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

@cyanheads/interpro-mcp-server 0.1.1 → 0.1.3

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Files changed (40) hide show

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

@@ -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;
@@ -21,13 +21,17 @@ 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()
@@ -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 CHANGED Viewed

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

@@ -112,6 +112,18 @@ export declare const interproSearchEntries: import("@cyanheads/mcp-ts-core").Too
     }, z.core.$strip>;
     sourceUrl: z.ZodString;
 }, z.core.$strip>, readonly [{
+    readonly reason: "incompatible_go_filters";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "Both goTerm and goCategory are supplied.";
+    readonly retryable: false;
+    readonly recovery: "Search with goTerm alone or goCategory alone; either supports query and entryType filters.";
+}, {
+    readonly reason: "go_filters_require_interpro";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "goTerm or goCategory is supplied for a member sourceDatabase.";
+    readonly retryable: false;
+    readonly recovery: "Search interpro_search_entries with sourceDatabase interpro and the GO filter, then read each result's member_databases with interpro_get_entry or search the member database with integratedInto set to that InterPro accession.";
+}, {
     readonly reason: "database_mismatch";
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "Integration filtering is requested on the integrating database.";

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

	@@ -1 +1 @@
1	- {"version":3,"file":"interpro-search-entries.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/interpro-search-entries.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmCjE,wEAAwE;AACxE,eAAO,MAAM,qBAAqB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4JhC~~,CAAC"}
1	+ {"version":3,"file":"interpro-search-entries.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/interpro-search-entries.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmCjE,wEAAwE;AACxE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAuLhC,CAAC"}

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

@@ -25,7 +25,7 @@ const RowSchema = z
 /** 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.',
+    description: 'Search InterPro entries or member signatures by text or entry type. GO filters require sourceDatabase interpro; integratedInto selects member signatures for an 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({
@@ -35,8 +35,8 @@ export const interproSearchEntries = tool('interpro_search_entries', {
         goTerm: optionalString(z
             .string()
             .trim()
-            .regex(/^GO:\d{7}$/)).describe('GO annotation identifier such as GO:0003677.'),
-        goCategory: optionalString(z.enum(['P', 'F', 'C'])).describe('GO category: P biological process, F molecular function, C cellular component.'),
+            .regex(/^GO:\d{7}$/)).describe('GO annotation identifier such as GO:0003677; requires sourceDatabase interpro and cannot combine with goCategory.'),
+        goCategory: optionalString(z.enum(['P', 'F', 'C'])).describe('GO category: P biological process, F molecular function, C cellular component; requires sourceDatabase interpro and cannot combine with goTerm.'),
         integratedInto: optionalString(z
             .string()
             .trim()
@@ -45,9 +45,8 @@ export const interproSearchEntries = tool('interpro_search_entries', {
             .number()
             .int()
             .min(1)
-            .max(MAX_LIMIT)
             .default(20)
-            .describe('Page size, from 1 to 100; defaults to 20.'),
+            .describe('Positive integer 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 from this tool with unchanged filters; limit may change.'),
     }),
     output: z.object({
@@ -63,10 +62,24 @@ export const interproSearchEntries = tool('interpro_search_entries', {
         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.'),
+        cap: z.number().int().optional().describe('Effective page size after clamping.'),
         effectiveQuery: z.string().optional().describe('Applied filters as JSON.'),
     },
     errors: [
+        {
+            reason: 'incompatible_go_filters',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'Both goTerm and goCategory are supplied.',
+            retryable: false,
+            recovery: 'Search with goTerm alone or goCategory alone; either supports query and entryType filters.',
+        },
+        {
+            reason: 'go_filters_require_interpro',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'goTerm or goCategory is supplied for a member sourceDatabase.',
+            retryable: false,
+            recovery: "Search interpro_search_entries with sourceDatabase interpro and the GO filter, then read each result's member_databases with interpro_get_entry or search the member database with integratedInto set to that InterPro accession.",
+        },
         {
             reason: 'database_mismatch',
             code: JsonRpcErrorCode.ValidationError,
@@ -101,6 +114,12 @@ export const interproSearchEntries = tool('interpro_search_entries', {
         ...UPSTREAM_ERRORS,
     ],
     async handler(input, ctx) {
+        if (input.sourceDatabase !== 'interpro' && (input.goTerm || input.goCategory))
+            throw ctx.fail('go_filters_require_interpro', 'GO filters select InterPro annotations and require sourceDatabase interpro.');
+        if (input.goTerm && input.goCategory)
+            throw ctx.fail('incompatible_go_filters', 'goTerm and goCategory cannot be combined.');
+        const limit = Math.min(input.limit, MAX_LIMIT);
+        const notices = input.limit > limit ? [`Requested limit ${input.limit} was clamped to ${limit}.`] : [];
         if (input.integratedInto && input.sourceDatabase === 'interpro')
             throw ctx.fail('database_mismatch', 'integratedInto requires a member sourceDatabase.');
         const query = {
@@ -119,7 +138,7 @@ export const interproSearchEntries = tool('interpro_search_entries', {
             go_term: query.goTerm,
             go_category: query.goCategory,
             integrated: query.integratedInto,
-            page_size: input.limit,
+            page_size: limit,
             cursor,
         }, listSchema(RowSchema), { continuation: cursor !== undefined });
         const entries = normalizeImages(response.data?.results.map((row) => row.metadata) ?? []);
@@ -127,27 +146,27 @@ export const interproSearchEntries = tool('interpro_search_entries', {
         const page = {
             total: response.data?.count ?? 0,
             returned: entries.length,
-            limit: input.limit,
+            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.' +
+            notices.push('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.'
                     : ''));
         }
+        if (next) {
+            notices.push(pageGuidance('interpro_search_entries', 'entries', limit, MAX_LIMIT));
+            ctx.enrich.truncated({ shown: entries.length, cap: limit, guidance: notices.join(' ') });
+        }
+        else if (notices.length)
+            ctx.enrich.notice(notices.join(' '));
         return { query, entries, page, sourceUrl: response.sourceUrl };
     },
     format: formatInterpro,

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

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/services/interpro/description-text.d.ts ADDED Viewed

@@ -0,0 +1,3 @@
+/** Decode description fragments without executing markup or changing the source description. */
+export declare function descriptionText(description: unknown): string | undefined;
+//# sourceMappingURL=description-text.d.ts.map

package/dist/services/interpro/description-text.d.ts.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"file":"description-text.d.ts","sourceRoot":"","sources":["../../../src/services/interpro/description-text.ts"],"names":[],"mappings":"AAwBA,gGAAgG;AAChG,wBAAgB,eAAe,CAAC,WAAW,EAAE,OAAO,GAAG,MAAM,GAAG,SAAS,CA0IxE"}