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

package/dist/services/interpro/routing.js

@@ -0,0 +1,106 @@
+/**
+ * @fileoverview Validated accession routing and fixed-origin InterPro URLs.
+ * @module services/interpro/routing
+ */
+import { notFound, validationError } from '@cyanheads/mcp-ts-core/errors';
+import { AccessionSchema } from './schemas.js';
+/** Canonical API origin; no upstream continuation URL is fetched directly. */
+export const API_BASE = 'https://www.ebi.ac.uk/interpro/api/';
+/** Official reference documentation. */
+export const DOCUMENTATION_URL = 'https://interpro-documentation.readthedocs.io/en/latest/api.html';
+/** Routing patterns and examples are shared with the reference vocabulary. */
+export const ENTRY_ROUTES = [
+    { source: 'interpro', pattern: /^IPR\d{6}$/i, example: 'IPR011615' },
+    { source: 'pfam', pattern: /^PF\d{5}$/i, example: 'PF00870' },
+    { source: 'prosite', pattern: /^PS00\d{3}$/i, example: 'PS00107' },
+    { source: 'profile', pattern: /^PS5\d{4}$/i, example: 'PS50011' },
+    { source: 'smart', pattern: /^SM\d{5}$/i, example: 'SM00220' },
+    { source: 'cdd', pattern: /^cd\d+$/i, example: 'cd08367' },
+    { source: 'panther', pattern: /^PTHR\d+(?::SF\d+)?$/i, example: 'PTHR11447' },
+    { source: 'cathgene3d', pattern: /^G3DSA:\d+\.\d+\.\d+\.\d+$/i, example: 'G3DSA:3.30.200.20' },
+    { source: 'ssf', pattern: /^SSF\d+$/i, example: 'SSF56112' },
+    { source: 'ncbifam', pattern: /^(?:TIGR|NF)\d+$/i, example: 'TIGR00001' },
+    { source: 'hamap', pattern: /^MF_\d+$/i, example: 'MF_00001' },
+    { source: 'prints', pattern: /^PR\d+$/i, example: 'PR00386' },
+    { source: 'pirsf', pattern: /^PIRSF\d+$/i, example: 'PIRSF000047' },
+    { source: 'sfld', pattern: /^SFLD[A-Z]?\d+$/i, example: 'SFLDF00001' },
+    { source: 'antifam', pattern: /^ANF\d+$/i, example: 'ANF00001' },
+];
+/** Pfam clan (`CL`) and CDD superfamily (`cl`) accessions name sets, never entries. */
+const CLAN_PATTERN = /^cl\d+$/i;
+/** Resolve one entry accession without guessing alternate databases after a miss. */
+export function resolveEntry(accession, sourceDatabase) {
+    const safe = AccessionSchema.parse(accession);
+    if (CLAN_PATTERN.test(safe))
+        throw notFound(`${safe} is a set accession, not an entry accession.`, {
+            reason: 'entry_not_found',
+            retryable: false,
+            accession: safe,
+            recovery: {
+                hint: 'Call interpro_get_clan with this accession to read the set and its member entries.',
+            },
+        });
+    const inferred = ENTRY_ROUTES.find((route) => route.pattern.test(safe))?.source;
+    if (inferred && sourceDatabase && inferred !== sourceDatabase)
+        throw validationError(`Accession ${safe} routes to sourceDatabase ${inferred} by its prefix, not ${sourceDatabase}.`, {
+            reason: 'database_mismatch',
+            retryable: false,
+            accession: safe,
+            sourceDatabase,
+            inferredSourceDatabase: inferred,
+        });
+    const source = sourceDatabase ?? inferred;
+    if (!source)
+        throw validationError(`Accession ${safe} matches no standard prefix, and no sourceDatabase was supplied.`, { reason: 'accession_source_unknown', retryable: false, accession: safe });
+    return {
+        accession: inferred ? (source === 'cdd' ? safe.toLowerCase() : safe.toUpperCase()) : safe,
+        sourceDatabase: source,
+    };
+}
+/** Resolve case-sensitive CL clan prefixes, with explicit source disambiguation. */
+export function resolveClan(accession, sourceDatabase) {
+    const safe = AccessionSchema.parse(accession);
+    const isCl = CLAN_PATTERN.test(safe);
+    const isPirsf = /^PIRSF\d+$/i.test(safe);
+    const inferred = /^CL\d+$/.test(safe)
+        ? 'pfam'
+        : /^cl\d+$/.test(safe)
+            ? 'cdd'
+            : isPirsf
+                ? 'pirsf'
+                : undefined;
+    if ((isPirsf && sourceDatabase && sourceDatabase !== 'pirsf') ||
+        (isCl && sourceDatabase === 'pirsf'))
+        throw validationError(`Set accession ${safe} routes to sourceDatabase ${inferred ?? 'pfam or cdd'} by its prefix, not ${sourceDatabase}.`, {
+            reason: 'database_mismatch',
+            retryable: false,
+            accession: safe,
+            sourceDatabase,
+            ...(inferred ? { inferredSourceDatabase: inferred } : {}),
+        });
+    const source = sourceDatabase ?? inferred;
+    if (!source)
+        throw validationError(isCl
+            ? `Set accession ${safe} has a mixed-case CL prefix, which can name a Pfam or CDD set, and no sourceDatabase was supplied.`
+            : `Set accession ${safe} matches no set prefix, and no sourceDatabase was supplied.`, { reason: 'accession_source_unknown', retryable: false, accession: safe });
+    return {
+        accession: isCl
+            ? source === 'cdd'
+                ? safe.toLowerCase()
+                : safe.toUpperCase()
+            : inferred
+                ? safe.toUpperCase()
+                : safe,
+        sourceDatabase: source,
+    };
+}
+/** Build fixed-origin requests from independently validated, encoded path segments. */
+export function apiUrl(segments, query = {}) {
+    const path = segments.map((part) => encodeURIComponent(AccessionSchema.parse(part))).join('/');
+    const url = new URL(`${path}${path ? '/' : ''}`, API_BASE);
+    for (const [key, value] of Object.entries(query))
+        if (value !== undefined)
+            url.searchParams.set(key, String(value));
+    return url.href;
+}
+//# sourceMappingURL=routing.js.map

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

@@ -0,0 +1 @@
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package/dist/services/interpro/schemas.d.ts

@@ -0,0 +1,182 @@
+/**
+ * @fileoverview Lossless InterPro wire schemas and shared input vocabulary.
+ * @module services/interpro/schemas
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+/** JSON values retained verbatim from upstream records. */
+export declare const JsonValueSchema: z.ZodJSONSchema;
+/** An upstream object with every additional JSON field retained. */
+export declare const JsonObjectSchema: z.ZodRecord<z.ZodString, z.ZodJSONSchema>;
+/** Supported entry API routes, including separate PROSITE pattern and profile routes. */
+export declare const SourceDatabaseSchema: 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";
+}>;
+/** Entry annotation categories. */
+export declare const EntryTypeSchema: 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";
+}>;
+/** A validated database route. */
+export type SourceDatabase = z.infer<typeof SourceDatabaseSchema>;
+/** Form clients may submit blank optional strings. */
+export declare const optionalString: <T extends z.ZodType>(schema: T) => z.ZodPreprocess<z.ZodOptional<T>, unknown>;
+/** A blank string takes the `.default()` that `schema` declares, as an omitted one does. */
+export declare const defaultedString: <T extends z.ZodType>(schema: T) => z.ZodPreprocess<T, unknown>;
+/** Safe identifiers are encoded as a single path segment after validation. */
+export declare const AccessionSchema: z.ZodString;
+/**
+ * Whether an upstream value is exactly an accession, the only form server-written text may name
+ * it in. The schema trims, so a value padded with blank lines must not pass as one.
+ */
+export declare const isAccession: (value: unknown) => value is string;
+/** Canonical UniProt accessions exclude isoform suffixes. */
+export declare const ProteinAccessionSchema: z.ZodString;
+/** GO annotation returned by InterPro. */
+export declare const GoTermSchema: 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>>;
+/** Sparse list metadata; only routing fields are required. */
+export declare const EntrySummarySchema: 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.$catchall<z.ZodJSONSchema>>;
+/** Detail metadata differs from summary metadata: names are objects. */
+export declare const EntryMetadataSchema: z.ZodObject<{
+    accession: z.ZodString;
+    source_database: z.ZodString;
+    name: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+        name: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        short: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>>;
+}, z.core.$catchall<z.ZodJSONSchema>>;
+/** Complete location fragments retain discontinuity and arbitrary annotations. */
+export declare const LocationSchema: z.ZodObject<{
+    fragments: z.ZodArray<z.ZodObject<{
+        start: z.ZodNumber;
+        end: z.ZodNumber;
+        'dc-status': z.ZodOptional<z.ZodString>;
+    }, z.core.$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.$catchall<z.ZodJSONSchema>>;
+/** Protein metadata preserves omitted annotations and additional source fields. */
+export declare const ProteinMetadataSchema: z.ZodObject<{
+    accession: z.ZodString;
+    length: z.ZodNumber;
+    source_database: z.ZodString;
+    name: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    gene: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    source_organism: z.ZodOptional<z.ZodObject<{
+        taxId: z.ZodUnion<readonly [z.ZodString, z.ZodNumber]>;
+        scientificName: z.ZodString;
+        fullName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>;
+}, z.core.$catchall<z.ZodJSONSchema>>;
+/** Protein match rows retain complete nested source records. */
+export declare const MatchSchema: z.ZodObject<{
+    metadata: z.ZodObject<{
+        accession: z.ZodString;
+        source_database: z.ZodString;
+        name: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        type: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        integrated: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        member_databases: z.ZodOptional<z.ZodNullable<z.ZodRecord<z.ZodString, z.ZodRecord<z.ZodString, z.ZodString>>>>;
+        go_terms: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodObject<{
+            identifier: z.ZodString;
+            name: z.ZodString;
+            category: z.ZodObject<{
+                code: z.ZodString;
+                name: z.ZodString;
+            }, z.core.$catchall<z.ZodJSONSchema>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>>>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>;
+    proteins: z.ZodArray<z.ZodObject<{
+        accession: z.ZodString;
+        entry_protein_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.$catchall<z.ZodJSONSchema>>>;
+}, z.core.$catchall<z.ZodJSONSchema>>;
+/** Feature-keyed extra annotations, not a protein detail envelope. */
+export declare const ExtraFeaturesSchema: 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.$catchall<z.ZodJSONSchema>>>;
+/** Standard list envelope; callers select the operation-specific row schema. */
+export declare const listSchema: <T extends z.ZodType>(row: T) => z.ZodObject<{
+    count: z.ZodNumber;
+    next: z.ZodNullable<z.ZodString>;
+    previous: z.ZodNullable<z.ZodString>;
+    results: z.ZodArray<T>;
+}, z.core.$catchall<z.ZodJSONSchema>>;
+/** Detail response envelope. */
+export declare const detailSchema: <T extends z.ZodType>(metadata: T) => z.ZodObject<{
+    metadata: T;
+}, z.core.$catchall<z.ZodJSONSchema>>;
+/** Server-owned page metadata. */
+export declare const PageSchema: z.ZodObject<{
+    total: z.ZodNumber;
+    returned: z.ZodNumber;
+    limit: z.ZodNumber;
+    hasMore: z.ZodBoolean;
+    nextCursor: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>;
+//# sourceMappingURL=schemas.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/services/interpro/schemas.js

@@ -0,0 +1,215 @@
+/**
+ * @fileoverview Lossless InterPro wire schemas and shared input vocabulary.
+ * @module services/interpro/schemas
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+/** JSON values retained verbatim from upstream records. */
+export const JsonValueSchema = z.json().describe('An unmodified JSON value.');
+/** An upstream object with every additional JSON field retained. */
+export const JsonObjectSchema = z
+    .record(z.string(), JsonValueSchema)
+    .describe('Complete upstream JSON object.');
+/** Supported entry API routes, including separate PROSITE pattern and profile routes. */
+export const SourceDatabaseSchema = z
+    .enum([
+    'interpro',
+    'pfam',
+    'prosite',
+    'profile',
+    'smart',
+    'cdd',
+    'panther',
+    'cathgene3d',
+    'ssf',
+    'ncbifam',
+    'hamap',
+    'prints',
+    'pirsf',
+    'sfld',
+    'antifam',
+])
+    .describe('InterPro entry API database slug.');
+/** Entry annotation categories. */
+export const EntryTypeSchema = z
+    .enum([
+    'domain',
+    'family',
+    'repeat',
+    'homologous_superfamily',
+    'active_site',
+    'binding_site',
+    'conserved_site',
+    'ptm',
+    'region',
+    'coiled_coil',
+    'disordered',
+])
+    .describe('Entry annotation type.');
+/** A blank or whitespace-only string from a form client reads as omitted. */
+const omitBlank = (value) => typeof value === 'string' && value.trim() === '' ? undefined : value;
+/** Form clients may submit blank optional strings. */
+export const optionalString = (schema) => z.preprocess(omitBlank, schema.optional());
+/** A blank string takes the `.default()` that `schema` declares, as an omitted one does. */
+export const defaultedString = (schema) => z.preprocess(omitBlank, schema);
+/** Safe identifiers are encoded as a single path segment after validation. */
+export const AccessionSchema = z
+    .string()
+    .trim()
+    .min(1)
+    .max(100)
+    .regex(/^[A-Za-z0-9_.:-]+$/)
+    .refine((value) => value !== '.' && value !== '..', 'Dot segments are not accessions.')
+    .describe('Identifier encoded as one path segment; no URL syntax.');
+/**
+ * Whether an upstream value is exactly an accession, the only form server-written text may name
+ * it in. The schema trims, so a value padded with blank lines must not pass as one.
+ */
+export const isAccession = (value) => typeof value === 'string' && AccessionSchema.safeParse(value).data === value;
+/** Canonical UniProt accessions exclude isoform suffixes. */
+export const ProteinAccessionSchema = z
+    .string()
+    .trim()
+    .regex(/^(?:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2})$/i)
+    .describe('Canonical six- or ten-character UniProt accession, without an isoform suffix.');
+/** GO annotation returned by InterPro. */
+export const GoTermSchema = z
+    .object({
+    identifier: z.string().describe('GO identifier.'),
+    name: z.string().describe('GO term name.'),
+    category: z
+        .object({
+        code: z.string().describe('GO category code.'),
+        name: z.string().describe('GO category name.'),
+    })
+        .catchall(JsonValueSchema)
+        .describe('GO category.'),
+})
+    .catchall(JsonValueSchema)
+    .describe('GO annotation.');
+/** Sparse list metadata; only routing fields are required. */
+export const EntrySummarySchema = z
+    .object({
+    accession: z.string().describe('Entry accession.'),
+    source_database: z.string().describe('Upstream source database.'),
+    name: z.string().nullable().optional().describe('Entry name when supplied.'),
+    type: z.string().nullable().optional().describe('Entry type when supplied.'),
+    integrated: z.string().nullable().optional().describe('Integrated InterPro accession.'),
+    member_databases: z
+        .record(z.string(), z.record(z.string(), z.string()))
+        .nullable()
+        .optional()
+        .describe('Member signatures grouped by database.'),
+    go_terms: z.array(GoTermSchema).nullable().optional().describe('GO annotations when supplied.'),
+})
+    .catchall(JsonValueSchema);
+/** Detail metadata differs from summary metadata: names are objects. */
+export const EntryMetadataSchema = z
+    .object({
+    accession: z.string().describe('Entry accession.'),
+    source_database: z.string().describe('Upstream database.'),
+    name: z
+        .object({
+        name: z.string().nullable().optional().describe('Full name.'),
+        short: z.string().nullable().optional().describe('Short name.'),
+    })
+        .catchall(JsonValueSchema)
+        .nullable()
+        .optional()
+        .describe('Detail name object.'),
+})
+    .catchall(JsonValueSchema);
+/** Complete location fragments retain discontinuity and arbitrary annotations. */
+export const LocationSchema = z
+    .object({
+    fragments: z
+        .array(z
+        .object({
+        start: z.number().int().positive().describe('Inclusive 1-based start residue.'),
+        end: z.number().int().positive().describe('Inclusive 1-based end residue.'),
+        'dc-status': z.string().optional().describe('Discontinuity status.'),
+    })
+        .catchall(JsonValueSchema)
+        .refine((fragment) => fragment.start <= fragment.end, 'Fragment start exceeds end.')
+        .describe('Complete continuous or discontinuous sequence fragment.'))
+        .min(1)
+        .describe('Nonempty sequence fragments.'),
+    representative: z.boolean().nullable().optional().describe('Representative match flag.'),
+    model: z.string().nullable().optional().describe('Source model.'),
+    score: z.number().nullable().optional().describe('Upstream match score.'),
+})
+    .catchall(JsonValueSchema)
+    .describe('Complete upstream match location.');
+/** Protein metadata preserves omitted annotations and additional source fields. */
+export const ProteinMetadataSchema = z
+    .object({
+    accession: z.string().describe('Protein accession.'),
+    length: z.number().int().positive().describe('Sequence length in residues.'),
+    source_database: z.string().describe('Protein source database.'),
+    name: z.string().nullable().optional().describe('Protein name.'),
+    gene: z.string().nullable().optional().describe('Gene name.'),
+    source_organism: z
+        .object({
+        taxId: z
+            .union([
+            z.string().describe('Taxonomy identifier as supplied text.'),
+            z.number().int().describe('Taxonomy identifier as supplied integer.'),
+        ])
+            .describe('Taxonomy identifier.'),
+        scientificName: z.string().describe('Scientific organism name.'),
+        fullName: z.string().nullable().optional().describe('Full organism name.'),
+    })
+        .catchall(JsonValueSchema)
+        .optional()
+        .describe('Source organism.'),
+})
+    .catchall(JsonValueSchema);
+/** Protein match rows retain complete nested source records. */
+export const MatchSchema = z
+    .object({
+    metadata: EntrySummarySchema.describe('Entry metadata.'),
+    proteins: z
+        .array(z
+        .object({
+        accession: z.string().describe('Matched protein accession.'),
+        entry_protein_locations: z
+            .array(LocationSchema)
+            .min(1)
+            .describe('Complete match locations.'),
+    })
+        .catchall(JsonValueSchema)
+        .describe('Complete protein match object.'))
+        .min(1)
+        .describe('Protein match objects.'),
+})
+    .catchall(JsonValueSchema);
+/** Feature-keyed extra annotations, not a protein detail envelope. */
+export const ExtraFeaturesSchema = z.record(z.string(), z
+    .object({
+    accession: z.string().describe('Feature accession.'),
+    source_database: z.string().describe('Feature source.'),
+    locations: z.array(LocationSchema).describe('Feature locations.'),
+})
+    .catchall(JsonValueSchema));
+/** Standard list envelope; callers select the operation-specific row schema. */
+export const listSchema = (row) => z
+    .object({
+    count: z.number().int().nonnegative().describe('Total matching records.'),
+    next: z.string().nullable().describe('Upstream continuation URL.'),
+    previous: z.string().nullable().describe('Upstream previous URL.'),
+    results: z.array(row).describe('Current page records.'),
+})
+    .catchall(JsonValueSchema);
+/** Detail response envelope. */
+export const detailSchema = (metadata) => z.object({ metadata: metadata.describe('Complete detail metadata.') }).catchall(JsonValueSchema);
+/** Server-owned page metadata. */
+export const PageSchema = z.object({
+    total: z.number().int().nonnegative().describe('Upstream total records.'),
+    returned: z.number().int().nonnegative().describe('Records returned in this page.'),
+    limit: z.number().int().positive().describe('Requested page size.'),
+    hasMore: z.boolean().describe('Whether upstream advertises continuation.'),
+    nextCursor: z
+        .string()
+        .optional()
+        .describe('Opaque continuation with unchanged target and filters.'),
+});
+//# sourceMappingURL=schemas.js.map

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

@@ -0,0 +1 @@
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package/dist/services/interpro/upstream-errors.d.ts

@@ -0,0 +1,43 @@
+/**
+ * @fileoverview Error contracts for upstream failures the service raises identically for every tool.
+ * @module services/interpro/upstream-errors
+ */
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+/** Declared upstream failures every tool shares; spread after `upstream_shape_invalid`. */
+export declare const UPSTREAM_ERRORS: readonly [{
+    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';
+}];
+//# sourceMappingURL=upstream-errors.d.ts.map

package/dist/services/interpro/upstream-errors.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"upstream-errors.d.ts","sourceRoot":"","sources":["../../../src/services/interpro/upstream-errors.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE,2FAA2F;AAC3F,eAAO,MAAM,eAAe;aAExB,MAAM,EAAE,6BAA6B;aACrC,IAAI;aACJ,IAAI,EAAE,qCAAqC;aAC3C,SAAS;aACT,QAAQ,EACN,wHAAwH;aAC1H,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,mBAAmB;aAC3B,IAAI;aACJ,IAAI,EAAE,6DAA6D;aACnE,SAAS;aACT,QAAQ,EACN,4GAA4G;aAC9G,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,sBAAsB;aAC9B,IAAI;aACJ,IAAI,EAAE,sEAAsE;aAC5E,SAAS;aACT,QAAQ,EACN,4GAA4G;aAC9G,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,kBAAkB;aAC1B,IAAI;aACJ,IAAI,EAAE,mEAAmE;aACzE,SAAS;aACT,QAAQ,EACN,sFAAsF;aACxF,QAAQ,EAAE,SAAS;;aAGnB,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,4BAA4B;aAClC,SAAS;aACT,QAAQ,EACN,2FAA2F;aAC7F,QAAQ,EAAE,SAAS;EAEb,CAAC"}

package/dist/services/interpro/upstream-errors.js

@@ -0,0 +1,49 @@
+/**
+ * @fileoverview Error contracts for upstream failures the service raises identically for every tool.
+ * @module services/interpro/upstream-errors
+ */
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+/** Declared upstream failures every tool shares; spread after `upstream_shape_invalid`. */
+export const UPSTREAM_ERRORS = [
+    {
+        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: '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',
+    },
+];
+//# sourceMappingURL=upstream-errors.js.map

package/dist/services/interpro/upstream-errors.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"upstream-errors.js","sourceRoot":"","sources":["../../../src/services/interpro/upstream-errors.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE,2FAA2F;AAC3F,MAAM,CAAC,MAAM,eAAe,GAAG;IAC7B;QACE,MAAM,EAAE,6BAA6B;QACrC,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,qCAAqC;QAC3C,SAAS,EAAE,KAAK;QAChB,QAAQ,EACN,wHAAwH;QAC1H,QAAQ,EAAE,SAAS;KACpB;IACD;QACE,MAAM,EAAE,mBAAmB;QAC3B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,6DAA6D;QACnE,SAAS,EAAE,KAAK;QAChB,QAAQ,EACN,4GAA4G;QAC9G,QAAQ,EAAE,SAAS;KACpB;IACD;QACE,MAAM,EAAE,sBAAsB;QAC9B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,sEAAsE;QAC5E,SAAS,EAAE,IAAI;QACf,QAAQ,EACN,4GAA4G;QAC9G,QAAQ,EAAE,SAAS;KACpB;IACD;QACE,MAAM,EAAE,kBAAkB;QAC1B,IAAI,EAAE,gBAAgB,CAAC,OAAO;QAC9B,IAAI,EAAE,mEAAmE;QACzE,SAAS,EAAE,IAAI;QACf,QAAQ,EACN,sFAAsF;QACxF,QAAQ,EAAE,SAAS;KACpB;IACD;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,WAAW;QAClC,IAAI,EAAE,4BAA4B;QAClC,SAAS,EAAE,IAAI;QACf,QAAQ,EACN,2FAA2F;QAC7F,QAAQ,EAAE,SAAS;KACpB;CACO,CAAC"}