@cyanheads/brapi-mcp-server 0.3.5

package/dist/services/dataset-store/types.d.ts

@@ -0,0 +1,65 @@
+/**
+ * @fileoverview Dataset lifecycle types — provenance, metadata, paginated
+ * load responses. All JSON-serializable so they round-trip through `ctx.state`.
+ *
+ * @module services/dataset-store/types
+ */
+export interface CreateDatasetInput {
+    /** BrAPI base URL the dataset was pulled from. */
+    baseUrl: string;
+    /** Optional column list; inferred from the first row when omitted. */
+    columns?: string[];
+    /** Cap the producer applied — number of rows that would have been pulled without truncation. Omit when no cap was applied. */
+    maxRows?: number;
+    /** Full query params / filter map — required for reproducibility. */
+    query: unknown;
+    /** Row payload. */
+    rows: Record<string, unknown>[];
+    /** Original tool / operation that produced the dataset (e.g. 'find_studies'). */
+    source: string;
+    /** True when the producer hit a cap before exhausting the upstream result set. */
+    truncated?: boolean;
+}
+export interface DatasetMetadata {
+    baseUrl: string;
+    columns: string[];
+    /** ISO 8601 create timestamp. */
+    createdAt: string;
+    datasetId: string;
+    /** ISO 8601 expiry — when the TTL will evict the dataset. */
+    expiresAt: string;
+    /** Cap that was applied at create time. Omitted when none. */
+    maxRows?: number;
+    query: unknown;
+    rowCount: number;
+    /** Serialized payload size in bytes (UTF-8 JSON). */
+    sizeBytes: number;
+    source: string;
+    /** True when the dataset rows were capped before exhausting upstream. */
+    truncated?: boolean;
+}
+export interface DatasetLoadOptions {
+    /** Subset of columns to return. Omitted → all columns. */
+    columns?: string[];
+    /** 1-indexed page number. Default 1. */
+    page?: number;
+    /** Rows per page. Default 100, max 1000. */
+    pageSize?: number;
+}
+export interface DatasetPage {
+    datasetId: string;
+    page: number;
+    pageSize: number;
+    rows: Record<string, unknown>[];
+    totalPages: number;
+    totalRows: number;
+}
+export interface DatasetListOptions {
+    cursor?: string;
+    limit?: number;
+}
+export interface DatasetListPage {
+    cursor?: string;
+    datasets: DatasetMetadata[];
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/services/dataset-store/types.d.ts.map

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package/dist/services/dataset-store/types.js

@@ -0,0 +1,8 @@
+/**
+ * @fileoverview Dataset lifecycle types — provenance, metadata, paginated
+ * load responses. All JSON-serializable so they round-trip through `ctx.state`.
+ *
+ * @module services/dataset-store/types
+ */
+export {};
+//# sourceMappingURL=types.js.map

package/dist/services/dataset-store/types.js.map

@@ -0,0 +1 @@
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package/dist/services/ontology-resolver/index.d.ts

@@ -0,0 +1,8 @@
+/**
+ * @fileoverview Public API barrel for the OntologyResolver service.
+ *
+ * @module services/ontology-resolver
+ */
+export { getOntologyResolver, initOntologyResolver, OntologyResolver, resetOntologyResolver, type VariableLike, } from './ontology-resolver.js';
+export type { OntologyCandidate, ResolveOptions } from './types.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/services/ontology-resolver/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/services/ontology-resolver/index.js

@@ -0,0 +1,7 @@
+/**
+ * @fileoverview Public API barrel for the OntologyResolver service.
+ *
+ * @module services/ontology-resolver
+ */
+export { getOntologyResolver, initOntologyResolver, OntologyResolver, resetOntologyResolver, } from './ontology-resolver.js';
+//# sourceMappingURL=index.js.map

package/dist/services/ontology-resolver/index.js.map

@@ -0,0 +1 @@
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package/dist/services/ontology-resolver/ontology-resolver.d.ts

@@ -0,0 +1,49 @@
+/**
+ * @fileoverview Free-text → ontology-term matcher for observation variables.
+ * The default backend scores each variable record against the query using
+ * substring + synonym matching; no network I/O of its own (variable lists
+ * are fetched upstream by the caller). Designed to be swappable — embedding-
+ * backed implementations can replace this one without changing the tool
+ * surface.
+ *
+ * @module services/ontology-resolver/ontology-resolver
+ */
+import type { OntologyCandidate, ResolveOptions } from './types.js';
+/**
+ * Loose shape of a BrAPI observation-variable record. Every field is
+ * optional because server implementations vary in what they populate.
+ */
+export interface VariableLike {
+    method?: {
+        methodName?: string;
+    };
+    observationVariableDbId?: string;
+    observationVariableName?: string;
+    observationVariablePUI?: string;
+    ontologyDbId?: string;
+    ontologyName?: string;
+    scale?: {
+        scaleName?: string;
+    };
+    synonyms?: string[] | undefined;
+    trait?: {
+        traitClass?: string;
+        description?: string;
+        name?: string;
+        synonyms?: string[];
+    };
+}
+export declare class OntologyResolver {
+    /**
+     * Rank a pool of variables against a free-text query. Returns up to
+     * `limit` candidates sorted by match quality (exact PUI > name match >
+     * synonym match). When the query is empty, returns the pool unchanged
+     * (up to the limit).
+     */
+    match(query: string, variables: readonly VariableLike[], options?: ResolveOptions): OntologyCandidate[];
+    private scoreOne;
+}
+export declare function initOntologyResolver(): void;
+export declare function getOntologyResolver(): OntologyResolver;
+export declare function resetOntologyResolver(): void;
+//# sourceMappingURL=ontology-resolver.d.ts.map

package/dist/services/ontology-resolver/ontology-resolver.d.ts.map

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package/dist/services/ontology-resolver/ontology-resolver.js

@@ -0,0 +1,99 @@
+/**
+ * @fileoverview Free-text → ontology-term matcher for observation variables.
+ * The default backend scores each variable record against the query using
+ * substring + synonym matching; no network I/O of its own (variable lists
+ * are fetched upstream by the caller). Designed to be swappable — embedding-
+ * backed implementations can replace this one without changing the tool
+ * surface.
+ *
+ * @module services/ontology-resolver/ontology-resolver
+ */
+export class OntologyResolver {
+    /**
+     * Rank a pool of variables against a free-text query. Returns up to
+     * `limit` candidates sorted by match quality (exact PUI > name match >
+     * synonym match). When the query is empty, returns the pool unchanged
+     * (up to the limit).
+     */
+    match(query, variables, options = {}) {
+        const limit = options.limit ?? 10;
+        const normalized = query.trim().toLowerCase();
+        if (!normalized) {
+            return variables.slice(0, limit).map((v) => toCandidate(v, 'nameMatch'));
+        }
+        const scored = [];
+        for (const variable of variables) {
+            if (options.ontologyDbId && variable.ontologyDbId !== options.ontologyDbId)
+                continue;
+            const match = this.scoreOne(variable, normalized);
+            if (match)
+                scored.push(match);
+        }
+        scored.sort((a, b) => b.score - a.score);
+        return scored.slice(0, limit).map((s) => s.candidate);
+    }
+    scoreOne(variable, query) {
+        const pui = variable.observationVariablePUI?.toLowerCase();
+        if (pui && pui === query) {
+            return { candidate: toCandidate(variable, 'puiMatch'), score: 100 };
+        }
+        const name = variable.observationVariableName?.toLowerCase();
+        if (name) {
+            if (name === query)
+                return { candidate: toCandidate(variable, 'nameMatch'), score: 90 };
+            if (name.includes(query))
+                return { candidate: toCandidate(variable, 'nameMatch'), score: 60 };
+        }
+        const synonymMatch = variable.synonyms?.find((s) => s.toLowerCase().includes(query));
+        if (synonymMatch) {
+            return { candidate: toCandidate(variable, 'synonymMatch'), score: 50 };
+        }
+        const traitSynonymMatch = variable.trait?.synonyms?.find((s) => s.toLowerCase().includes(query));
+        if (traitSynonymMatch) {
+            return { candidate: toCandidate(variable, 'synonymMatch'), score: 40 };
+        }
+        const traitName = variable.trait?.name?.toLowerCase();
+        if (traitName?.includes(query)) {
+            return { candidate: toCandidate(variable, 'nameMatch'), score: 35 };
+        }
+        const traitClass = variable.trait?.traitClass?.toLowerCase();
+        if (traitClass && traitClass === query) {
+            return { candidate: toCandidate(variable, 'traitClassMatch'), score: 30 };
+        }
+        const traitDescription = variable.trait?.description?.toLowerCase();
+        if (traitDescription?.includes(query)) {
+            return { candidate: toCandidate(variable, 'nameMatch'), score: 20 };
+        }
+        return;
+    }
+}
+function toCandidate(variable, source) {
+    const candidate = { source };
+    if (variable.observationVariablePUI)
+        candidate.termId = variable.observationVariablePUI;
+    const name = variable.observationVariableName ?? variable.trait?.name;
+    if (name)
+        candidate.name = name;
+    if (variable.trait?.description)
+        candidate.description = variable.trait.description;
+    if (variable.ontologyDbId)
+        candidate.ontologyDbId = variable.ontologyDbId;
+    const combinedSynonyms = [...(variable.synonyms ?? []), ...(variable.trait?.synonyms ?? [])];
+    if (combinedSynonyms.length > 0)
+        candidate.synonyms = Array.from(new Set(combinedSynonyms));
+    return candidate;
+}
+let _resolver;
+export function initOntologyResolver() {
+    _resolver = new OntologyResolver();
+}
+export function getOntologyResolver() {
+    if (!_resolver) {
+        throw new Error('OntologyResolver not initialized — call initOntologyResolver() in setup()');
+    }
+    return _resolver;
+}
+export function resetOntologyResolver() {
+    _resolver = undefined;
+}
+//# sourceMappingURL=ontology-resolver.js.map

package/dist/services/ontology-resolver/ontology-resolver.js.map

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package/dist/services/ontology-resolver/types.d.ts

@@ -0,0 +1,38 @@
+/**
+ * @fileoverview Types for OntologyResolver — resolved ontology-URI candidates
+ * with score and source attribution.
+ *
+ * @module services/ontology-resolver/types
+ */
+/**
+ * One candidate match returned by `OntologyResolver.resolve`. `source`
+ * reports how the match was produced so downstream tooling can surface the
+ * degradation path to users (e.g. "substring match — server has no /ontologies").
+ */
+export interface OntologyCandidate {
+    /** Short definition or description, when available. */
+    description?: string;
+    /** Display name of the trait/variable/term. */
+    name?: string;
+    /** Originating ontology (e.g. "CO_334"). */
+    ontologyDbId?: string;
+    /**
+     * How the candidate was surfaced:
+     *  - `puiMatch`  — exact match on `observationVariablePUIs`
+     *  - `nameMatch` — substring match on `observationVariableNames`
+     *  - `synonymMatch` — match on a registered synonym
+     *  - `traitClassMatch` — match via trait class
+     */
+    source: 'puiMatch' | 'nameMatch' | 'synonymMatch' | 'traitClassMatch';
+    /** Synonyms registered for this term. */
+    synonyms?: string[];
+    /** Persistent ontology URI or term ID (e.g. "CO_334:0000013"). */
+    termId?: string;
+}
+export interface ResolveOptions {
+    /** Max candidates to return. Default 10. */
+    limit?: number;
+    /** Optional ontology scope (e.g. "CO_334"). */
+    ontologyDbId?: string;
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/services/ontology-resolver/types.d.ts.map

@@ -0,0 +1 @@
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package/dist/services/ontology-resolver/types.js

@@ -0,0 +1,8 @@
+/**
+ * @fileoverview Types for OntologyResolver — resolved ontology-URI candidates
+ * with score and source attribution.
+ *
+ * @module services/ontology-resolver/types
+ */
+export {};
+//# sourceMappingURL=types.js.map

package/dist/services/ontology-resolver/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/services/ontology-resolver/types.ts"],"names":[],"mappings":"AAAA;;;;;GAKG"}

package/dist/services/reference-data-cache/index.d.ts

@@ -0,0 +1,9 @@
+/**
+ * @fileoverview Public API barrel for the ReferenceDataCache service.
+ *
+ * @module services/reference-data-cache
+ */
+export type { ReferenceLookupOptions } from './reference-data-cache.js';
+export { getReferenceDataCache, initReferenceDataCache, ReferenceDataCache, resetReferenceDataCache, } from './reference-data-cache.js';
+export type { Location, Program, Trial } from './types.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/services/reference-data-cache/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/services/reference-data-cache/index.js

@@ -0,0 +1,7 @@
+/**
+ * @fileoverview Public API barrel for the ReferenceDataCache service.
+ *
+ * @module services/reference-data-cache
+ */
+export { getReferenceDataCache, initReferenceDataCache, ReferenceDataCache, resetReferenceDataCache, } from './reference-data-cache.js';
+//# sourceMappingURL=index.js.map

package/dist/services/reference-data-cache/index.js.map

@@ -0,0 +1 @@
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package/dist/services/reference-data-cache/reference-data-cache.d.ts

@@ -0,0 +1,31 @@
+/**
+ * @fileoverview Per-connection batch cache for BrAPI reference nouns —
+ * programs, trials, locations. Used by tools (e.g. `find_studies`) to
+ * resolve foreign keys in a single upstream call per noun instead of N+1
+ * per-row lookups. Cache keys are tenant-scoped via `ctx.state` with TTL
+ * from `BRAPI_REFERENCE_CACHE_TTL_SECONDS`.
+ *
+ * @module services/reference-data-cache/reference-data-cache
+ */
+import type { Context } from '@cyanheads/mcp-ts-core';
+import type { ServerConfig } from '../../config/server-config.js';
+import { type BrapiClient, type BrapiRequestOptions } from '../../services/brapi-client/index.js';
+import type { Location, Program, Trial } from './types.js';
+export type ReferenceLookupOptions = Pick<BrapiRequestOptions, 'auth'>;
+export declare class ReferenceDataCache {
+    private readonly serverConfig;
+    private readonly client;
+    constructor(serverConfig: ServerConfig, client?: () => BrapiClient);
+    getPrograms(baseUrl: string, programDbIds: readonly string[], ctx: Context, options?: ReferenceLookupOptions): Promise<Map<string, Program>>;
+    getTrials(baseUrl: string, trialDbIds: readonly string[], ctx: Context, options?: ReferenceLookupOptions): Promise<Map<string, Trial>>;
+    getLocations(baseUrl: string, locationDbIds: readonly string[], ctx: Context, options?: ReferenceLookupOptions): Promise<Map<string, Location>>;
+    /** Drop every cached entry for a base URL across all reference nouns. */
+    invalidate(baseUrl: string, ctx: Context): Promise<void>;
+    private batchResolve;
+    private fetchBatch;
+    private deletePrefix;
+}
+export declare function initReferenceDataCache(serverConfig: ServerConfig): void;
+export declare function getReferenceDataCache(): ReferenceDataCache;
+export declare function resetReferenceDataCache(): void;
+//# sourceMappingURL=reference-data-cache.d.ts.map

package/dist/services/reference-data-cache/reference-data-cache.d.ts.map

@@ -0,0 +1 @@
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package/dist/services/reference-data-cache/reference-data-cache.js

@@ -0,0 +1,131 @@
+/**
+ * @fileoverview Per-connection batch cache for BrAPI reference nouns —
+ * programs, trials, locations. Used by tools (e.g. `find_studies`) to
+ * resolve foreign keys in a single upstream call per noun instead of N+1
+ * per-row lookups. Cache keys are tenant-scoped via `ctx.state` with TTL
+ * from `BRAPI_REFERENCE_CACHE_TTL_SECONDS`.
+ *
+ * @module services/reference-data-cache/reference-data-cache
+ */
+import { getBrapiClient, } from '../../services/brapi-client/index.js';
+const PROGRAM_CFG = {
+    endpoint: '/programs',
+    idFilter: 'programDbIds',
+    idField: 'programDbId',
+    cachePrefix: 'program',
+};
+const TRIAL_CFG = {
+    endpoint: '/trials',
+    idFilter: 'trialDbIds',
+    idField: 'trialDbId',
+    cachePrefix: 'trial',
+};
+const LOCATION_CFG = {
+    endpoint: '/locations',
+    idFilter: 'locationDbIds',
+    idField: 'locationDbId',
+    cachePrefix: 'location',
+};
+export class ReferenceDataCache {
+    serverConfig;
+    client;
+    constructor(serverConfig, client = getBrapiClient) {
+        this.serverConfig = serverConfig;
+        this.client = client;
+    }
+    getPrograms(baseUrl, programDbIds, ctx, options) {
+        return this.batchResolve(PROGRAM_CFG, baseUrl, programDbIds, ctx, options);
+    }
+    getTrials(baseUrl, trialDbIds, ctx, options) {
+        return this.batchResolve(TRIAL_CFG, baseUrl, trialDbIds, ctx, options);
+    }
+    getLocations(baseUrl, locationDbIds, ctx, options) {
+        return this.batchResolve(LOCATION_CFG, baseUrl, locationDbIds, ctx, options);
+    }
+    /** Drop every cached entry for a base URL across all reference nouns. */
+    async invalidate(baseUrl, ctx) {
+        const serverSlug = sanitizeKey(baseUrl);
+        await Promise.all([
+            this.deletePrefix(ctx, `brapi/ref/${PROGRAM_CFG.cachePrefix}/${serverSlug}/`),
+            this.deletePrefix(ctx, `brapi/ref/${TRIAL_CFG.cachePrefix}/${serverSlug}/`),
+            this.deletePrefix(ctx, `brapi/ref/${LOCATION_CFG.cachePrefix}/${serverSlug}/`),
+        ]);
+    }
+    async batchResolve(cfg, baseUrl, ids, ctx, options = {}) {
+        if (ids.length === 0)
+            return new Map();
+        const uniqueIds = Array.from(new Set(ids));
+        const serverSlug = sanitizeKey(baseUrl);
+        const keyFor = (id) => `brapi/ref/${cfg.cachePrefix}/${serverSlug}/${id}`;
+        const cached = await ctx.state.getMany(uniqueIds.map(keyFor));
+        const results = new Map();
+        const missing = [];
+        for (const id of uniqueIds) {
+            const hit = cached.get(keyFor(id));
+            if (hit)
+                results.set(id, hit);
+            else
+                missing.push(id);
+        }
+        if (missing.length === 0)
+            return results;
+        const fetched = await this.fetchBatch(cfg, baseUrl, missing, ctx, options);
+        const ttl = this.serverConfig.referenceCacheTtlSeconds;
+        await Promise.all(fetched.map(async (item) => {
+            const id = String(item[cfg.idField] ?? '');
+            if (!id)
+                return;
+            await ctx.state.set(keyFor(id), item, { ttl });
+            results.set(id, item);
+        }));
+        return results;
+    }
+    async fetchBatch(cfg, baseUrl, ids, ctx, options) {
+        const requestOptions = {
+            params: { [cfg.idFilter]: ids, pageSize: ids.length },
+        };
+        if (options.auth)
+            requestOptions.auth = options.auth;
+        const env = await this.client().get(baseUrl, cfg.endpoint, ctx, requestOptions);
+        return extractDataArray(env);
+    }
+    async deletePrefix(ctx, prefix) {
+        let cursor;
+        do {
+            const listOpts = { limit: 100 };
+            if (cursor !== undefined)
+                listOpts.cursor = cursor;
+            const page = await ctx.state.list(prefix, listOpts);
+            if (page.items.length > 0) {
+                await ctx.state.deleteMany(page.items.map((item) => item.key));
+            }
+            cursor = page.cursor;
+        } while (cursor);
+    }
+}
+function extractDataArray(envelope) {
+    const result = envelope.result;
+    if (Array.isArray(result))
+        return result;
+    if (result && typeof result === 'object' && 'data' in result && Array.isArray(result.data)) {
+        return result.data;
+    }
+    return [];
+}
+function sanitizeKey(value) {
+    return value.replace(/[^a-zA-Z0-9]/g, '-');
+}
+let _cache;
+export function initReferenceDataCache(serverConfig) {
+    _cache = new ReferenceDataCache(serverConfig);
+}
+export function getReferenceDataCache() {
+    if (!_cache) {
+        throw new Error('ReferenceDataCache not initialized — call initReferenceDataCache() in setup()');
+    }
+    return _cache;
+}
+export function resetReferenceDataCache() {
+    _cache = undefined;
+}
+//# sourceMappingURL=reference-data-cache.js.map

package/dist/services/reference-data-cache/reference-data-cache.js.map

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package/dist/services/reference-data-cache/types.d.ts

@@ -0,0 +1,42 @@
+/**
+ * @fileoverview Reference-data shapes for FK resolution — programs, trials,
+ * locations. Every non-id field is optional because BrAPI server
+ * implementations vary wildly in what they populate.
+ *
+ * @module services/reference-data-cache/types
+ */
+export interface Program {
+    abbreviation?: string;
+    commonCropName?: string;
+    documentationURL?: string;
+    leadPersonDbId?: string;
+    leadPersonName?: string;
+    objective?: string;
+    programDbId: string;
+    programName?: string;
+}
+export interface Trial {
+    active?: boolean;
+    commonCropName?: string;
+    documentationURL?: string;
+    endDate?: string;
+    programDbId?: string;
+    programName?: string;
+    startDate?: string;
+    trialDbId: string;
+    trialDescription?: string;
+    trialName?: string;
+}
+export interface Location {
+    abbreviation?: string;
+    altitude?: number;
+    countryCode?: string;
+    countryName?: string;
+    documentationURL?: string;
+    latitude?: number;
+    locationDbId: string;
+    locationName?: string;
+    locationType?: string;
+    longitude?: number;
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/services/reference-data-cache/types.d.ts.map

@@ -0,0 +1 @@
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package/dist/services/reference-data-cache/types.js

@@ -0,0 +1,9 @@
+/**
+ * @fileoverview Reference-data shapes for FK resolution — programs, trials,
+ * locations. Every non-id field is optional because BrAPI server
+ * implementations vary wildly in what they populate.
+ *
+ * @module services/reference-data-cache/types
+ */
+export {};
+//# sourceMappingURL=types.js.map

package/dist/services/reference-data-cache/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/services/reference-data-cache/types.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG"}

package/dist/services/server-registry/index.d.ts

@@ -0,0 +1,9 @@
+/**
+ * @fileoverview Public API barrel for the ServerRegistry service.
+ *
+ * @module services/server-registry
+ */
+export type { RegisterInput, TokenFetcher } from './server-registry.js';
+export { DEFAULT_ALIAS, getServerRegistry, initServerRegistry, resetServerRegistry, ServerRegistry, } from './server-registry.js';
+export type { AuthMode, ConnectAuth, RegisteredServer } from './types.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/services/server-registry/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/services/server-registry/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,YAAY,EAAE,aAAa,EAAE,YAAY,EAAE,MAAM,sBAAsB,CAAC;AACxE,OAAO,EACL,aAAa,EACb,iBAAiB,EACjB,kBAAkB,EAClB,mBAAmB,EACnB,cAAc,GACf,MAAM,sBAAsB,CAAC;AAC9B,YAAY,EAAE,QAAQ,EAAE,WAAW,EAAE,gBAAgB,EAAE,MAAM,YAAY,CAAC"}

package/dist/services/server-registry/index.js

@@ -0,0 +1,7 @@
+/**
+ * @fileoverview Public API barrel for the ServerRegistry service.
+ *
+ * @module services/server-registry
+ */
+export { DEFAULT_ALIAS, getServerRegistry, initServerRegistry, resetServerRegistry, ServerRegistry, } from './server-registry.js';
+//# sourceMappingURL=index.js.map

package/dist/services/server-registry/index.js.map

@@ -0,0 +1 @@
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