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

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

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package/dist/tools/functions.d.ts

@@ -1,14 +0,0 @@
-/**
- * Special function tools for the MCP server.
- * Provides tools for classify, extract_concepts, and similar documents search.
- * @module mcp/tools/functions
- */
-import { type DimensionsClient } from "@digital-science/dimensions-dsl";
-import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-/**
- * Registers all special function tools with the MCP server.
- * @param server - MCP server instance
- * @param client - Dimensions client instance
- */
-export declare function registerFunctionTools(server: McpServer, client: DimensionsClient): void;
-//# sourceMappingURL=functions.d.ts.map

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

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

@@ -1,294 +0,0 @@
-/**
- * Special function tools for the MCP server.
- * Provides tools for classify, extract_concepts, and similar documents search.
- * @module mcp/tools/functions
- */
-import { CLASSIFICATION_SYSTEMS, } from "@digital-science/dimensions-dsl";
-import { ErrorCode, McpError } from "@modelcontextprotocol/sdk/types.js";
-import { z } from "zod";
-import { withFieldAliases } from "../middleware/field-aliases.js";
-import { formatErrorResult, formatToolResult, READ_ONLY_API_ANNOTATIONS } from "../utils.js";
-/**
- * Registers all special function tools with the MCP server.
- * @param server - MCP server instance
- * @param client - Dimensions client instance
- */
-export function registerFunctionTools(server, client) {
-    // Classify Text
-    server.registerTool("classify_text", {
-        description: "Classify text (title and/or abstract) using Dimensions classification systems. " +
-            "Supports FOR (Fields of Research), SDG (Sustainable Development Goals), RCDC, " +
-            "HRCS, and other research classification taxonomies. Returns classification codes with names.",
-        inputSchema: {
-            title: z
-                .string()
-                .optional()
-                .describe("Document title for classification (at least title or abstract required)"),
-            abstract: z
-                .string()
-                .optional()
-                .describe("Document abstract for classification (at least title or abstract required)"),
-            system: z
-                .enum(CLASSIFICATION_SYSTEMS)
-                .describe("Classification system to use: FOR (Fields of Research), FOR_2020, " +
-                "SDG (Sustainable Development Goals), SDG_2021, RCDC, HRCS_HC, HRCS_RAC, " +
-                "HRA, BRA, ICRP_CSO, ICRP_CT, UOA"),
-        },
-        outputSchema: {
-            system: z.string().describe("Classification system used"),
-            classifications: z
-                .array(z.record(z.string(), z.unknown()))
-                .describe("Classification results"),
-        },
-        annotations: READ_ONLY_API_ANNOTATIONS,
-    }, async (args) => {
-        if (!args.title && !args.abstract) {
-            throw new McpError(ErrorCode.InvalidParams, "At least one of title or abstract must be provided");
-        }
-        try {
-            const result = await client.classify({
-                title: args.title,
-                abstract: args.abstract,
-                system: args.system,
-            });
-            return formatToolResult({
-                system: args.system,
-                classifications: result[args.system],
-            });
-        }
-        catch (error) {
-            return formatErrorResult(error);
-        }
-    });
-    // Extract Concepts
-    server.registerTool("extract_concepts", {
-        description: "Extract research concepts from text using Dimensions natural language processing. " +
-            "Identifies key scientific concepts, terms, and topics from abstracts or descriptions.",
-        inputSchema: {
-            text: z
-                .string()
-                .min(1)
-                .describe("Text to extract concepts from (e.g., abstract, description)"),
-            return_scores: z
-                .boolean()
-                .optional()
-                .default(false)
-                .describe("Include relevance scores for each concept (0-1 scale)"),
-        },
-        outputSchema: {
-            concepts: z.array(z.record(z.string(), z.unknown())).describe("Extracted concepts"),
-            returnedWithScores: z.boolean().describe("Whether relevance scores are included"),
-        },
-        annotations: READ_ONLY_API_ANNOTATIONS,
-    }, async (args) => {
-        try {
-            const result = await client.extractConcepts(args.text, {
-                returnScores: args.return_scores,
-            });
-            return formatToolResult({
-                concepts: result.extracted_concepts,
-                returnedWithScores: args.return_scores,
-            });
-        }
-        catch (error) {
-            return formatErrorResult(error);
-        }
-    });
-    // Find Similar Publications
-    server.registerTool("find_similar_publications", {
-        description: "Find publications semantically similar to provided text. " +
-            "Uses the similar_documents() function to match publications based on meaning, " +
-            "not just keywords. Great for finding related research based on an abstract.",
-        inputSchema: {
-            text: z
-                .string()
-                .min(1)
-                .describe("Abstract or description text to find similar publications for"),
-            year_from: z
-                .number()
-                .int()
-                .optional()
-                .describe("Filter publications from this year (inclusive)"),
-            year_to: z
-                .number()
-                .int()
-                .optional()
-                .describe("Filter publications up to this year (inclusive)"),
-            limit: z
-                .number()
-                .int()
-                .min(1)
-                .max(1000)
-                .default(10)
-                .describe("Maximum results to return (max 1000)"),
-            fields: z
-                .array(z.string())
-                .optional()
-                .describe("Fields to return (e.g., ['id', 'title', 'doi', 'year', 'times_cited'])"),
-        },
-        outputSchema: {
-            totalCount: z.number().describe("Total matching records"),
-            returnedCount: z.number().describe("Records returned in this response"),
-            publications: z.array(z.record(z.string(), z.unknown())).describe("Similar publications"),
-        },
-        annotations: READ_ONLY_API_ANNOTATIONS,
-    }, withFieldAliases({ entitySource: { kind: "static", entity: "publications" }, fieldArrayArgs: ["fields"] }, async (args) => {
-        try {
-            let builder = client.publications().forSimilar(args.text);
-            if (args.year_from !== undefined) {
-                builder = builder.where("year", ">=", args.year_from);
-            }
-            if (args.year_to !== undefined) {
-                builder = builder.where("year", "<=", args.year_to);
-            }
-            if (args.fields && args.fields.length > 0) {
-                builder = builder.fields(args.fields);
-            }
-            const result = await builder.limit(args.limit).execute();
-            return formatToolResult({
-                totalCount: result.totalCount,
-                returnedCount: result.data.length,
-                publications: result.data,
-            });
-        }
-        catch (error) {
-            return formatErrorResult(error);
-        }
-    }));
-    // Extract Affiliations
-    server.registerTool("extract_affiliations", {
-        description: "Resolve and disambiguate organization affiliations using Dimensions entity resolution. " +
-            "Takes freetext affiliation strings or structured organization data and returns matched " +
-            "organizations with GRID/ROR identifiers and confidence scores.",
-        inputSchema: {
-            affiliations: z
-                .array(z.object({
-                affiliation: z
-                    .string()
-                    .optional()
-                    .describe("Freetext affiliation string (e.g., 'University of Oxford, UK')"),
-                name: z.string().optional().describe("Organization name"),
-                city: z.string().optional().describe("City"),
-                state: z.string().optional().describe("State/province"),
-                country: z.string().optional().describe("Country"),
-            }))
-                .min(1)
-                .describe("Array of affiliations to resolve. Each must have either 'affiliation' or 'name'"),
-        },
-        outputSchema: {
-            matchCount: z.number().describe("Number of resolved affiliations"),
-            affiliations: z.array(z.record(z.string(), z.unknown())).describe("Resolved affiliations"),
-        },
-        annotations: READ_ONLY_API_ANNOTATIONS,
-    }, async (args) => {
-        try {
-            const result = await client.extractAffiliations(args.affiliations);
-            return formatToolResult({
-                matchCount: result.extracted_affiliations.length,
-                affiliations: result.extracted_affiliations,
-            });
-        }
-        catch (error) {
-            return formatErrorResult(error);
-        }
-    });
-    // Extract Grants
-    server.registerTool("extract_grants", {
-        description: "Resolve grant numbers to Dimensions grant records. " +
-            "Takes a grant number and optional funder information to find matching grants " +
-            "with full metadata including funding amounts, dates, and funder details.",
-        inputSchema: {
-            grant_number: z.string().min(1).describe("Grant number to look up (e.g., 'R01HL117329')"),
-            fundref: z
-                .string()
-                .optional()
-                .describe("FundRef ID of the funder (e.g., '100000050' for NIH)"),
-            funder_name: z
-                .string()
-                .optional()
-                .describe("Funder name as alternative to FundRef ID (e.g., 'NIH')"),
-        },
-        outputSchema: {
-            matchCount: z.number().describe("Number of matched grants"),
-            grants: z.array(z.record(z.string(), z.unknown())).describe("Matched grant records"),
-        },
-        annotations: READ_ONLY_API_ANNOTATIONS,
-    }, async (args) => {
-        try {
-            const result = await client.extractGrants({
-                grantNumber: args.grant_number,
-                fundref: args.fundref,
-                funderName: args.funder_name,
-            });
-            return formatToolResult({
-                matchCount: result.grant_id ? 1 : 0,
-                grants: result.grant_id ? [{ grant_id: result.grant_id }] : [],
-            });
-        }
-        catch (error) {
-            return formatErrorResult(error);
-        }
-    });
-    // Find Similar Grants
-    server.registerTool("find_similar_grants", {
-        description: "Find grants semantically similar to provided text. " +
-            "Uses the similar_documents() function to match grants based on meaning. " +
-            "Useful for identifying similar funding opportunities or research projects.",
-        inputSchema: {
-            text: z
-                .string()
-                .min(1)
-                .describe("Project description or abstract to find similar grants for"),
-            start_year_from: z
-                .number()
-                .int()
-                .optional()
-                .describe("Filter grants starting from this year (inclusive)"),
-            start_year_to: z
-                .number()
-                .int()
-                .optional()
-                .describe("Filter grants starting up to this year (inclusive)"),
-            limit: z
-                .number()
-                .int()
-                .min(1)
-                .max(1000)
-                .default(10)
-                .describe("Maximum results to return (max 1000)"),
-            fields: z
-                .array(z.string())
-                .optional()
-                .describe("Fields to return (e.g., ['id', 'title', 'funder_org_name', 'funding_usd'])"),
-        },
-        outputSchema: {
-            totalCount: z.number().describe("Total matching records"),
-            returnedCount: z.number().describe("Records returned in this response"),
-            grants: z.array(z.record(z.string(), z.unknown())).describe("Similar grants"),
-        },
-        annotations: READ_ONLY_API_ANNOTATIONS,
-    }, withFieldAliases({ entitySource: { kind: "static", entity: "grants" }, fieldArrayArgs: ["fields"] }, async (args) => {
-        try {
-            let builder = client.grants().forSimilar(args.text);
-            if (args.start_year_from !== undefined) {
-                builder = builder.where("start_year", ">=", args.start_year_from);
-            }
-            if (args.start_year_to !== undefined) {
-                builder = builder.where("start_year", "<=", args.start_year_to);
-            }
-            if (args.fields && args.fields.length > 0) {
-                builder = builder.fields(args.fields);
-            }
-            const result = await builder.limit(args.limit).execute();
-            return formatToolResult({
-                totalCount: result.totalCount,
-                returnedCount: result.data.length,
-                grants: result.data,
-            });
-        }
-        catch (error) {
-            return formatErrorResult(error);
-        }
-    }));
-}
-//# sourceMappingURL=functions.js.map

package/dist/tools/functions.js.map

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package/dist/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 { DimensionsClient } from "@digital-science/dimensions-dsl";
-import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.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/tools/impact-chain.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"impact-chain.d.ts","sourceRoot":"","sources":["../../src/tools/impact-chain.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,iCAAiC,CAAC;AACxE,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAiCzE;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,gBAAgB,GAAG,IAAI,CAqE1F"}

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

@@ -1 +0,0 @@
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