@digital-science-dsl/dimensions-analytics-mcp 0.5.3 → 1.0.0

package/dist/mcp/tools/dataset-profile.js

@@ -1,194 +0,0 @@
-/**
- * Dataset profile tool for the MCP server.
- * Provides deep profiling of Dimensions datasets including structural links
- * to associated publications and grants.
- * @module mcp/tools/dataset-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 dataset_profile tool with the MCP server.
- * @param server - MCP server instance
- * @param client - Dimensions client instance
- */
-export function registerDatasetProfileTools(server, client) {
-    server.registerTool("dataset_profile", {
-        description: "Get a comprehensive profile for a research dataset including its associated publication, linked grants, and related publications. Uses structural links (associated_publication_id, associated_grant_ids) rather than free-text search.",
-        inputSchema: {
-            datasetId: z.string().optional().describe("Dimensions dataset ID"),
-            query: z
-                .string()
-                .optional()
-                .describe("Search term to find datasets (used when datasetId is not known)"),
-            includeLinkedPublications: z
-                .boolean()
-                .default(true)
-                .describe("Include the associated publication and related publications"),
-            includeLinkedGrants: z.boolean().default(true).describe("Include associated grants"),
-            publicationLimit: z
-                .number()
-                .int()
-                .min(1)
-                .max(50)
-                .default(10)
-                .describe("Max related publications to return"),
-        },
-        outputSchema: {
-            found: z.boolean().describe("Whether the dataset was found"),
-            profile: z
-                .record(z.string(), z.unknown())
-                .optional()
-                .describe("Dataset profile with linked entities"),
-            message: z.string().optional().describe("Message when not found"),
-        },
-        annotations: READ_ONLY_API_ANNOTATIONS,
-    }, async (args) => {
-        if (!args.datasetId && !args.query) {
-            throw new McpError(ErrorCode.InvalidParams, "Must provide at least one of: datasetId or query");
-        }
-        try {
-            // Step 1: Find the dataset
-            let datasetDsl;
-            if (args.datasetId) {
-                datasetDsl = client
-                    .createQueryBuilder()
-                    .search("datasets")
-                    .where("id", "=", args.datasetId)
-                    .fields([
-                    "id",
-                    "title",
-                    "doi",
-                    "year",
-                    "repository",
-                    "description",
-                    "associated_publication_id",
-                    "associated_grant_ids",
-                ])
-                    .limit(1)
-                    .build();
-            }
-            else {
-                datasetDsl = client
-                    .createQueryBuilder()
-                    .search("datasets")
-                    .for(args.query)
-                    .fields([
-                    "id",
-                    "title",
-                    "doi",
-                    "year",
-                    "repository",
-                    "description",
-                    "associated_publication_id",
-                    "associated_grant_ids",
-                ])
-                    .limit(5)
-                    .build();
-            }
-            const datasetResponse = await client.rawQuery(datasetDsl);
-            const datasets = asArray(datasetResponse.datasets);
-            if (datasets.length === 0) {
-                return formatToolResult({
-                    found: false,
-                    message: args.datasetId
-                        ? `No dataset found with ID: ${args.datasetId}`
-                        : `No dataset found matching: ${args.query}`,
-                });
-            }
-            const dataset = datasets[0];
-            const profile = {
-                dataset,
-                matchCount: datasets.length,
-            };
-            // Extract structural link IDs
-            const associatedPubId = typeof dataset.associated_publication_id === "string"
-                ? dataset.associated_publication_id
-                : undefined;
-            const associatedGrantIds = Array.isArray(dataset.associated_grant_ids)
-                ? dataset.associated_grant_ids
-                : undefined;
-            const datasetTitle = typeof dataset.title === "string" ? dataset.title : undefined;
-            // Step 2: Concurrent linked entity fetches
-            const queries = [];
-            if (args.includeLinkedPublications !== false) {
-                // Linked publication via structural ID
-                if (associatedPubId) {
-                    queries.push((async () => {
-                        const pubDsl = client
-                            .createQueryBuilder()
-                            .search("publications")
-                            .where("id", "=", associatedPubId)
-                            .fields([
-                            "id",
-                            "title",
-                            "doi",
-                            "year",
-                            "times_cited",
-                            "journal",
-                            "authors",
-                            "research_orgs",
-                        ])
-                            .limit(1)
-                            .build();
-                        const pubResponse = await client.rawQuery(pubDsl);
-                        const pubs = asArray(pubResponse.publications);
-                        if (pubs.length > 0) {
-                            profile.linkedPublication = pubs[0];
-                        }
-                    })());
-                }
-                // Related publications on same topic
-                if (datasetTitle) {
-                    queries.push((async () => {
-                        const relDsl = client
-                            .createQueryBuilder()
-                            .search("publications")
-                            .for(datasetTitle)
-                            .fields(["id", "title", "doi", "year", "times_cited", "journal"])
-                            .sort("times_cited", "desc")
-                            .limit(args.publicationLimit)
-                            .build();
-                        const relResponse = await client.rawQuery(relDsl);
-                        const relPubs = asArray(relResponse.publications);
-                        profile.relatedPublications = {
-                            totalCount: typeof relResponse._stats?.total_count === "number"
-                                ? relResponse._stats.total_count
-                                : relPubs.length,
-                            returnedCount: relPubs.length,
-                            items: relPubs,
-                        };
-                    })());
-                }
-            }
-            if (args.includeLinkedGrants !== false &&
-                associatedGrantIds &&
-                associatedGrantIds.length > 0) {
-                queries.push((async () => {
-                    const grantDsl = client
-                        .createQueryBuilder()
-                        .search("grants")
-                        .whereIn("id", associatedGrantIds)
-                        .fields(["id", "title", "funding_usd", "funder_org_name", "start_year"])
-                        .limit(10)
-                        .build();
-                    const grantResponse = await client.rawQuery(grantDsl);
-                    const grants = asArray(grantResponse.grants);
-                    profile.linkedGrants = {
-                        totalCount: grants.length,
-                        items: grants,
-                    };
-                })());
-            }
-            await Promise.all(queries);
-            return formatToolResult({
-                found: true,
-                profile,
-            });
-        }
-        catch (error) {
-            return formatErrorResult(error);
-        }
-    });
-}
-//# sourceMappingURL=dataset-profile.js.map

package/dist/mcp/tools/dataset-profile.js.map

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package/dist/mcp/tools/impact-chain.d.ts

@@ -1,15 +0,0 @@
-/**
- * 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 type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import type { DimensionsClient } from "../../dsl/index.js";
-/**
- * Registers the research_impact_chain tool with the MCP server.
- * @param server - MCP server instance
- * @param client - Dimensions client instance
- */
-export declare function registerImpactChainTools(server: McpServer, client: DimensionsClient): void;
-//# sourceMappingURL=impact-chain.d.ts.map

package/dist/mcp/tools/impact-chain.d.ts.map

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

@@ -1,96 +0,0 @@
-/**
- * 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

@@ -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 { 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

@@ -1 +0,0 @@
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package/dist/mcp/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 { 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/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 { 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

@@ -1 +0,0 @@
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