npm - @cyanheads/interpro-mcp-server - Versions diffs - 0.1.1 → 0.1.3 - Mend

@cyanheads/interpro-mcp-server 0.1.1 → 0.1.3

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 (40) hide show

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

	@@ -1 +1 @@
1	- {"version":3,"file":"interpro-get-clan.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/interpro-get-clan.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkEjE,yEAAyE;AACzE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EAuQ1B~~,CAAC"}
1	+ {"version":3,"file":"interpro-get-clan.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/interpro-get-clan.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkEjE,yEAAyE;AACzE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA0Q1B,CAAC"}

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

@@ -71,9 +71,8 @@ export const interproGetClan = tool('interpro_get_clan', {
             .number()
             .int()
             .min(1)
-            .max(MAX_LIMIT)
             .default(20)
-            .describe('Member page size from 1 to 100; defaults to 20.'),
+            .describe('Positive integer member page size; values above 100 are clamped to 100 with a notice; defaults to 20.'),
         cursor: optionalString(z.string().trim().max(4096)).describe('Opaque nextCursor with unchanged accession, sourceDatabase, and includeRelationships; limit, relationshipOffset, and includeThumbnail may change.'),
     }),
     output: z.object({
@@ -97,7 +96,7 @@ export const interproGetClan = tool('interpro_get_clan', {
         totalCount: z.number().optional().describe('Total matching members.'),
         truncated: z.boolean().optional().describe('More members remain.'),
         shown: z.number().int().optional().describe('Members returned in this page.'),
-        cap: z.number().int().optional().describe('Requested member page size.'),
+        cap: z.number().int().optional().describe('Effective member page size after clamping.'),
         effectiveQuery: z
             .string()
             .optional()
@@ -162,6 +161,7 @@ export const interproGetClan = tool('interpro_get_clan', {
         ...UPSTREAM_ERRORS,
     ],
     async handler(input, ctx) {
+        const limit = Math.min(input.limit, MAX_LIMIT);
         if (input.relationshipOffset > 0 && !input.includeRelationships)
             throw ctx.fail('relationships_not_requested', `relationshipOffset ${input.relationshipOffset} pages the relationship graph, which this call did not request.`);
         const target = resolveClan(input.accession, input.sourceDatabase);
@@ -173,7 +173,7 @@ export const interproGetClan = tool('interpro_get_clan', {
         const detail = await service.request(call, ['set', target.sourceDatabase, target.accession], {}, detailSchema(ClanMetadataSchema), { missing: { reason: 'clan_not_found', ...target } });
         if (!detail.data)
             throw ctx.fail('upstream_shape_invalid', 'Clan metadata response is missing.');
-        const response = await service.request(call, ['entry', target.sourceDatabase, 'set', target.sourceDatabase, target.accession], { page_size: input.limit, cursor }, listSchema(MemberSchema), { continuation: cursor !== undefined });
+        const response = await service.request(call, ['entry', target.sourceDatabase, 'set', target.sourceDatabase, target.accession], { page_size: limit, cursor }, listSchema(MemberSchema), { continuation: cursor !== undefined });
         const thumbnails = projectWikipediaThumbnails(detail.data.metadata, input.includeThumbnail, 'interpro_get_clan');
         const { relationships: graph, ...clan } = normalizeImages(thumbnails.metadata);
         const members = normalizeImages(response.data?.results ?? []);
@@ -181,7 +181,7 @@ export const interproGetClan = tool('interpro_get_clan', {
         const page = {
             total: response.data?.count ?? 0,
             returned: members.length,
-            limit: input.limit,
+            limit,
             hasMore: next !== undefined,
             ...(next ? { nextCursor: encodeCursor('interpro_get_clan', scope, next) } : {}),
         };
@@ -197,7 +197,7 @@ export const interproGetClan = tool('interpro_get_clan', {
             url: `https://www.ebi.ac.uk/interpro/set/${target.sourceDatabase}/${encodeURIComponent(target.accession)}/`,
             sourceUrl: detail.sourceUrl,
         });
-        const notices = [];
+        const notices = input.limit > limit ? [`Requested limit ${input.limit} was clamped to ${limit}.`] : [];
         let output = result(clan);
         if (!input.includeRelationships)
             notices.push('Relationships are omitted; set includeRelationships=true to page the relationship graph.');
@@ -221,7 +221,7 @@ export const interproGetClan = tool('interpro_get_clan', {
             if (fit.oversized) {
                 const roomier = [
                     ...(input.includeThumbnail ? ['includeThumbnail: false'] : []),
-                    ...(input.limit > 1 ? ['a smaller limit'] : []),
+                    ...(limit > 1 ? ['a smaller limit'] : []),
                 ];
                 notices.push(`The clan metadata and member page leave no room in the ${BUDGET_LABEL}, so this slice holds one item and exceeds it${roomier.length ? `; repeat with ${roomier.join(' or ')} for larger slices` : ''}.`);
             }
@@ -231,11 +231,11 @@ export const interproGetClan = tool('interpro_get_clan', {
                     sourceDatabase: target.sourceDatabase,
                     includeRelationships: true,
                     relationshipOffset: nextOffset,
-                    limit: input.limit,
+                    limit,
                     ...(input.includeThumbnail ? { includeThumbnail: true } : {}),
                     ...(input.cursor ? { cursor: input.cursor } : {}),
                 };
-                notices.push(`This relationship slice holds items ${offset} to ${nextOffset - 1} of ${total}, nodes first, then links (${returnedNodes} of ${totalNodes} nodes, ${returnedLinks} of ${totalLinks} links). Continue with interpro_get_clan ${JSON.stringify(nextCall)}${input.limit > 1 ? '; a smaller limit leaves more of the response budget to each slice' : ''}.`);
+                notices.push(`This relationship slice holds items ${offset} to ${nextOffset - 1} of ${total}, nodes first, then links (${returnedNodes} of ${totalNodes} nodes, ${returnedLinks} of ${totalLinks} links). Continue with interpro_get_clan ${JSON.stringify(nextCall)}${limit > 1 ? '; a smaller limit leaves more of the response budget to each slice' : ''}.`);
             }
         }
         if (thumbnails.notice)
@@ -243,10 +243,10 @@ export const interproGetClan = tool('interpro_get_clan', {
         if (!members.length)
             notices.push('This member page is empty; the clan metadata remains available.');
         if (next) {
-            notices.push(pageGuidance('interpro_get_clan', 'members', input.limit, MAX_LIMIT));
+            notices.push(pageGuidance('interpro_get_clan', 'members', limit, MAX_LIMIT));
             ctx.enrich.truncated({
                 shown: members.length,
-                cap: input.limit,
+                cap: limit,
                 guidance: notices.join(' '),
             });
         }

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

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

@@ -25,6 +25,19 @@ export declare const interproGetEntry: import("@cyanheads/mcp-ts-core").ToolDefi
         ssf: "ssf";
     }>>, unknown>;
     includeThumbnail: z.ZodDefault<z.ZodBoolean>;
+    sections: z.ZodOptional<z.ZodArray<z.ZodEnum<{
+        counters: "counters";
+        cross_references: "cross_references";
+        description: "description";
+        go_terms: "go_terms";
+        hierarchy: "hierarchy";
+        literature: "literature";
+        member_databases: "member_databases";
+        overlaps_with: "overlaps_with";
+        wikipedia: "wikipedia";
+    }>>>;
+    overlapLimit: z.ZodOptional<z.ZodNumber>;
+    overlapOffset: z.ZodOptional<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     accession: z.ZodString;
     sourceDatabase: z.ZodEnum<{
@@ -51,10 +64,56 @@ export declare const interproGetEntry: import("@cyanheads/mcp-ts-core").ToolDefi
             name: z.ZodOptional<z.ZodNullable<z.ZodString>>;
             short: z.ZodOptional<z.ZodNullable<z.ZodString>>;
         }, z.core.$catchall<z.ZodJSONSchema>>>>;
+        descriptionText: z.ZodOptional<z.ZodString>;
     }, z.core.$catchall<z.ZodJSONSchema>>;
     url: z.ZodString;
     sourceUrl: z.ZodString;
+    sections: z.ZodOptional<z.ZodArray<z.ZodEnum<{
+        counters: "counters";
+        cross_references: "cross_references";
+        description: "description";
+        go_terms: "go_terms";
+        hierarchy: "hierarchy";
+        literature: "literature";
+        member_databases: "member_databases";
+        overlaps_with: "overlaps_with";
+        wikipedia: "wikipedia";
+    }>>>;
+    omittedSections: z.ZodOptional<z.ZodArray<z.ZodEnum<{
+        counters: "counters";
+        cross_references: "cross_references";
+        description: "description";
+        go_terms: "go_terms";
+        hierarchy: "hierarchy";
+        literature: "literature";
+        member_databases: "member_databases";
+        overlaps_with: "overlaps_with";
+        wikipedia: "wikipedia";
+    }>>>;
+    overlapsPage: z.ZodOptional<z.ZodDiscriminatedUnion<[z.ZodObject<{
+        available: z.ZodLiteral<true>;
+        total: z.ZodNumber;
+        offset: z.ZodNumber;
+        returned: z.ZodNumber;
+        hasMore: z.ZodBoolean;
+        nextOffset: z.ZodOptional<z.ZodNumber>;
+    }, z.core.$strip>, z.ZodObject<{
+        available: z.ZodLiteral<false>;
+        offset: z.ZodNumber;
+    }, z.core.$strip>], "available">>;
 }, z.core.$strip>, readonly [{
+    readonly reason: "overlap_limit_required";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "overlapOffset is supplied without overlapLimit.";
+    readonly retryable: false;
+    readonly recovery: "Supply overlapLimit to enable paging, or omit overlapOffset for full overlaps.";
+}, {
+    readonly reason: "overlaps_not_selected";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "Overlap paging is requested but sections excludes overlaps_with.";
+    readonly retryable: false;
+    readonly recovery: "Include overlaps_with in sections or omit sections, then retry with overlapLimit.";
+}, {
     readonly reason: "database_mismatch";
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "Explicit database conflicts with accession routing.";
@@ -125,6 +184,7 @@ export declare const interproGetEntry: import("@cyanheads/mcp-ts-core").ToolDefi
     readonly recovery: 'Wait for retryAfter when supplied, then repeat the same tool with fewer concurrent calls.';
     readonly thrownBy: 'service';
 }], {
+    readonly totalCount: z.ZodOptional<z.ZodNumber>;
     readonly notice: z.ZodOptional<z.ZodString>;
 }>;
 //# sourceMappingURL=interpro-get-entry.tool.d.ts.map

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"interpro-get-entry.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/interpro-get-entry.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAuDjE,wEAAwE;AACxE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2O3B,CAAC"}

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

@@ -4,15 +4,51 @@
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { descriptionText } from '../../../services/interpro/description-text.js';
 import { formatInterpro, normalizeImages, projectWikipediaThumbnails, } from '../../../services/interpro/format.js';
 import { getInterproService } from '../../../services/interpro/interpro-service.js';
 import { resolveEntry } from '../../../services/interpro/routing.js';
-import { AccessionSchema, detailSchema, EntryMetadataSchema, optionalString, SourceDatabaseSchema, } from '../../../services/interpro/schemas.js';
+import { AccessionSchema, detailSchema, EntryDetailMetadataSchema, EntryMetadataSchema, optionalString, SourceDatabaseSchema, } from '../../../services/interpro/schemas.js';
 import { UPSTREAM_ERRORS } from '../../../services/interpro/upstream-errors.js';
+const SECTIONS = [
+    'description',
+    'hierarchy',
+    'member_databases',
+    'go_terms',
+    'literature',
+    'cross_references',
+    'wikipedia',
+    'counters',
+    'overlaps_with',
+];
+const SectionSchema = z.enum(SECTIONS);
+const OverlapsPageSchema = z.discriminatedUnion('available', [
+    z
+        .object({
+        available: z.literal(true).describe('Overlap array was supplied.'),
+        total: z.number().int().nonnegative().describe('Complete upstream overlap count.'),
+        offset: z.number().int().nonnegative().describe('Requested record offset.'),
+        returned: z.number().int().nonnegative().describe('Complete records returned.'),
+        hasMore: z.boolean().describe('More overlap records remain.'),
+        nextOffset: z
+            .number()
+            .int()
+            .nonnegative()
+            .optional()
+            .describe('Next offset when more records remain.'),
+    })
+        .describe('Page of complete upstream overlap records.'),
+    z
+        .object({
+        available: z.literal(false).describe('Overlap array was not supplied.'),
+        offset: z.number().int().nonnegative().describe('Requested record offset.'),
+    })
+        .describe('Overlap paging unavailable for a missing or null source section.'),
+]);
 /** Retrieve one complete entry with deterministic accession routing. */
 export const interproGetEntry = tool('interpro_get_entry', {
     title: 'InterPro entry metadata',
-    description: 'Retrieve one InterPro or member-database entry, including description, hierarchy, member signatures, GO terms, literature, cross-references, clan membership, and coverage counters.',
+    description: 'Retrieve one InterPro or member-database entry with full metadata by default. Select optional sections while retaining core and unknown metadata, or supply overlapLimit to page whole overlap records in upstream order; offsets are not a snapshot across calls.',
     annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
     auth: ['tool:interpro_get_entry:read'],
     input: z.object({
@@ -22,21 +58,68 @@ export const interproGetEntry = tool('interpro_get_entry', {
             .boolean()
             .default(false)
             .describe('Include each Wikipedia thumbnail image, base64 data often hundreds of KB; defaults to false.'),
+        sections: z
+            .array(SectionSchema.describe('Optional metadata section to retain.'))
+            .optional()
+            .describe('Retain these named sections and all core or unknown metadata; omitted means full detail, and an empty array retains core metadata only.'),
+        overlapLimit: z
+            .number()
+            .int()
+            .positive()
+            .max(Number.MAX_SAFE_INTEGER)
+            .optional()
+            .describe('Positive safe integer number of whole overlap records; supplying it enables overlap paging.'),
+        overlapOffset: z
+            .number()
+            .int()
+            .nonnegative()
+            .max(Number.MAX_SAFE_INTEGER)
+            .optional()
+            .describe('Nonnegative safe integer overlap offset; requires overlapLimit, defaults to zero.'),
     }),
     output: z.object({
         accession: z.string().describe('Canonical requested accession.'),
         sourceDatabase: SourceDatabaseSchema,
-        entry: EntryMetadataSchema.describe('Complete upstream metadata, preserving sparse annotations; Wikipedia thumbnails are omitted unless includeThumbnail is true.'),
+        entry: EntryDetailMetadataSchema.describe('Upstream metadata after explicit section selection and overlap paging, with readable descriptionText when description is retained; raw description shapes and sparse annotations survive. Wikipedia thumbnails are omitted unless includeThumbnail is true.'),
         url: z.string().describe('Canonical InterPro website URL.'),
         sourceUrl: z.string().describe('Official API source URL.'),
+        sections: z
+            .array(SectionSchema.describe('Retained optional section.'))
+            .optional()
+            .describe('Canonical selected sections, when explicitly selected.'),
+        omittedSections: z
+            .array(SectionSchema.describe('Omitted source section.'))
+            .optional()
+            .describe('Named sections actually removed from upstream metadata.'),
+        overlapsPage: OverlapsPageSchema.optional().describe('Explicit overlap paging state; unavailable arrays have no fabricated total.'),
     }),
     enrichment: {
+        totalCount: z
+            .number()
+            .int()
+            .nonnegative()
+            .optional()
+            .describe('Total upstream overlap records when explicit paging has an available array.'),
         notice: z
             .string()
             .optional()
-            .describe('Omitted Wikipedia thumbnail size and how to include it.'),
+            .describe('Section selection, overlap page continuation or availability, and omitted Wikipedia thumbnail guidance.'),
     },
     errors: [
+        {
+            reason: 'overlap_limit_required',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'overlapOffset is supplied without overlapLimit.',
+            retryable: false,
+            recovery: 'Supply overlapLimit to enable paging, or omit overlapOffset for full overlaps.',
+        },
+        {
+            reason: 'overlaps_not_selected',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'Overlap paging is requested but sections excludes overlaps_with.',
+            retryable: false,
+            recovery: 'Include overlaps_with in sections or omit sections, then retry with overlapLimit.',
+        },
         {
             reason: 'database_mismatch',
             code: JsonRpcErrorCode.ValidationError,
@@ -80,19 +163,75 @@ export const interproGetEntry = tool('interpro_get_entry', {
         ...UPSTREAM_ERRORS,
     ],
     async handler(input, ctx) {
+        if (input.overlapOffset !== undefined && input.overlapLimit === undefined)
+            throw ctx.fail('overlap_limit_required');
+        if (input.overlapLimit !== undefined &&
+            input.sections &&
+            !input.sections.includes('overlaps_with'))
+            throw ctx.fail('overlaps_not_selected');
         const target = resolveEntry(input.accession, input.sourceDatabase);
         const service = getInterproService();
         const response = await service.request(service.begin(ctx), ['entry', target.sourceDatabase, target.accession], {}, detailSchema(EntryMetadataSchema), { missing: { reason: 'entry_not_found', ...target } });
         if (!response.data)
             throw ctx.fail('upstream_shape_invalid', 'Entry metadata response is missing.');
-        const { metadata, notice } = projectWikipediaThumbnails(response.data.metadata, input.includeThumbnail, 'interpro_get_entry');
+        const sourceMetadata = response.data.metadata;
+        const selected = input.sections === undefined
+            ? undefined
+            : SECTIONS.filter((section) => input.sections?.includes(section));
+        const omittedSections = selected === undefined
+            ? undefined
+            : SECTIONS.filter((section) => !selected.includes(section) && Object.hasOwn(sourceMetadata, section));
+        const projected = { ...sourceMetadata };
+        for (const section of omittedSections ?? [])
+            delete projected[section];
+        const notices = [];
+        if (selected)
+            notices.push(`Selected sections: ${JSON.stringify(selected)}; omitted source sections: ${JSON.stringify(omittedSections)}. Core and unknown metadata are retained.`);
+        let overlapsPage;
+        if (input.overlapLimit !== undefined) {
+            const offset = input.overlapOffset ?? 0;
+            const overlaps = projected.overlaps_with;
+            if (overlaps === undefined || overlaps === null) {
+                overlapsPage = { available: false, offset };
+                notices.push('Overlap paging is unavailable because upstream overlaps_with is missing or null; no total is known.');
+            }
+            else {
+                if (!Array.isArray(overlaps))
+                    throw ctx.fail('upstream_shape_invalid', 'Entry overlaps_with is not an array.');
+                const slice = overlaps.slice(offset, offset + Math.min(input.overlapLimit, overlaps.length));
+                projected.overlaps_with = slice;
+                const nextOffset = offset + slice.length;
+                const hasMore = nextOffset < overlaps.length;
+                ctx.enrich.total(overlaps.length);
+                overlapsPage = {
+                    available: true,
+                    total: overlaps.length,
+                    offset,
+                    returned: slice.length,
+                    hasMore,
+                    ...(hasMore ? { nextOffset } : {}),
+                };
+                notices.push(`Overlap page returned ${slice.length} of ${overlaps.length} records at offset ${offset}.`);
+                if (hasMore)
+                    notices.push(`Continue with interpro_get_entry ${JSON.stringify({ ...target, includeThumbnail: input.includeThumbnail, ...(selected ? { sections: selected } : {}), overlapLimit: input.overlapLimit, overlapOffset: nextOffset })}.`);
+            }
+        }
+        const { metadata, notice } = projectWikipediaThumbnails(projected, input.includeThumbnail, 'interpro_get_entry');
         if (notice)
-            ctx.enrich.notice(notice);
+            notices.push(notice);
+        if (notices.length)
+            ctx.enrich.notice(notices.join(' '));
+        const readable = descriptionText(metadata.description);
+        const entry = normalizeImages(metadata);
+        if (readable)
+            entry.descriptionText = readable;
         return {
             ...target,
-            entry: normalizeImages(metadata),
+            entry,
             url: `https://www.ebi.ac.uk/interpro/entry/${target.sourceDatabase}/${encodeURIComponent(target.accession)}/`,
             sourceUrl: response.sourceUrl,
+            ...(selected ? { sections: selected, omittedSections } : {}),
+            ...(overlapsPage ? { overlapsPage } : {}),
         };
     },
     format: formatInterpro,

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

@@ -9,6 +9,7 @@ export declare const interproGetProteinDomains: import("@cyanheads/mcp-ts-core")
     accession: z.ZodString;
     residuePosition: z.ZodOptional<z.ZodNumber>;
     includeExtraFeatures: z.ZodDefault<z.ZodBoolean>;
+    includeResidueAnnotations: z.ZodDefault<z.ZodBoolean>;
     cursor: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
 }, z.core.$strip>, z.ZodObject<{
     accession: z.ZodString;
@@ -69,9 +70,24 @@ export declare const interproGetProteinDomains: import("@cyanheads/mcp-ts-core")
             score: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
         }, z.core.$catchall<z.ZodJSONSchema>>>;
     }, z.core.$catchall<z.ZodJSONSchema>>>>;
+    residueAnnotations: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodObject<{
+        accession: z.ZodString;
+        source_database: z.ZodString;
+        locations: z.ZodArray<z.ZodObject<{
+            fragments: z.ZodArray<z.ZodObject<{
+                start: z.ZodNumber;
+                end: z.ZodNumber;
+                'dc-status': z.ZodOptional<z.ZodString>;
+            }, z.core.$catchall<z.ZodJSONSchema>>>;
+            representative: z.ZodOptional<z.ZodNullable<z.ZodBoolean>>;
+            model: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+            score: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>>;
     selection: z.ZodObject<{
         residuePosition: z.ZodOptional<z.ZodNumber>;
         includeExtraFeatures: z.ZodBoolean;
+        includeResidueAnnotations: z.ZodOptional<z.ZodLiteral<true>>;
     }, z.core.$strip>;
     coverage: z.ZodObject<{
         totalMatches: z.ZodNumber;
@@ -79,6 +95,8 @@ export declare const interproGetProteinDomains: import("@cyanheads/mcp-ts-core")
         returnedMatches: z.ZodNumber;
         totalFeatures: z.ZodOptional<z.ZodNumber>;
         returnedFeatures: z.ZodOptional<z.ZodNumber>;
+        totalResidueAnnotations: z.ZodOptional<z.ZodNumber>;
+        returnedResidueAnnotations: z.ZodOptional<z.ZodNumber>;
         complete: z.ZodBoolean;
         hasMore: z.ZodBoolean;
         nextCursor: z.ZodOptional<z.ZodString>;
@@ -88,9 +106,9 @@ export declare const interproGetProteinDomains: import("@cyanheads/mcp-ts-core")
 }, z.core.$strip>, readonly [{
     readonly reason: "retry_deadline_exceeded";
     readonly code: JsonRpcErrorCode.Timeout;
-    readonly when: "The shared fifty-second budget expires across protein metadata, match pages, and extra features.";
+    readonly when: "The shared fifty-second budget expires across metadata, match pages, extra features, and residue rules.";
     readonly retryable: true;
-    readonly recovery: "Retry interpro_get_protein_domains after waiting; omit extra features when they are not needed.";
+    readonly recovery: "Retry interpro_get_protein_domains after waiting; omit optional annotations when they are not needed.";
     readonly thrownBy: "service";
 }, {
     readonly reason: "invalid_cursor";

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

	@@ -1 +1 @@
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