@digital-science-dsl/dimensions-analytics-mcp 1.0.4 → 1.2.0

package/test/examples/usage-scenarios.test.ts

@@ -8,6 +8,7 @@ import { registerAnalyticsTools } from "../../src/mcp/tools/analytics.js";
 import { registerLookupTools } from "../../src/mcp/tools/lookup.js";
 import { registerQueryTools } from "../../src/mcp/tools/query.js";
 import { registerSearchTools } from "../../src/mcp/tools/search.js";
+import { registerSimilarDocumentsTool } from "../../src/mcp/tools/similar-documents.js";
 import { testSchemaStore } from "../helpers/schema-fixture.js";
 import {
   callTool,
@@ -34,11 +35,12 @@ describe("usage-scenarios", () => {
     registerLookupTools(server as never, client as never);
     registerAnalyticsTools(server as never, client as never, schemaStore);
     registerQueryTools(server as never, client as never, schemaStore);
+    registerSimilarDocumentsTool(server as never, client as never);
   });
 
-  it("documents eleven natural-language workflows", () => {
-    expect(USAGE_SCENARIOS).toHaveLength(11);
-    expect(new Set(USAGE_SCENARIOS.map((s) => s.id)).size).toBe(11);
+  it("documents twelve natural-language workflows", () => {
+    expect(USAGE_SCENARIOS).toHaveLength(12);
+    expect(new Set(USAGE_SCENARIOS.map((s) => s.id)).size).toBe(12);
   });
 
   for (const scenario of USAGE_SCENARIOS) {

package/test/fixtures/describe-schema.json

@@ -3801,6 +3801,80 @@
       "fieldsets": ["basics", "categories"],
       "metrics": { "count": { "name": "count", "description": "Total count" } },
       "search_fields": ["full_data", "title_abstract_only", "concepts"]
+    },
+    "funder_groups": {
+      "fields": {
+        "id": {
+          "type": "string",
+          "description": "The Dimensions ID of the group.",
+          "long_description": null,
+          "is_entity": false,
+          "is_filter": true,
+          "is_facet": false,
+          "is_multivalue": false,
+          "solr_fields": { "return": "id", "filter": "id" }
+        },
+        "name": {
+          "type": "string",
+          "description": "The name of the group.",
+          "long_description": null,
+          "is_entity": false,
+          "is_filter": true,
+          "is_facet": false,
+          "is_multivalue": false,
+          "solr_fields": { "return": "name", "filter": "name" }
+        },
+        "organization_ids": {
+          "type": "string",
+          "description": "The GRID IDs of the organizations which are members of this group.",
+          "long_description": null,
+          "is_entity": false,
+          "is_filter": true,
+          "is_facet": false,
+          "is_multivalue": true,
+          "solr_fields": { "return": "values", "filter": "values" }
+        }
+      },
+      "fieldsets": ["basics"],
+      "metrics": { "count": { "name": "count", "description": "Total count" } },
+      "search_fields": ["name"]
+    },
+    "research_org_groups": {
+      "fields": {
+        "id": {
+          "type": "string",
+          "description": "The Dimensions ID of the group.",
+          "long_description": null,
+          "is_entity": false,
+          "is_filter": true,
+          "is_facet": false,
+          "is_multivalue": false,
+          "solr_fields": { "return": "id", "filter": "id" }
+        },
+        "name": {
+          "type": "string",
+          "description": "The name of the group.",
+          "long_description": null,
+          "is_entity": false,
+          "is_filter": true,
+          "is_facet": false,
+          "is_multivalue": false,
+          "solr_fields": { "return": "name", "filter": "name" }
+        },
+        "organization_ids": {
+          "type": "string",
+          "description": "The GRID IDs of the organizations which are members of this group.",
+          "long_description": null,
+          "is_entity": false,
+          "is_filter": true,
+          "is_facet": false,
+          "is_multivalue": true,
+          "solr_fields": { "return": "values", "filter": "values" }
+        }
+      },
+      "fieldsets": ["basics"],
+      "metrics": { "count": { "name": "count", "description": "Total count" } },
+      "search_fields": ["name"]
     }
   },
   "entities": {

package/test/integration/suites/index.ts

@@ -10,6 +10,7 @@ import { lookupSuite } from "./lookup.integration.js";
 import { querySuite } from "./query.integration.js";
 import { resourcesSuite } from "./resources.integration.js";
 import { searchSuite } from "./search.integration.js";
+import { similarDocumentsSuite } from "./similar-documents.integration.js";
 
 /** All integration test suites, in execution order. */
 export const allSuites: readonly EvalSuite[] = [
@@ -17,6 +18,7 @@ export const allSuites: readonly EvalSuite[] = [
   lookupSuite,
   querySuite,
   functionsSuite,
+  similarDocumentsSuite,
   analyticsSuite,
   resourcesSuite,
 ];

package/test/integration/suites/search.integration.ts

@@ -76,5 +76,29 @@ export const searchSuite: EvalSuite = {
       args: { query: "Massachusetts Institute of Technology", limit: 5 },
       assertions: [isSuccess(), hasField("totalCount"), arrayMinLength("organizations", 1)],
     },
+    {
+      name: "search reports for climate",
+      tool: "search_reports",
+      args: { query: "climate change", limit: 5 },
+      assertions: [isSuccess(), hasField("totalCount"), arrayMinLength("reports", 1)],
+    },
+    {
+      name: "search source titles for Nature",
+      tool: "search_source_titles",
+      args: { query: "Nature", limit: 5 },
+      assertions: [isSuccess(), hasField("totalCount"), arrayMinLength("source_titles", 1)],
+    },
+    {
+      name: "search funder groups for NIH",
+      tool: "search_funder_groups",
+      args: { query: "NIH", limit: 5 },
+      assertions: [isSuccess(), hasField("totalCount"), arrayMinLength("funder_groups", 1)],
+    },
+    {
+      name: "search research org groups",
+      tool: "search_research_org_groups",
+      args: { query: "University", limit: 5 },
+      assertions: [isSuccess(), hasField("totalCount"), arrayMinLength("research_org_groups", 1)],
+    },
   ],
 };

package/test/integration/suites/similar-documents.integration.ts

@@ -0,0 +1,51 @@
+/**
+ * Eval suite for similar_documents tool.
+ * @module test/integration/suites/similar-documents
+ */
+
+import { arrayMinLength, fieldAtLeast, hasField, isSuccess } from "../assertions.js";
+import type { EvalSuite } from "../types.js";
+
+const SAMPLE_ABSTRACT =
+  "After spinal cord injury, macrophages infiltrate the lesion site and contribute to both tissue damage and repair processes. Understanding macrophage polarization could lead to novel therapeutic strategies.";
+
+const SAMPLE_GRANT_TEXT =
+  "Development of novel cancer immunotherapy approaches using checkpoint inhibitors and CAR-T cell engineering for solid tumors.";
+
+export const similarDocumentsSuite: EvalSuite = {
+  name: "similar_documents",
+  description: "Concept-based similar document search for publications and grants",
+  cases: [
+    {
+      name: "similar publications from abstract text",
+      tool: "similar_documents",
+      args: {
+        entityType: "publications",
+        text: SAMPLE_ABSTRACT,
+        yearFrom: 2016,
+        limit: 5,
+        fields: ["id", "title", "year"],
+      },
+      assertions: [
+        isSuccess(),
+        hasField("totalCount"),
+        fieldAtLeast("totalCount", 1),
+        arrayMinLength("publications", 1),
+      ],
+      timeout: 60_000,
+    },
+    {
+      name: "similar grants from description text",
+      tool: "similar_documents",
+      args: {
+        entityType: "grants",
+        text: SAMPLE_GRANT_TEXT,
+        yearFrom: 2020,
+        limit: 5,
+        fields: ["id", "title"],
+      },
+      assertions: [isSuccess(), hasField("totalCount"), arrayMinLength("grants", 1)],
+      timeout: 60_000,
+    },
+  ],
+};

package/test/schema/store.test.ts

@@ -41,5 +41,10 @@ describe("SchemaStore", () => {
     const types = store.structuredEntityTypes();
     expect(types).toContain("publications");
     expect(types).toContain("organizations");
+    expect(types).toContain("reports");
+    expect(types).toContain("source_titles");
+    expect(types).toContain("funder_groups");
+    expect(types).toContain("research_org_groups");
+    expect(types).toHaveLength(12);
   });
 });

package/test/server.test.ts

@@ -60,6 +60,10 @@ describe("createMcpServerAsync", () => {
     expect(instructions).toContain("search_researchers matches names only");
     expect(instructions).toContain("research_orgs.id");
     expect(instructions).toContain("funder_orgs");
+    expect(instructions).toContain("search_organizations for institution lookup");
+    expect(instructions).toContain("search_source_titles");
+    expect(instructions).toContain("search_reports");
+    expect(instructions).toContain("similar_documents");
     expect(instructions).toContain("fetch_search_pages");
     expect(instructions).toContain("dimensions://schema/policy");
   });
@@ -134,6 +138,7 @@ describe("MCP protocol", () => {
     const toolNames = tools.tools.map((t) => t.name);
     expect(toolNames).toContain("search_publications");
     expect(toolNames).toContain("fetch_search_pages");
+    expect(toolNames).toContain("similar_documents");
     expect(toolNames).toContain("execute_dsl");
     expect(toolNames).not.toContain("validate_dsl");
 

package/test/tools/search.test.ts

@@ -37,7 +37,7 @@ describe("search tools", () => {
     registerSearchTools(server as never, client as never, testSchemaStore());
   });
 
-  it("registers all 8 search tools", () => {
+  it("registers all 12 search tools", () => {
     const expectedTools = [
       "search_publications",
       "search_grants",
@@ -47,11 +47,15 @@ describe("search tools", () => {
       "search_datasets",
       "search_policy_documents",
       "search_organizations",
+      "search_reports",
+      "search_source_titles",
+      "search_funder_groups",
+      "search_research_org_groups",
     ];
     for (const name of expectedTools) {
       expect(handlers.has(name)).toBe(true);
     }
-    expect(handlers.size).toBe(8);
+    expect(handlers.size).toBe(12);
   });
 
   describe("search_publications", () => {
@@ -243,6 +247,42 @@ describe("search tools", () => {
     });
   });
 
+  describe("search_reports", () => {
+    it("applies year filters and returns reports", async () => {
+      client.rawQuery.mockResolvedValue(apiRows("reports", [{ id: "rep.1", title: "Report" }], 1));
+
+      const result = await callTool(handlers, "search_reports", {
+        query: "climate",
+        yearFrom: 2020,
+        yearTo: 2024,
+        limit: 10,
+      });
+
+      const dsl = client.rawQuery.mock.calls[0][0] as string;
+      expect(dsl).toContain("search reports");
+      expect(dsl).toContain("year >= 2020");
+      expect(dsl).toContain("year <= 2024");
+      expect(parseToolResult(result).reports).toHaveLength(1);
+    });
+  });
+
+  describe("search_funder_groups", () => {
+    it("searches funder groups by name", async () => {
+      client.rawQuery.mockResolvedValue(
+        apiRows("funder_groups", [{ id: "fg.1", name: "NIH Institutes" }], 1),
+      );
+
+      const result = await callTool(handlers, "search_funder_groups", {
+        query: "NIH",
+        limit: 10,
+      });
+
+      const dsl = client.rawQuery.mock.calls[0][0] as string;
+      expect(dsl).toContain("search funder_groups");
+      expect(parseToolResult(result).funder_groups).toHaveLength(1);
+    });
+  });
+
   describe("truncation warnings", () => {
     it("includes truncation warning when totalCount exceeds returnedCount", async () => {
       client.rawQuery.mockResolvedValue(

package/test/tools/similar-documents.test.ts

@@ -0,0 +1,173 @@
+/**
+ * Tests for the similar_documents MCP tool.
+ * @module test/tools/similar-documents
+ */
+
+import { beforeEach, describe, expect, it } from "vitest";
+import { registerSimilarDocumentsTool } from "../../src/mcp/tools/similar-documents.js";
+import {
+  callTool,
+  createMockClient,
+  createMockServer,
+  parseToolResult,
+} from "../helpers/tool-test-harness.js";
+
+/** API-shaped mock response for parseEntityResponse. */
+function apiRows(
+  entity: string,
+  rows: Record<string, unknown>[],
+  totalCount?: number,
+): Record<string, unknown> {
+  return {
+    [entity]: rows,
+    _stats: { total_count: totalCount ?? rows.length },
+  };
+}
+
+const SAMPLE_ABSTRACT =
+  "After spinal cord injury, macrophages infiltrate the lesion site and contribute to both tissue damage and repair.";
+
+describe("similar_documents tool", () => {
+  let handlers: ReturnType<typeof createMockServer>["handlers"];
+  let client: ReturnType<typeof createMockClient>;
+
+  beforeEach(() => {
+    const { server, handlers: h } = createMockServer();
+    client = createMockClient();
+    handlers = h;
+    registerSimilarDocumentsTool(server as never, client as never);
+  });
+
+  it("registers similar_documents", () => {
+    expect(handlers.has("similar_documents")).toBe(true);
+  });
+
+  it("builds similar_documents DSL with default score sort and limit 20", async () => {
+    client.rawQuery.mockResolvedValue(apiRows("publications", [{ id: "pub.1", title: "A" }], 1));
+
+    await callTool(handlers, "similar_documents", {
+      entityType: "publications",
+      text: SAMPLE_ABSTRACT,
+    });
+
+    expect(client.rawQuery).toHaveBeenCalledTimes(1);
+    const dsl = client.rawQuery.mock.calls[0][0] as string;
+    expect(dsl).toContain("search publications for similar_documents(");
+    expect(dsl).toContain(SAMPLE_ABSTRACT);
+    expect(dsl).toContain("sort by score desc");
+    expect(dsl).toContain("limit 20");
+  });
+
+  it("applies year filters on publications and custom limit/fields", async () => {
+    client.rawQuery.mockResolvedValue(apiRows("publications", [], 0));
+
+    await callTool(handlers, "similar_documents", {
+      entityType: "publications",
+      text: SAMPLE_ABSTRACT,
+      yearFrom: 2018,
+      yearTo: 2024,
+      limit: 5,
+      fields: ["id", "title", "year"],
+    });
+
+    const dsl = client.rawQuery.mock.calls[0][0] as string;
+    expect(dsl).toContain("year >= 2018");
+    expect(dsl).toContain("year <= 2024");
+    expect(dsl).toContain("limit 5");
+    expect(dsl).toContain("return publications[id+title+year]");
+  });
+
+  it("uses start_year for grants year filters", async () => {
+    client.rawQuery.mockResolvedValue(apiRows("grants", [{ id: "grant.1" }], 1));
+
+    await callTool(handlers, "similar_documents", {
+      entityType: "grants",
+      text: "Cancer immunotherapy CAR-T solid tumors",
+      yearFrom: 2020,
+      limit: 5,
+      fields: ["id", "title"],
+    });
+
+    const dsl = client.rawQuery.mock.calls[0][0] as string;
+    expect(dsl).toContain("search grants for similar_documents(");
+    expect(dsl).toContain("start_year >= 2020");
+    expect(dsl).toContain("return grants[id+title]");
+  });
+
+  it("formats publication results", async () => {
+    const pubs = [
+      { id: "pub.1", title: "Paper A" },
+      { id: "pub.2", title: "Paper B" },
+    ];
+    client.rawQuery.mockResolvedValue(apiRows("publications", pubs, 2));
+
+    const result = await callTool(handlers, "similar_documents", {
+      entityType: "publications",
+      text: SAMPLE_ABSTRACT,
+      limit: 5,
+    });
+    const data = parseToolResult(result);
+
+    expect(result.isError).toBeUndefined();
+    expect(data.entityType).toBe("publications");
+    expect(data.totalCount).toBe(2);
+    expect(data.returnedCount).toBe(2);
+    expect(data.publications).toEqual(pubs);
+  });
+
+  it("formats grant results", async () => {
+    const grants = [{ id: "grant.1", title: "Grant A" }];
+    client.rawQuery.mockResolvedValue(apiRows("grants", grants, 1));
+
+    const result = await callTool(handlers, "similar_documents", {
+      entityType: "grants",
+      text: "Climate adaptation funding",
+      limit: 5,
+    });
+    const data = parseToolResult(result);
+
+    expect(data.entityType).toBe("grants");
+    expect(data.grants).toEqual(grants);
+    expect(data.publications).toBeUndefined();
+  });
+
+  it("applies extra filters", async () => {
+    client.rawQuery.mockResolvedValue(apiRows("publications", [], 0));
+
+    await callTool(handlers, "similar_documents", {
+      entityType: "publications",
+      text: SAMPLE_ABSTRACT,
+      filters: [{ field: "type", operator: "=", value: "article" }],
+      limit: 5,
+    });
+
+    const dsl = client.rawQuery.mock.calls[0][0] as string;
+    expect(dsl).toContain('type = "article"');
+  });
+
+  it("escapes quotes in text", async () => {
+    client.rawQuery.mockResolvedValue(apiRows("publications", [], 0));
+
+    await callTool(handlers, "similar_documents", {
+      entityType: "publications",
+      text: 'Text with "quotes" inside',
+      limit: 5,
+    });
+
+    const dsl = client.rawQuery.mock.calls[0][0] as string;
+    expect(dsl).toContain('similar_documents("Text with \\"quotes\\" inside")');
+  });
+
+  it("handles API errors gracefully", async () => {
+    client.rawQuery.mockRejectedValueOnce(new Error("Similarity search failed"));
+
+    const result = await callTool(handlers, "similar_documents", {
+      entityType: "publications",
+      text: SAMPLE_ABSTRACT,
+    });
+    const data = parseToolResult(result);
+
+    expect(result.isError).toBe(true);
+    expect(data.error).toBe("Similarity search failed");
+  });
+});

package/tsconfig.tsbuildinfo

@@ -1 +1 @@
-{"root":["./src/http-main.ts","./src/index.ts","./src/main.ts","./src/client/command.ts","./src/client/config.ts","./src/client/deployment-config.ts","./src/client/errors.ts","./src/client/http-client.ts","./src/client/index.ts","./src/client/internal-dsl-client.ts","./src/client/rate-limiter.ts","./src/client/request-retry.ts","./src/client/resolve-api-key-user.ts","./src/client/types.ts","./src/client/usage-context.ts","./src/client/usage-headers.ts","./src/client/auth/config-loaders.ts","./src/client/auth/factory.ts","./src/client/auth/index.ts","./src/client/auth/jwt-utils.ts","./src/client/auth/node.ts","./src/client/auth/schemas.ts","./src/client/auth/types.ts","./src/client/auth/decorators/index.ts","./src/client/auth/decorators/with-caching.ts","./src/client/auth/providers/index.ts","./src/client/auth/providers/jwt-auth-provider.ts","./src/client/config/index.ts","./src/client/config/loader.ts","./src/client/config/node.ts","./src/client/config/schemas.ts","./src/client/config/types.ts","./src/client/config/unified-loader.ts","./src/dsl/client.ts","./src/dsl/create-client.ts","./src/dsl/fluent-query-builder.ts","./src/dsl/index.ts","./src/dsl/pagination.ts","./src/dsl/query-builder.ts","./src/dsl/response-parser.ts","./src/dsl/usage-policy.ts","./src/dsl/commands/apply-filters.ts","./src/dsl/commands/index.ts","./src/dsl/commands/validate-input.ts","./src/dsl/commands/facet/index.ts","./src/dsl/commands/facet/schemas.ts","./src/dsl/commands/functions/ClassifyCommand.ts","./src/dsl/commands/functions/ExtractAffiliationsCommand.ts","./src/dsl/commands/functions/ExtractConceptsCommand.ts","./src/dsl/commands/functions/ExtractGrantsCommand.ts","./src/dsl/commands/functions/index.ts","./src/dsl/schema/cache.ts","./src/dsl/schema/extract.ts","./src/dsl/schema/index.ts","./src/dsl/schema/load.ts","./src/dsl/schema/store.ts","./src/dsl/schema/structured-entities.ts","./src/dsl/schema/summary.ts","./src/dsl/schema/types.ts","./src/dsl/schema/validation.ts","./src/dsl/types/buckets.ts","./src/dsl/types/common.ts","./src/dsl/types/entities.ts","./src/dsl/types/index.ts","./src/dsl/types/return-clauses.ts","./src/dsl/types/special-functions.ts","./src/dsl/types/vocabulary.ts","./src/dsl/utils/escape.ts","./src/dsl/utils/sanitize.ts","./src/dsl/utils/string-utils.ts","./src/dsl/utils/validate-field-name.ts","./src/mcp/batch-fetch.ts","./src/mcp/export-format.ts","./src/mcp/funder-org-names.ts","./src/mcp/http-server.ts","./src/mcp/server.ts","./src/mcp/shared-schema.ts","./src/mcp/usage-tracking.ts","./src/mcp/utils.ts","./src/mcp/examples/dsl-examples.ts","./src/mcp/examples/usage-scenarios.ts","./src/mcp/middleware/field-aliases.ts","./src/mcp/resources/schema.ts","./src/mcp/schema/context.ts","./src/mcp/schema/index.ts","./src/mcp/tools/analytics-filters.ts","./src/mcp/tools/analytics.ts","./src/mcp/tools/fetch-search-pages.ts","./src/mcp/tools/functions.ts","./src/mcp/tools/lookup.ts","./src/mcp/tools/query.ts","./src/mcp/tools/schema.ts","./src/mcp/tools/search-entity-metadata.ts","./src/mcp/tools/search-input.ts","./src/mcp/tools/search.ts"],"version":"5.9.3"}
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