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

package/dist/mcp/tools/impact-chain.js

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+/**
+ * Research impact chain tool for the MCP server.
+ * Traces how a research topic flows from publications through patents,
+ * clinical trials, and policy documents.
+ * @module mcp/tools/impact-chain
+ */
+import { z } from "zod";
+import { asArray, formatErrorResult, formatToolResult, READ_ONLY_API_ANNOTATIONS, } from "../utils.js";
+/** Impact chain stages in translation order. */
+const CHAIN_STAGES = [
+    {
+        entityType: "publications",
+        fields: ["id", "title", "doi", "year", "times_cited", "journal"],
+        sortField: "year",
+    },
+    {
+        entityType: "patents",
+        fields: ["id", "title", "year", "filing_date", "assignees"],
+        sortField: "year",
+    },
+    {
+        entityType: "clinical_trials",
+        fields: ["id", "title", "phase", "overall_status", "conditions"],
+        sortField: "date_inserted",
+    },
+    {
+        entityType: "policy_documents",
+        fields: ["id", "title", "year", "publisher_org"],
+        sortField: "year",
+    },
+];
+/**
+ * Registers the research_impact_chain tool with the MCP server.
+ * @param server - MCP server instance
+ * @param client - Dimensions client instance
+ */
+export function registerImpactChainTools(server, client) {
+    server.registerTool("research_impact_chain", {
+        description: "Trace how a research topic translates from basic science through real-world impact. Shows publications, patents, clinical trials, and policy documents for a query.",
+        inputSchema: {
+            query: z.string().describe("Seed topic or concept (e.g., 'gene therapy', 'CRISPR')"),
+            entityLimit: z.number().int().min(1).max(50).default(10).describe("Max entities per stage"),
+        },
+        outputSchema: {
+            found: z.boolean().describe("Whether results were found"),
+            query: z.string().optional().describe("The seed query"),
+            profile: z
+                .record(z.string(), z.unknown())
+                .optional()
+                .describe("Impact chain profile with stages"),
+        },
+        annotations: READ_ONLY_API_ANNOTATIONS,
+    }, async (args) => {
+        try {
+            const profile = {};
+            const stageResults = await Promise.all(CHAIN_STAGES.map(async (stage) => {
+                const builder = client
+                    .createQueryBuilder()
+                    .search(stage.entityType)
+                    .for(args.query)
+                    .fields([...stage.fields])
+                    .sort(stage.sortField, "desc")
+                    .limit(args.entityLimit);
+                const dsl = builder.build();
+                const response = await client.rawQuery(dsl);
+                const items = asArray(response[stage.entityType]);
+                return {
+                    entityType: stage.entityType,
+                    totalCount: typeof response._stats?.total_count === "number"
+                        ? response._stats.total_count
+                        : items.length,
+                    returnedCount: items.length,
+                    items,
+                };
+            }));
+            const stages = {};
+            for (const result of stageResults) {
+                stages[result.entityType] = {
+                    totalCount: result.totalCount,
+                    returnedCount: result.returnedCount,
+                    items: result.items,
+                };
+            }
+            profile.stages = stages;
+            return formatToolResult({
+                found: true,
+                query: args.query,
+                profile,
+            });
+        }
+        catch (error) {
+            return formatErrorResult(error);
+        }
+    });
+}
+//# sourceMappingURL=impact-chain.js.map

package/dist/mcp/tools/impact-chain.js.map

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

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+/**
+ * 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 { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import type { DimensionsClient } from "../../dsl/index.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/mcp/tools/kwq.d.ts.map

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package/dist/mcp/tools/kwq.js

@@ -0,0 +1,156 @@
+/**
+ * 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 { z } from "zod";
+import { buildQuery, conceptGroupsToQuerySpec, ensembleQueries } from "../../kwq/index.js";
+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/mcp/tools/kwq.js.map

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

@@ -0,0 +1,14 @@
+/**
+ * Lookup tools for the MCP server.
+ * Provides direct lookup by identifiers (DOI, PMID, Dimensions ID).
+ * @module mcp/tools/lookup
+ */
+import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { type DimensionsClient } from "../../dsl/index.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/mcp/tools/lookup.d.ts.map

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

@@ -0,0 +1,146 @@
+/**
+ * Lookup tools for the MCP server.
+ * Provides direct lookup by identifiers (DOI, PMID, Dimensions ID).
+ * @module mcp/tools/lookup
+ */
+import { z } from "zod";
+import { EntitySchema } from "../../dsl/index.js";
+import { withFieldAliases } from "../middleware/field-aliases.js";
+import { asArray, formatErrorResult, formatToolResult, READ_ONLY_API_ANNOTATIONS, } 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);
+        }
+    }));
+}
+//# sourceMappingURL=lookup.js.map

package/dist/mcp/tools/lookup.js.map

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

@@ -0,0 +1,15 @@
+/**
+ * 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 { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import type { DimensionsClient } from "../../dsl/index.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/mcp/tools/policy-profile.d.ts.map

@@ -0,0 +1 @@
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