-get-protein-domains.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/interpro-get-protein-domains.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmLjE,gGAAgG;AAChG,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAoYpC,CAAC"}

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

@@ -36,7 +36,7 @@ const CoverageSchema = z.object({
         .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()

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

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

@@ -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 ADDED Viewed

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package/dist/mcp-server/tools/definitions/interpro-get-scan-result.tool.js ADDED Viewed

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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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