@digital-science-dsl/dimensions-analytics-mcp 0.5.3 → 1.0.1

package/dist/tools/kwq.d.ts

@@ -1,19 +0,0 @@
-/**
- * KWQ (Keyword Query) tools for the MCP server.
- * Provides structured query building and RRF ensemble fusion via the Dimensions API.
- * @module mcp/tools/kwq
- */
-import type { DimensionsClient } from "@digital-science/dimensions-dsl";
-import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import type { SchemaStore } from "../schema/index.js";
-/**
- * Registers KWQ tools with the MCP server.
- * - build_query: always registered (pure computation)
- * - ensemble_queries: always registered (uses Dimensions API via client)
- *
- * @param server - MCP server instance
- * @param client - Dimensions API client (for ensemble query execution)
- * @param schemaStore - Loaded describe schema for search index hints
- */
-export declare function registerKwqTools(server: McpServer, client: DimensionsClient, schemaStore: SchemaStore): void;
-//# sourceMappingURL=kwq.d.ts.map

package/dist/tools/kwq.d.ts.map

@@ -1 +0,0 @@
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package/dist/tools/kwq.js

@@ -1,156 +0,0 @@
-/**
- * KWQ (Keyword Query) tools for the MCP server.
- * Provides structured query building and RRF ensemble fusion via the Dimensions API.
- * @module mcp/tools/kwq
- */
-import { buildQuery, conceptGroupsToQuerySpec, ensembleQueries, } from "@digital-science/dimensions-kwq";
-import { z } from "zod";
-import { formatErrorResult, formatToolResult } from "../utils.js";
-// #region Shared schemas
-const ENTITY_ENUM = z.enum([
-    "publications",
-    "grants",
-    "researchers",
-    "patents",
-    "clinical_trials",
-    "datasets",
-    "policy_documents",
-    "organizations",
-]);
-const ConceptGroupSchema = z.object({
-    terms: z.array(z.string()).min(1).describe("Terms OR'd together (synonyms)"),
-    role: z.enum(["include", "exclude"]).describe("include = AND into query, exclude = NOT"),
-});
-const FilterSchema = z.object({
-    field: z.string(),
-    op: z.string(),
-    value: z.union([z.string(), z.number(), z.array(z.string()), z.array(z.number())]),
-});
-// #endregion
-// #region Tool registration
-/**
- * Registers KWQ tools with the MCP server.
- * - build_query: always registered (pure computation)
- * - ensemble_queries: always registered (uses Dimensions API via client)
- *
- * @param server - MCP server instance
- * @param client - Dimensions API client (for ensemble query execution)
- * @param schemaStore - Loaded describe schema for search index hints
- */
-export function registerKwqTools(server, client, schemaStore) {
-    const indexHints = ENTITY_ENUM.options
-        .map((entity) => `${entity}: ${schemaStore.searchIndexes(entity).join(", ") || "default"}`)
-        .join("; ");
-    // --- build_query ---
-    server.registerTool("build_query", {
-        description: `Build a validated Dimensions DSL query from structured concept groups.
-
-Use concept_groups for the common pattern: groups of synonym terms, AND'd together, with optional exclusions.
-Each group's terms are OR'd (synonyms), include groups are AND'd, exclude groups are NOT'd.
-
-Search indexes by entity: ${indexHints}
-
-For advanced nested boolean logic, use search_json with a SearchExpr tree instead.
-Returns the validated DSL string, validation status, human-readable description, and complexity metrics.`,
-        inputSchema: {
-            entity: ENTITY_ENUM.describe("Target entity type"),
-            concept_groups: z
-                .array(ConceptGroupSchema)
-                .optional()
-                .describe("Concept groups: include groups AND'd, each group's terms OR'd, exclude groups NOT'd"),
-            search_json: z
-                .string()
-                .optional()
-                .describe("Advanced: raw SearchExpr JSON tree (overrides concept_groups). Use for nested boolean logic."),
-            index: z
-                .string()
-                .optional()
-                .describe("Search index (e.g. title_abstract_only, full_data, title_only)"),
-            filters: z.array(FilterSchema).optional().describe("WHERE clause filters"),
-            fields: z.array(z.string()).optional().describe("Fields to return"),
-            sort_by: z.string().optional().describe("Sort field"),
-            sort_order: z.enum(["asc", "desc"]).optional().describe("Sort order"),
-            limit: z
-                .number()
-                .int()
-                .min(1)
-                .max(1000)
-                .optional()
-                .default(20)
-                .describe("Result limit (default 20, max 1000)"),
-            skip: z.number().int().min(0).optional().describe("Result offset"),
-        },
-        annotations: {
-            readOnlyHint: true,
-            destructiveHint: false,
-            idempotentHint: true,
-            openWorldHint: false,
-        },
-    }, async (args) => {
-        try {
-            if (args.concept_groups && args.search_json) {
-                return formatErrorResult(new Error("Provide either concept_groups or search_json, not both."));
-            }
-            const spec = conceptGroupsToQuerySpec(args);
-            const result = buildQuery(spec);
-            return formatToolResult({
-                dsl: result.dsl,
-                valid: result.validation._tag === "valid",
-                errors: result.validation._tag === "invalid" ? result.validation.errors : undefined,
-                warnings: result.validation._tag === "valid" && result.validation.warnings.length > 0
-                    ? result.validation.warnings
-                    : undefined,
-                description: result.description,
-                complexity: result.complexity,
-            });
-        }
-        catch (error) {
-            return formatErrorResult(error);
-        }
-    });
-    // --- ensemble_queries ---
-    server.registerTool("ensemble_queries", {
-        description: `Execute 2-10 query specs in parallel and fuse results using Reciprocal Rank Fusion (RRF).
-
-Each spec uses the same concept_groups model as build_query. RRF produces a
-variance-reduced ranking by combining multiple retrieval strategies — different
-keyword formulations, different indexes, or different filter configurations.
-
-RRF score: score(d) = Σ 1/(k + rank_i(d)) across all lists containing document d.
-Higher k (default 60) weights more evenly; lower k favors top-ranked documents.`,
-        inputSchema: {
-            specs: z
-                .array(z.object({
-                entity: ENTITY_ENUM.default("publications"),
-                concept_groups: z.array(ConceptGroupSchema).optional(),
-                search_json: z.string().optional(),
-                index: z.string().optional(),
-                filters: z.array(FilterSchema).optional(),
-                fields: z.array(z.string()).optional(),
-                limit: z.number().int().optional().default(100).describe("Per-query result limit"),
-            }))
-                .min(2)
-                .max(10)
-                .describe("2-10 query specs to execute and fuse"),
-            k: z.number().int().optional().default(60).describe("RRF k parameter (default 60)"),
-            limit: z.number().int().optional().default(100).describe("Max fused results to return"),
-        },
-        annotations: {
-            readOnlyHint: true,
-            destructiveHint: false,
-            idempotentHint: false,
-            openWorldHint: true,
-        },
-    }, async (args) => {
-        try {
-            const querySpecs = args.specs.map((spec) => conceptGroupsToQuerySpec(spec));
-            const result = await ensembleQueries((dsl) => client.rawQuery(dsl), querySpecs, { k: args.k, limit: args.limit });
-            return formatToolResult(result);
-        }
-        catch (error) {
-            return formatErrorResult(error);
-        }
-    });
-}
-// #endregion
-//# sourceMappingURL=kwq.js.map

package/dist/tools/kwq.js.map

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package/dist/tools/lookup.d.ts

@@ -1,14 +0,0 @@
-/**
- * Lookup tools for the MCP server.
- * Provides direct lookup by identifiers (DOI, PMID, Dimensions ID).
- * @module mcp/tools/lookup
- */
-import { type DimensionsClient } from "@digital-science/dimensions-dsl";
-import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-/**
- * Registers all lookup tools with the MCP server.
- * @param server - MCP server instance
- * @param client - Dimensions client instance
- */
-export declare function registerLookupTools(server: McpServer, client: DimensionsClient): void;
-//# sourceMappingURL=lookup.d.ts.map

package/dist/tools/lookup.d.ts.map

@@ -1 +0,0 @@
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package/dist/tools/lookup.js

@@ -1,213 +0,0 @@
-/**
- * Lookup tools for the MCP server.
- * Provides direct lookup by identifiers (DOI, PMID, Dimensions ID).
- * @module mcp/tools/lookup
- */
-import { EntitySchema, } from "@digital-science/dimensions-dsl";
-import { z } from "zod";
-import { withFieldAliases } from "../middleware/field-aliases.js";
-import { asArray, formatErrorResult, formatToolResult, READ_ONLY_API_ANNOTATIONS, withTruncationWarning, } from "../utils.js";
-/**
- * Registers all lookup tools with the MCP server.
- * @param server - MCP server instance
- * @param client - Dimensions client instance
- */
-export function registerLookupTools(server, client) {
-    // Get publication by DOI
-    server.registerTool("get_by_doi", {
-        description: "Retrieve a publication by its Digital Object Identifier (DOI). Returns full publication details including abstract, citations, and authors.",
-        inputSchema: {
-            doi: z.string().describe("The DOI to look up (e.g., '10.1038/nature12373')"),
-            fields: z
-                .array(z.string())
-                .optional()
-                .describe("Fields to return (e.g., ['id', 'title', 'abstract', 'times_cited'])"),
-        },
-        outputSchema: {
-            found: z.boolean().describe("Whether the entity was found"),
-            publication: z.record(z.string(), z.unknown()).optional().describe("The found entity"),
-            message: z.string().optional().describe("Message when not found"),
-        },
-        annotations: READ_ONLY_API_ANNOTATIONS,
-    }, withFieldAliases({ entitySource: { kind: "static", entity: "publications" }, fieldArrayArgs: ["fields"] }, async (args) => {
-        try {
-            const qb = client
-                .createQueryBuilder()
-                .search("publications")
-                .where("doi", "=", args.doi)
-                .limit(1);
-            if (args.fields?.length)
-                qb.fields(args.fields);
-            const dsl = qb.build();
-            const response = await client.rawQuery(dsl);
-            const publications = asArray(response.publications);
-            if (publications.length === 0) {
-                return formatToolResult({
-                    found: false,
-                    message: `No publication found with DOI: ${args.doi}`,
-                });
-            }
-            return formatToolResult({
-                found: true,
-                publication: publications[0],
-            });
-        }
-        catch (error) {
-            return formatErrorResult(error);
-        }
-    }));
-    // Get publication by PubMed ID
-    server.registerTool("get_by_pmid", {
-        description: "Retrieve a publication by its PubMed ID (PMID). Returns full publication details from Dimensions.",
-        inputSchema: {
-            pmid: z.string().describe("The PubMed ID to look up (e.g., '23846567')"),
-            fields: z
-                .array(z.string())
-                .optional()
-                .describe("Fields to return (e.g., ['id', 'title', 'abstract', 'times_cited'])"),
-        },
-        outputSchema: {
-            found: z.boolean().describe("Whether the entity was found"),
-            publication: z.record(z.string(), z.unknown()).optional().describe("The found entity"),
-            message: z.string().optional().describe("Message when not found"),
-        },
-        annotations: READ_ONLY_API_ANNOTATIONS,
-    }, withFieldAliases({ entitySource: { kind: "static", entity: "publications" }, fieldArrayArgs: ["fields"] }, async (args) => {
-        try {
-            const qb = client
-                .createQueryBuilder()
-                .search("publications")
-                .where("pmid", "=", args.pmid)
-                .limit(1);
-            if (args.fields?.length)
-                qb.fields(args.fields);
-            const dsl = qb.build();
-            const response = await client.rawQuery(dsl);
-            const publications = asArray(response.publications);
-            if (publications.length === 0) {
-                return formatToolResult({
-                    found: false,
-                    message: `No publication found with PMID: ${args.pmid}`,
-                });
-            }
-            return formatToolResult({
-                found: true,
-                publication: publications[0],
-            });
-        }
-        catch (error) {
-            return formatErrorResult(error);
-        }
-    }));
-    // Get entity by Dimensions ID
-    server.registerTool("get_by_id", {
-        description: "Retrieve any entity by its Dimensions ID. Supports publications, grants, patents, clinical trials, datasets, policy documents, researchers, and organizations.",
-        inputSchema: {
-            entityType: EntitySchema.describe("The type of entity to look up"),
-            id: z.string().describe("The Dimensions ID to look up"),
-            fields: z.array(z.string()).optional().describe("Fields to return"),
-        },
-        outputSchema: {
-            found: z.boolean().describe("Whether the entity was found"),
-            entity: z.record(z.string(), z.unknown()).optional().describe("The found entity"),
-            entityType: z.string().optional().describe("The type of the found entity"),
-            message: z.string().optional().describe("Message when not found"),
-        },
-        annotations: READ_ONLY_API_ANNOTATIONS,
-    }, withFieldAliases({ entitySource: { kind: "dynamic", argName: "entityType" }, fieldArrayArgs: ["fields"] }, async (args) => {
-        try {
-            const qb = client
-                .createQueryBuilder()
-                .search(args.entityType)
-                .where("id", "=", args.id)
-                .limit(1);
-            if (args.fields?.length)
-                qb.fields(args.fields);
-            const dsl = qb.build();
-            const response = await client.rawQuery(dsl);
-            const entities = asArray(response[args.entityType]);
-            if (entities.length === 0) {
-                return formatToolResult({
-                    found: false,
-                    message: `No ${args.entityType.slice(0, -1)} found with ID: ${args.id}`,
-                });
-            }
-            return formatToolResult({
-                found: true,
-                entity: entities[0],
-                entityType: args.entityType,
-            });
-        }
-        catch (error) {
-            return formatErrorResult(error);
-        }
-    }));
-    // Get recent high impact publications
-    server.registerTool("recent_high_impact", {
-        description: "Find the most cited publications in a topic area from recent years. Useful for identifying influential recent research.",
-        inputSchema: {
-            query: z
-                .string()
-                .describe("Search query for the topic area (e.g., 'deep learning', 'immunotherapy')"),
-            years: z
-                .number()
-                .int()
-                .min(1)
-                .max(10)
-                .default(5)
-                .describe("Number of recent years to consider (default: 5)"),
-            limit: z
-                .number()
-                .int()
-                .min(1)
-                .max(100)
-                .default(20)
-                .describe("Number of publications to return (max 100)"),
-            fields: z.array(z.string()).optional().describe("Fields to return"),
-        },
-        outputSchema: {
-            query: z.string().describe("The search query used"),
-            yearRange: z.string().describe("Year range searched (e.g., '2020-2025')"),
-            totalCount: z.number().describe("Total matching records"),
-            returnedCount: z.number().describe("Records returned in this response"),
-            truncated: z.boolean().optional().describe("True when results are truncated"),
-            truncationWarning: z.string().optional().describe("Warning message when truncated"),
-            publications: z.array(z.record(z.string(), z.unknown())).describe("Result records"),
-        },
-        annotations: READ_ONLY_API_ANNOTATIONS,
-    }, withFieldAliases({ entitySource: { kind: "static", entity: "publications" }, fieldArrayArgs: ["fields"] }, async (args) => {
-        try {
-            const currentYear = new Date().getFullYear();
-            const startYear = currentYear - args.years;
-            const qb = client
-                .createQueryBuilder()
-                .search("publications")
-                .for(args.query)
-                .where("year", ">=", startYear)
-                .sort("times_cited", "desc")
-                .limit(args.limit);
-            if (args.fields?.length) {
-                qb.fields(args.fields);
-            }
-            else {
-                qb.fields(["id", "title", "doi", "year", "times_cited", "authors", "journal"]);
-            }
-            const dsl = qb.build();
-            const response = await client.rawQuery(dsl);
-            const publications = asArray(response.publications);
-            const totalCount = response._stats?.total_count ?? publications.length;
-            const returnedCount = publications.length;
-            return formatToolResult(withTruncationWarning({
-                query: args.query,
-                yearRange: `${startYear}-${currentYear}`,
-                totalCount,
-                returnedCount,
-                publications,
-            }, totalCount, returnedCount));
-        }
-        catch (error) {
-            return formatErrorResult(error);
-        }
-    }));
-}
-//# sourceMappingURL=lookup.js.map

package/dist/tools/lookup.js.map

@@ -1 +0,0 @@
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package/dist/tools/policy-profile.d.ts

@@ -1,15 +0,0 @@
-/**
- * Policy document profile tool for the MCP server.
- * Provides deep profiling of policy documents including structural links
- * to cited publications and their supporting grants.
- * @module mcp/tools/policy-profile
- */
-import type { DimensionsClient } from "@digital-science/dimensions-dsl";
-import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-/**
- * Registers the policy_document_profile tool with the MCP server.
- * @param server - MCP server instance
- * @param client - Dimensions client instance
- */
-export declare function registerPolicyProfileTools(server: McpServer, client: DimensionsClient): void;
-//# sourceMappingURL=policy-profile.d.ts.map

package/dist/tools/policy-profile.d.ts.map

@@ -1 +0,0 @@
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package/dist/tools/policy-profile.js

@@ -1,174 +0,0 @@
-/**
- * Policy document profile tool for the MCP server.
- * Provides deep profiling of policy documents including structural links
- * to cited publications and their supporting grants.
- * @module mcp/tools/policy-profile
- */
-import { ErrorCode, McpError } from "@modelcontextprotocol/sdk/types.js";
-import { z } from "zod";
-import { asArray, formatErrorResult, formatToolResult, READ_ONLY_API_ANNOTATIONS, } from "../utils.js";
-/**
- * Registers the policy_document_profile tool with the MCP server.
- * @param server - MCP server instance
- * @param client - Dimensions client instance
- */
-export function registerPolicyProfileTools(server, client) {
-    server.registerTool("policy_document_profile", {
-        description: "Get a comprehensive profile for a policy document including its cited publications and their supporting grants. Uses structural links (publication_ids) rather than free-text search to trace the evidence chain from policy back to funded research.",
-        inputSchema: {
-            policyDocId: z.string().optional().describe("Dimensions policy document ID"),
-            query: z
-                .string()
-                .optional()
-                .describe("Search term to find policy documents (used when policyDocId is not known)"),
-            includeLinkedPublications: z
-                .boolean()
-                .default(true)
-                .describe("Include cited publications and their supporting grants"),
-            publicationLimit: z
-                .number()
-                .int()
-                .min(1)
-                .max(50)
-                .default(20)
-                .describe("Max linked publications to return"),
-        },
-        outputSchema: {
-            found: z.boolean().describe("Whether the policy document was found"),
-            profile: z
-                .record(z.string(), z.unknown())
-                .optional()
-                .describe("Policy document profile with linked entities"),
-            message: z.string().optional().describe("Message when not found"),
-        },
-        annotations: READ_ONLY_API_ANNOTATIONS,
-    }, async (args) => {
-        if (!args.policyDocId && !args.query) {
-            throw new McpError(ErrorCode.InvalidParams, "Must provide at least one of: policyDocId or query");
-        }
-        try {
-            // Step 1: Find the policy document
-            let policyDsl;
-            if (args.policyDocId) {
-                policyDsl = client
-                    .createQueryBuilder()
-                    .search("policy_documents")
-                    .where("id", "=", args.policyDocId)
-                    .fields([
-                    "id",
-                    "title",
-                    "year",
-                    "publisher_org",
-                    "linkout",
-                    "publisher_org",
-                    "publication_ids",
-                ])
-                    .limit(1)
-                    .build();
-            }
-            else {
-                policyDsl = client
-                    .createQueryBuilder()
-                    .search("policy_documents")
-                    .for(args.query)
-                    .fields([
-                    "id",
-                    "title",
-                    "year",
-                    "publisher_org",
-                    "linkout",
-                    "publisher_org",
-                    "publication_ids",
-                ])
-                    .limit(5)
-                    .build();
-            }
-            const policyResponse = await client.rawQuery(policyDsl);
-            const policyDocs = asArray(policyResponse.policy_documents);
-            if (policyDocs.length === 0) {
-                return formatToolResult({
-                    found: false,
-                    message: args.policyDocId
-                        ? `No policy document found with ID: ${args.policyDocId}`
-                        : `No policy document found matching: ${args.query}`,
-                });
-            }
-            const policyDoc = policyDocs[0];
-            const profile = {
-                policyDocument: policyDoc,
-                matchCount: policyDocs.length,
-            };
-            // Extract structural link IDs
-            const publicationIds = Array.isArray(policyDoc.publication_ids)
-                ? policyDoc.publication_ids
-                : undefined;
-            // Step 2: Fetch linked publications
-            if (args.includeLinkedPublications !== false &&
-                publicationIds &&
-                publicationIds.length > 0) {
-                const pubSlice = publicationIds.slice(0, args.publicationLimit);
-                const pubDsl = client
-                    .createQueryBuilder()
-                    .search("publications")
-                    .whereIn("id", pubSlice)
-                    .fields([
-                    "id",
-                    "title",
-                    "doi",
-                    "year",
-                    "times_cited",
-                    "journal",
-                    "authors",
-                    "research_orgs",
-                    "funders",
-                    "supporting_grant_ids",
-                ])
-                    .limit(args.publicationLimit)
-                    .build();
-                const pubResponse = await client.rawQuery(pubDsl);
-                const publications = asArray(pubResponse.publications);
-                profile.linkedPublications = {
-                    totalLinked: publicationIds.length,
-                    returnedCount: publications.length,
-                    items: publications,
-                };
-                // Second-wave: fetch grants behind the publications
-                const allGrantIds = new Set();
-                for (const pub of publications) {
-                    if (Array.isArray(pub.supporting_grant_ids)) {
-                        for (const gid of pub.supporting_grant_ids) {
-                            if (typeof gid === "string") {
-                                allGrantIds.add(gid);
-                            }
-                        }
-                    }
-                }
-                if (allGrantIds.size > 0) {
-                    const grantIds = [...allGrantIds].slice(0, 50);
-                    const grantDsl = client
-                        .createQueryBuilder()
-                        .search("grants")
-                        .whereIn("id", grantIds)
-                        .fields(["id", "title", "funding_usd", "funder_org_name", "start_year"])
-                        .limit(50)
-                        .build();
-                    const grantResponse = await client.rawQuery(grantDsl);
-                    const grants = asArray(grantResponse.grants);
-                    profile.supportingGrants = {
-                        totalLinked: allGrantIds.size,
-                        returnedCount: grants.length,
-                        items: grants,
-                    };
-                }
-            }
-            return formatToolResult({
-                found: true,
-                profile,
-            });
-        }
-        catch (error) {
-            return formatErrorResult(error);
-        }
-    });
-}
-//# sourceMappingURL=policy-profile.js.map

package/dist/tools/policy-profile.js.map

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package/dist/tools/profile.d.ts

@@ -1,14 +0,0 @@
-/**
- * Profile tools for the MCP server.
- * Provides researcher and organization profile aggregation.
- * @module mcp/tools/profile
- */
-import type { DimensionsClient } from "@digital-science/dimensions-dsl";
-import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-/**
- * Registers all profile tools with the MCP server.
- * @param server - MCP server instance
- * @param client - Dimensions client instance
- */
-export declare function registerProfileTools(server: McpServer, client: DimensionsClient): void;
-//# sourceMappingURL=profile.d.ts.map