@cyanheads/interpro-mcp-server 0.0.0-stage → 0.1.1

package/dist/mcp-server/tools/definitions/interpro-list-reference.tool.d.ts

@@ -0,0 +1,89 @@
+/**
+ * @fileoverview InterPro vocabulary and live release reference tool.
+ * @module mcp-server/tools/definitions/interpro-list-reference.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+/** Decode supported vocabulary or retrieve coherent current release counts. */
+export declare const interproListReference: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    topic: z.ZodEnum<{
+        accession_patterns: "accession_patterns";
+        databases: "databases";
+        entry_types: "entry_types";
+        release: "release";
+        taxa: "taxa";
+    }>;
+}, z.core.$strip>, z.ZodObject<{
+    topic: z.ZodEnum<{
+        accession_patterns: "accession_patterns";
+        databases: "databases";
+        entry_types: "entry_types";
+        release: "release";
+        taxa: "taxa";
+    }>;
+    items: z.ZodArray<z.ZodObject<{
+        id: z.ZodString;
+        label: z.ZodString;
+        description: z.ZodOptional<z.ZodString>;
+        sourceDatabase: z.ZodOptional<z.ZodString>;
+        accessionPattern: z.ZodOptional<z.ZodString>;
+        example: z.ZodOptional<z.ZodString>;
+        taxonId: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>>;
+    sourceUrls: z.ZodArray<z.ZodString>;
+    release: z.ZodOptional<z.ZodObject<{
+        version: z.ZodString;
+        date: z.ZodString;
+        databaseCounts: z.ZodRecord<z.ZodString, z.ZodJSONSchema>;
+    }, z.core.$strip>>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "upstream_shape_invalid";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "Upstream JSON or response structure is incompatible.";
+    readonly retryable: false;
+    readonly recovery: "Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.";
+    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: "Retry list tools with a smaller limit, or retrieve individual members with interpro_get_entry instead of a large clan.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "release_changed";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "Release metadata and count responses advertise different versions.";
+    readonly retryable: true;
+    readonly recovery: "Retry interpro_list_reference with topic release after the upstream release update finishes.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_rejected";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "InterPro returns an unhandled redirect or client rejection.";
+    readonly retryable: false;
+    readonly recovery: "Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_unavailable";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "InterPro has a network or server failure; HTTP 501 is not retryable.";
+    readonly retryable: true;
+    readonly recovery: "Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_timeout";
+    readonly code: JsonRpcErrorCode.Timeout;
+    readonly when: "InterPro returns HTTP 408/504 or an attempt exceeds its deadline.";
+    readonly retryable: true;
+    readonly recovery: "Retry with a smaller limit where available, then repeat the same tool after waiting.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_rate_limited";
+    readonly code: JsonRpcErrorCode.RateLimited;
+    readonly when: "InterPro returns HTTP 429.";
+    readonly retryable: true;
+    readonly recovery: "Wait for retryAfter when supplied, then repeat the same tool with fewer concurrent calls.";
+    readonly thrownBy: "service";
+}], undefined>;
+//# sourceMappingURL=interpro-list-reference.tool.d.ts.map

package/dist/mcp-server/tools/definitions/interpro-list-reference.tool.d.ts.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/interpro-list-reference.tool.js

@@ -0,0 +1,99 @@
+/**
+ * @fileoverview InterPro vocabulary and live release reference tool.
+ * @module mcp-server/tools/definitions/interpro-list-reference.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 { getInterproService } from '../../../services/interpro/interpro-service.js';
+import { ReferenceItemSchema, ReferenceTopicSchema, staticReference, } from '../../../services/interpro/reference.js';
+import { JsonObjectSchema } from '../../../services/interpro/schemas.js';
+/** Decode supported vocabulary or retrieve coherent current release counts. */
+export const interproListReference = tool('interpro_list_reference', {
+    title: 'InterPro reference vocabulary',
+    description: 'List supported InterPro database slugs, entry types, accession routing patterns, common taxon IDs, or current release information.',
+    annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
+    auth: ['tool:interpro_list_reference:read'],
+    input: z.object({ topic: ReferenceTopicSchema }),
+    output: z.object({
+        topic: ReferenceTopicSchema,
+        items: z
+            .array(ReferenceItemSchema)
+            .describe('Applicable reference vocabulary; empty for release.'),
+        sourceUrls: z.array(z.string()).describe('Official reference sources.'),
+        release: z
+            .object({
+            version: z.string().describe('Greatest numeric release version.'),
+            date: z.string().describe('Release date supplied by InterPro.'),
+            databaseCounts: JsonObjectSchema.describe('Complete entry aggregate response.'),
+        })
+            .optional()
+            .describe('Current live release metadata when requested.'),
+    }),
+    errors: [
+        {
+            reason: 'upstream_shape_invalid',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'Upstream JSON or response structure is incompatible.',
+            retryable: false,
+            recovery: 'Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_response_too_large',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'An upstream response exceeds 4 MiB.',
+            retryable: false,
+            recovery: 'Retry list tools with a smaller limit, or retrieve individual members with interpro_get_entry instead of a large clan.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'release_changed',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'Release metadata and count responses advertise different versions.',
+            retryable: true,
+            recovery: 'Retry interpro_list_reference with topic release after the upstream release update finishes.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_rejected',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'InterPro returns an unhandled redirect or client rejection.',
+            retryable: false,
+            recovery: 'Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_unavailable',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'InterPro has a network or server failure; HTTP 501 is not retryable.',
+            retryable: true,
+            recovery: 'Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_timeout',
+            code: JsonRpcErrorCode.Timeout,
+            when: 'InterPro returns HTTP 408/504 or an attempt exceeds its deadline.',
+            retryable: true,
+            recovery: 'Retry with a smaller limit where available, then repeat the same tool after waiting.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_rate_limited',
+            code: JsonRpcErrorCode.RateLimited,
+            when: 'InterPro returns HTTP 429.',
+            retryable: true,
+            recovery: 'Wait for retryAfter when supplied, then repeat the same tool with fewer concurrent calls.',
+            thrownBy: 'service',
+        },
+    ],
+    async handler(input, ctx) {
+        if (input.topic !== 'release')
+            return { topic: input.topic, ...staticReference(input.topic) };
+        const { sourceUrls, ...release } = await getInterproService().release(ctx);
+        return { topic: input.topic, items: [], sourceUrls, release };
+    },
+    format: formatInterpro,
+});
+//# sourceMappingURL=interpro-list-reference.tool.js.map

package/dist/mcp-server/tools/definitions/interpro-list-reference.tool.js.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/interpro-search-entries.tool.d.ts

@@ -0,0 +1,184 @@
+/**
+ * @fileoverview Cursor-paged entry and signature discovery.
+ * @module mcp-server/tools/definitions/interpro-search-entries.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+/** Search or browse one database without per-record detail requests. */
+export declare const interproSearchEntries: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    sourceDatabase: z.ZodPreprocess<z.ZodDefault<z.ZodEnum<{
+        antifam: "antifam";
+        cathgene3d: "cathgene3d";
+        cdd: "cdd";
+        hamap: "hamap";
+        interpro: "interpro";
+        ncbifam: "ncbifam";
+        panther: "panther";
+        pfam: "pfam";
+        pirsf: "pirsf";
+        prints: "prints";
+        profile: "profile";
+        prosite: "prosite";
+        sfld: "sfld";
+        smart: "smart";
+        ssf: "ssf";
+    }>>, unknown>;
+    query: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+    entryType: z.ZodPreprocess<z.ZodOptional<z.ZodEnum<{
+        active_site: "active_site";
+        binding_site: "binding_site";
+        coiled_coil: "coiled_coil";
+        conserved_site: "conserved_site";
+        disordered: "disordered";
+        domain: "domain";
+        family: "family";
+        homologous_superfamily: "homologous_superfamily";
+        ptm: "ptm";
+        region: "region";
+        repeat: "repeat";
+    }>>, unknown>;
+    goTerm: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+    goCategory: z.ZodPreprocess<z.ZodOptional<z.ZodEnum<{
+        C: "C";
+        F: "F";
+        P: "P";
+    }>>, unknown>;
+    integratedInto: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+    limit: z.ZodDefault<z.ZodNumber>;
+    cursor: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+}, z.core.$strip>, z.ZodObject<{
+    query: z.ZodObject<{
+        sourceDatabase: z.ZodEnum<{
+            antifam: "antifam";
+            cathgene3d: "cathgene3d";
+            cdd: "cdd";
+            hamap: "hamap";
+            interpro: "interpro";
+            ncbifam: "ncbifam";
+            panther: "panther";
+            pfam: "pfam";
+            pirsf: "pirsf";
+            prints: "prints";
+            profile: "profile";
+            prosite: "prosite";
+            sfld: "sfld";
+            smart: "smart";
+            ssf: "ssf";
+        }>;
+        query: z.ZodOptional<z.ZodString>;
+        entryType: z.ZodOptional<z.ZodEnum<{
+            active_site: "active_site";
+            binding_site: "binding_site";
+            coiled_coil: "coiled_coil";
+            conserved_site: "conserved_site";
+            disordered: "disordered";
+            domain: "domain";
+            family: "family";
+            homologous_superfamily: "homologous_superfamily";
+            ptm: "ptm";
+            region: "region";
+            repeat: "repeat";
+        }>>;
+        goTerm: z.ZodOptional<z.ZodString>;
+        goCategory: z.ZodOptional<z.ZodEnum<{
+            C: "C";
+            F: "F";
+            P: "P";
+        }>>;
+        integratedInto: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>;
+    entries: z.ZodArray<z.ZodObject<{
+        accession: z.ZodString;
+        source_database: z.ZodString;
+        name: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        type: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        integrated: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        member_databases: z.ZodOptional<z.ZodNullable<z.ZodRecord<z.ZodString, z.ZodRecord<z.ZodString, z.ZodString>>>>;
+        go_terms: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodObject<{
+            identifier: z.ZodString;
+            name: z.ZodString;
+            category: z.ZodObject<{
+                code: z.ZodString;
+                name: z.ZodString;
+            }, z.core.$catchall<z.ZodJSONSchema>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>>>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>;
+    page: z.ZodObject<{
+        total: z.ZodNumber;
+        returned: z.ZodNumber;
+        limit: z.ZodNumber;
+        hasMore: z.ZodBoolean;
+        nextCursor: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>;
+    sourceUrl: z.ZodString;
+}, z.core.$strip>, readonly [{
+    readonly reason: "database_mismatch";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "Integration filtering is requested on the integrating database.";
+    readonly retryable: false;
+    readonly recovery: "Call interpro_list_reference with topic accession_patterns, then retry with the matching sourceDatabase.";
+}, {
+    readonly reason: "invalid_cursor";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "Cursor decoding or scope fails, or upstream rejects continuation.";
+    readonly retryable: false;
+    readonly recovery: "Repeat the same tool without cursor to restart pagination, keeping the intended filters.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "entry_withdrawn";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "InterPro answers the search with HTTP 410, reporting a withdrawn record.";
+    readonly retryable: false;
+    readonly recovery: "Repeat interpro_search_entries with integratedInto set to a current InterPro accession, or without it; consult interpro_list_reference with topic databases for source names.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_shape_invalid";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "Upstream JSON, structure, or continuation is incompatible.";
+    readonly retryable: false;
+    readonly recovery: "Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.";
+    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: 'Retry list tools with a smaller limit, or retrieve individual members with interpro_get_entry instead of a large clan.';
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: 'upstream_rejected';
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: 'InterPro returns an unhandled redirect or client rejection.';
+    readonly retryable: false;
+    readonly recovery: 'Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.';
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: 'upstream_unavailable';
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: 'InterPro has a network or server failure; HTTP 501 is not retryable.';
+    readonly retryable: true;
+    readonly recovery: 'Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.';
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: 'upstream_timeout';
+    readonly code: JsonRpcErrorCode.Timeout;
+    readonly when: 'InterPro returns HTTP 408/504 or an attempt exceeds its deadline.';
+    readonly retryable: true;
+    readonly recovery: 'Retry with a smaller limit where available, then repeat the same tool after waiting.';
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: 'upstream_rate_limited';
+    readonly code: JsonRpcErrorCode.RateLimited;
+    readonly when: 'InterPro returns HTTP 429.';
+    readonly retryable: true;
+    readonly recovery: 'Wait for retryAfter when supplied, then repeat the same tool with fewer concurrent calls.';
+    readonly thrownBy: 'service';
+}], {
+    readonly notice: z.ZodOptional<z.ZodString>;
+    readonly totalCount: z.ZodOptional<z.ZodNumber>;
+    readonly truncated: z.ZodOptional<z.ZodBoolean>;
+    readonly shown: z.ZodOptional<z.ZodNumber>;
+    readonly cap: z.ZodOptional<z.ZodNumber>;
+    readonly effectiveQuery: z.ZodOptional<z.ZodString>;
+}>;
+//# sourceMappingURL=interpro-search-entries.tool.d.ts.map

package/dist/mcp-server/tools/definitions/interpro-search-entries.tool.d.ts.map

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package/dist/mcp-server/tools/definitions/interpro-search-entries.tool.js

@@ -0,0 +1,155 @@
+/**
+ * @fileoverview Cursor-paged entry and signature discovery.
+ * @module mcp-server/tools/definitions/interpro-search-entries.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { continuation, decodeCursor, encodeCursor, pageGuidance, } from '../../../services/interpro/cursors.js';
+import { formatInterpro, normalizeImages } from '../../../services/interpro/format.js';
+import { getInterproService } from '../../../services/interpro/interpro-service.js';
+import { ENTRY_ROUTES } from '../../../services/interpro/routing.js';
+import { defaultedString, EntrySummarySchema, EntryTypeSchema, JsonValueSchema, listSchema, optionalString, PageSchema, SourceDatabaseSchema, } from '../../../services/interpro/schemas.js';
+import { UPSTREAM_ERRORS } from '../../../services/interpro/upstream-errors.js';
+const MAX_LIMIT = 100;
+const QuerySchema = z.object({
+    sourceDatabase: SourceDatabaseSchema,
+    query: z.string().optional().describe('Applied text search.'),
+    entryType: EntryTypeSchema.optional().describe('Applied entry type.'),
+    goTerm: z.string().optional().describe('Applied GO identifier.'),
+    goCategory: z.enum(['P', 'F', 'C']).optional().describe('Applied GO category.'),
+    integratedInto: z.string().optional().describe('Applied integrating InterPro accession.'),
+});
+const RowSchema = z
+    .object({ metadata: EntrySummarySchema.describe('Entry summary.') })
+    .catchall(JsonValueSchema);
+/** Search or browse one database without per-record detail requests. */
+export const interproSearchEntries = tool('interpro_search_entries', {
+    title: 'Search InterPro entries',
+    description: 'Search InterPro entries or member signatures by text, entry type, GO annotation, or integrated InterPro accession. Results are cursor-paged; use interpro_get_entry for full metadata.',
+    annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
+    auth: ['tool:interpro_search_entries:read'],
+    input: z.object({
+        sourceDatabase: defaultedString(SourceDatabaseSchema.default('interpro')).describe('Database to search; defaults to interpro.'),
+        query: optionalString(z.string().trim().min(1).max(300)).describe('Text to search; omit all filters to browse the database.'),
+        entryType: optionalString(EntryTypeSchema).describe('Entry annotation type.'),
+        goTerm: optionalString(z
+            .string()
+            .trim()
+            .regex(/^GO:\d{7}$/)).describe('GO annotation identifier such as GO:0003677.'),
+        goCategory: optionalString(z.enum(['P', 'F', 'C'])).describe('GO category: P biological process, F molecular function, C cellular component.'),
+        integratedInto: optionalString(z
+            .string()
+            .trim()
+            .regex(/^IPR\d{6}$/i)).describe('Integrating InterPro accession; requires a member sourceDatabase.'),
+        limit: z
+            .number()
+            .int()
+            .min(1)
+            .max(MAX_LIMIT)
+            .default(20)
+            .describe('Page size, from 1 to 100; defaults to 20.'),
+        cursor: optionalString(z.string().trim().max(4096)).describe('Opaque nextCursor from this tool with unchanged filters; limit may change.'),
+    }),
+    output: z.object({
+        query: QuerySchema.describe('Applied canonical filters.'),
+        entries: z
+            .array(EntrySummarySchema.describe('Complete entry summary.'))
+            .describe('Complete entry summaries from this page.'),
+        page: PageSchema.describe('Continuation and upstream total.'),
+        sourceUrl: z.string().describe('Official API source URL.'),
+    }),
+    enrichment: {
+        notice: z.string().optional().describe('Interpretation or recovery guidance.'),
+        totalCount: z.number().optional().describe('Upstream total matching records.'),
+        truncated: z.boolean().optional().describe('More records remain.'),
+        shown: z.number().int().optional().describe('Records returned in this page.'),
+        cap: z.number().int().optional().describe('Requested page size.'),
+        effectiveQuery: z.string().optional().describe('Applied filters as JSON.'),
+    },
+    errors: [
+        {
+            reason: 'database_mismatch',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'Integration filtering is requested on the integrating database.',
+            retryable: false,
+            recovery: 'Call interpro_list_reference with topic accession_patterns, then retry with the matching sourceDatabase.',
+        },
+        {
+            reason: 'invalid_cursor',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'Cursor decoding or scope fails, or upstream rejects continuation.',
+            retryable: false,
+            recovery: 'Repeat the same tool without cursor to restart pagination, keeping the intended filters.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'entry_withdrawn',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'InterPro answers the search with HTTP 410, reporting a withdrawn record.',
+            retryable: false,
+            recovery: 'Repeat interpro_search_entries with integratedInto set to a current InterPro accession, or without it; consult interpro_list_reference with topic databases for source names.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_shape_invalid',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'Upstream JSON, structure, or continuation is incompatible.',
+            retryable: false,
+            recovery: 'Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.',
+            thrownBy: 'service',
+        },
+        ...UPSTREAM_ERRORS,
+    ],
+    async handler(input, ctx) {
+        if (input.integratedInto && input.sourceDatabase === 'interpro')
+            throw ctx.fail('database_mismatch', 'integratedInto requires a member sourceDatabase.');
+        const query = {
+            sourceDatabase: input.sourceDatabase,
+            ...(input.query ? { query: input.query } : {}),
+            ...(input.entryType ? { entryType: input.entryType } : {}),
+            ...(input.goTerm ? { goTerm: input.goTerm } : {}),
+            ...(input.goCategory ? { goCategory: input.goCategory } : {}),
+            ...(input.integratedInto ? { integratedInto: input.integratedInto.toUpperCase() } : {}),
+        };
+        const cursor = decodeCursor(input.cursor, 'interpro_search_entries', query);
+        const service = getInterproService();
+        const response = await service.request(service.begin(ctx), ['entry', query.sourceDatabase], {
+            search: query.query,
+            type: query.entryType,
+            go_term: query.goTerm,
+            go_category: query.goCategory,
+            integrated: query.integratedInto,
+            page_size: input.limit,
+            cursor,
+        }, listSchema(RowSchema), { continuation: cursor !== undefined });
+        const entries = normalizeImages(response.data?.results.map((row) => row.metadata) ?? []);
+        const next = continuation(response.data?.next ?? null, new Set(cursor ? [cursor] : []));
+        const page = {
+            total: response.data?.count ?? 0,
+            returned: entries.length,
+            limit: input.limit,
+            hasMore: next !== undefined,
+            ...(next ? { nextCursor: encodeCursor('interpro_search_entries', query, next) } : {}),
+        };
+        ctx.enrich.total(page.total);
+        ctx.enrich.echo(JSON.stringify(query));
+        if (next)
+            ctx.enrich.truncated({
+                shown: entries.length,
+                cap: input.limit,
+                guidance: pageGuidance('interpro_search_entries', 'entries', input.limit, MAX_LIMIT),
+            });
+        if (!entries.length) {
+            const memberText = input.sourceDatabase === 'interpro' &&
+                input.query &&
+                ENTRY_ROUTES.some((route) => route.source !== 'interpro' && route.pattern.test(input.query ?? ''));
+            ctx.enrich.notice('No entries matched the applied filters. Remove query, entryType, goTerm, goCategory, or integratedInto filters that are present; call interpro_list_reference with topic databases to check sourceDatabase.' +
+                (memberText
+                    ? ' Use interpro_get_entry with the accession to infer its member database.'
+                    : ''));
+        }
+        return { query, entries, page, sourceUrl: response.sourceUrl };
+    },
+    format: formatInterpro,
+});
+//# sourceMappingURL=interpro-search-entries.tool.js.map

package/dist/mcp-server/tools/definitions/interpro-search-entries.tool.js.map

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package/dist/services/interpro/budget.d.ts

@@ -0,0 +1,26 @@
+/**
+ * @fileoverview Shared byte budget for one tool result's domain output, and whole-item fitting.
+ * @module services/interpro/budget
+ */
+/** Most UTF-8 bytes one result's domain output may occupy when serialized as compact JSON. */
+export declare const RESPONSE_BYTE_BUDGET = 100000;
+/** UTF-8 bytes of a value serialized as compact JSON, the form both result surfaces carry. */
+export declare function jsonByteLength(value: unknown): number;
+/**
+ * The largest count from 1 to `max` whose `build(count)` fits {@link RESPONSE_BYTE_BUDGET},
+ * found by binary search on the assumption that the built size grows with the count. Returns 1
+ * when even one item overflows, so a continuation always advances, and 0 when none remain.
+ */
+export declare function largestFittingCount(max: number, build: (count: number) => unknown): number;
+/** The budget as it reads in notices. */
+export declare const BUDGET_LABEL: string;
+/**
+ * Builds the largest whole-item output that fits the budget. `oversized` is set when even the
+ * smallest non-empty output exceeds it, so the output carries one indivisible item alone.
+ */
+export declare function fitWithinBudget<T>(max: number, build: (count: number) => T): {
+    count: number;
+    output: T;
+    oversized: boolean;
+};
+//# sourceMappingURL=budget.d.ts.map

package/dist/services/interpro/budget.d.ts.map

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package/dist/services/interpro/budget.js

@@ -0,0 +1,41 @@
+/**
+ * @fileoverview Shared byte budget for one tool result's domain output, and whole-item fitting.
+ * @module services/interpro/budget
+ */
+/** Most UTF-8 bytes one result's domain output may occupy when serialized as compact JSON. */
+export const RESPONSE_BYTE_BUDGET = 100_000;
+/** UTF-8 bytes of a value serialized as compact JSON, the form both result surfaces carry. */
+export function jsonByteLength(value) {
+    return Buffer.byteLength(JSON.stringify(value), 'utf8');
+}
+/**
+ * The largest count from 1 to `max` whose `build(count)` fits {@link RESPONSE_BYTE_BUDGET},
+ * found by binary search on the assumption that the built size grows with the count. Returns 1
+ * when even one item overflows, so a continuation always advances, and 0 when none remain.
+ */
+export function largestFittingCount(max, build) {
+    if (max <= 0)
+        return 0;
+    let fits = 1;
+    let overflows = max + 1;
+    while (overflows - fits > 1) {
+        const middle = Math.floor((fits + overflows) / 2);
+        if (jsonByteLength(build(middle)) <= RESPONSE_BYTE_BUDGET)
+            fits = middle;
+        else
+            overflows = middle;
+    }
+    return fits;
+}
+/** The budget as it reads in notices. */
+export const BUDGET_LABEL = `${RESPONSE_BYTE_BUDGET.toLocaleString('en-US')}-byte response budget`;
+/**
+ * Builds the largest whole-item output that fits the budget. `oversized` is set when even the
+ * smallest non-empty output exceeds it, so the output carries one indivisible item alone.
+ */
+export function fitWithinBudget(max, build) {
+    const count = largestFittingCount(max, build);
+    const output = build(count);
+    return { count, output, oversized: count > 0 && jsonByteLength(output) > RESPONSE_BYTE_BUDGET };
+}
+//# sourceMappingURL=budget.js.map

package/dist/services/interpro/budget.js.map

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