@digital-science-dsl/dimensions-analytics-mcp 1.1.0 → 1.3.0

package/test/mcp/auto-update.test.ts

@@ -0,0 +1,347 @@
+/**
+ * @module test/mcp/auto-update
+ */
+
+import { join } from "node:path";
+import { afterEach, describe, expect, it, vi } from "vitest";
+import {
+  type AutoUpdateIo,
+  DEFAULT_UPDATE_INTERVAL_MS,
+  detectInstallLayout,
+  envFlagOff,
+  type InstallLayout,
+  NPM_PACKAGE,
+  PREFIX_DIR_NAME,
+  parseSemver,
+  readCurrentVersion,
+  resolveNpmBin,
+  resolvePackageRoot,
+  runUpdateCheck,
+  stampPathFor,
+  UPDATING_DOCS_URL,
+  type UpdateStamp,
+  upgradeGuidance,
+  upgradeRecipe,
+  versionRelation,
+} from "../../src/mcp/auto-update.js";
+
+const HOME = "/Users/test";
+const PREFIX_ROOT = join(
+  HOME,
+  PREFIX_DIR_NAME,
+  "node_modules",
+  "@digital-science-dsl",
+  "dimensions-analytics-mcp",
+);
+
+function fakeIo(overrides: Partial<AutoUpdateIo> & { stamps?: Map<string, UpdateStamp> } = {}): {
+  io: AutoUpdateIo;
+  logs: string[];
+  stamps: Map<string, UpdateStamp>;
+  reexec: ReturnType<typeof vi.fn>;
+  npmInstall: ReturnType<typeof vi.fn>;
+} {
+  const logs: string[] = [];
+  const stamps = overrides.stamps ?? new Map<string, UpdateStamp>();
+  const reexec = vi.fn();
+  const npmInstall = vi.fn<(version: string) => boolean>().mockReturnValue(true);
+  const stampPath = join(HOME, PREFIX_DIR_NAME, ".auto-update.json");
+
+  const io: AutoUpdateIo = {
+    now: () => 1_000_000,
+    env: {},
+    layout: "prefix",
+    currentVersion: "1.2.0",
+    allowInstall: true,
+    stampPath,
+    readStamp: (path) => stamps.get(path),
+    writeStamp: (path, stamp) => {
+      stamps.set(path, stamp);
+    },
+    npmView: () => "1.3.0",
+    npmInstall,
+    log: (message) => {
+      logs.push(message);
+    },
+    reexec,
+    ...overrides,
+  };
+
+  return { io, logs, stamps, reexec, npmInstall };
+}
+
+describe("envFlagOff", () => {
+  it("treats 0/false/off/no as off", () => {
+    expect(envFlagOff("0")).toBe(true);
+    expect(envFlagOff("false")).toBe(true);
+    expect(envFlagOff("OFF")).toBe(true);
+    expect(envFlagOff("no")).toBe(true);
+    expect(envFlagOff("1")).toBe(false);
+    expect(envFlagOff(undefined)).toBe(false);
+  });
+});
+
+describe("detectInstallLayout", () => {
+  it("detects the guided prefix install", () => {
+    expect(detectInstallLayout(PREFIX_ROOT, HOME)).toBe("prefix");
+    expect(detectInstallLayout(`${PREFIX_ROOT}/dist`, HOME)).toBe("prefix");
+  });
+
+  it("detects npx cache paths", () => {
+    expect(
+      detectInstallLayout(
+        "/Users/test/.npm/_npx/abc123/node_modules/@digital-science-dsl/dimensions-analytics-mcp",
+        HOME,
+      ),
+    ).toBe("npx");
+  });
+
+  it("detects global installs", () => {
+    expect(
+      detectInstallLayout(
+        "/usr/local/lib/node_modules/@digital-science-dsl/dimensions-analytics-mcp",
+        HOME,
+      ),
+    ).toBe("global");
+  });
+
+  it("detects source / workspace checkouts", () => {
+    expect(
+      detectInstallLayout("/Users/akovari/devel/dimensions-analytics-mcp/apps/mcp", HOME),
+    ).toBe("source");
+  });
+
+  it("normalizes Windows prefix paths", () => {
+    expect(
+      detectInstallLayout(
+        "C:\\Users\\test\\.dimensions-analytics-mcp\\node_modules\\@digital-science-dsl\\dimensions-analytics-mcp",
+        "C:\\Users\\test",
+      ),
+    ).toBe("prefix");
+  });
+});
+
+describe("versionRelation", () => {
+  it("classifies same, patch/minor, and major", () => {
+    expect(versionRelation("1.2.0", "1.2.0")).toBe("same");
+    expect(versionRelation("1.2.0", "1.2.1")).toBe("newer-same-major");
+    expect(versionRelation("1.2.0", "1.3.0")).toBe("newer-same-major");
+    expect(versionRelation("1.2.0", "2.0.0")).toBe("newer-major");
+    expect(versionRelation("1.3.0", "1.2.0")).toBe("older");
+    expect(versionRelation("nope", "1.0.0")).toBe("incomparable");
+  });
+});
+
+describe("parseSemver", () => {
+  it("reads leading v and ignores pre-release suffix for the numeric core", () => {
+    expect(parseSemver("v1.2.3")).toEqual({ major: 1, minor: 2, patch: 3 });
+    expect(parseSemver("1.2.3-beta.1")).toEqual({ major: 1, minor: 2, patch: 3 });
+  });
+});
+
+describe("upgradeGuidance", () => {
+  const layouts: InstallLayout[] = ["prefix", "npx", "global", "source", "hosted"];
+
+  it.each(layouts)("includes docs link and a recipe for %s", (layout) => {
+    const text = upgradeGuidance(layout, "1.0.3", "1.3.0");
+    expect(text).toContain("1.0.3");
+    expect(text).toContain("1.3.0");
+    expect(text).toContain(UPDATING_DOCS_URL);
+    expect(text).toContain(upgradeRecipe(layout).split("\n")[0]);
+  });
+
+  it("tells prefix users to re-run the installer or npm --prefix", () => {
+    const text = upgradeGuidance("prefix", "1.0.3", "1.3.0");
+    expect(text).toContain("install.sh");
+    expect(text).toContain("install.ps1");
+    expect(text).toContain(`npm install ${NPM_PACKAGE}@latest --prefix ~/${PREFIX_DIR_NAME}`);
+  });
+
+  it("tells npx users to pin @latest", () => {
+    expect(upgradeGuidance("npx", "1.0.3", "1.3.0")).toContain(`${NPM_PACKAGE}@latest`);
+    expect(upgradeGuidance("npx", "1.0.3", "1.3.0")).toContain("npx cache");
+  });
+
+  it("tells global users to npm install -g @latest", () => {
+    expect(upgradeGuidance("global", "1.0.3", "1.3.0")).toContain(
+      `npm install -g ${NPM_PACKAGE}@latest`,
+    );
+  });
+
+  it("tells source checkouts to pull and rebuild", () => {
+    expect(upgradeGuidance("source", "1.0.3", "1.3.0")).toContain(
+      "git pull && pnpm install && pnpm run build",
+    );
+  });
+
+  it("tells hosted operators to bump the pin, not run the stdio installer", () => {
+    const text = upgradeGuidance("hosted", "1.0.3", "1.3.0");
+    expect(text).toContain("deployed image");
+    expect(text).toContain("Do not run the stdio installer");
+  });
+
+  it("notes that majors are not auto-applied", () => {
+    expect(upgradeGuidance("prefix", "1.2.0", "2.0.0", { major: true })).toContain(
+      "auto-update will not apply it",
+    );
+  });
+});
+
+describe("stampPathFor", () => {
+  it("uses the prefix dir for stdio and tmpdir for hosted", () => {
+    expect(stampPathFor("prefix", HOME, "/tmp")).toBe(
+      join(HOME, PREFIX_DIR_NAME, ".auto-update.json"),
+    );
+    expect(stampPathFor("hosted", HOME, "/tmp")).toBe(
+      "/tmp/dimensions-analytics-mcp-auto-update.json",
+    );
+  });
+});
+
+describe("resolveNpmBin", () => {
+  it("prefers npm next to node", () => {
+    expect(resolveNpmBin("/usr/local/bin/node", "darwin", (p) => p === "/usr/local/bin/npm")).toBe(
+      "/usr/local/bin/npm",
+    );
+  });
+
+  it("falls back to npm.cmd on Windows", () => {
+    expect(resolveNpmBin("C:\\Program Files\\nodejs\\node.exe", "win32", () => false)).toBe(
+      "npm.cmd",
+    );
+  });
+});
+
+describe("resolvePackageRoot / readCurrentVersion", () => {
+  it("reads this workspace package version from import.meta.url", () => {
+    const root = resolvePackageRoot();
+    expect(readCurrentVersion(root)).toMatch(/^\d+\.\d+\.\d+/);
+  });
+});
+
+describe("runUpdateCheck", () => {
+  afterEach(() => {
+    vi.restoreAllMocks();
+  });
+
+  it("skips when DIMENSIONS_MCP_UPDATED=1", () => {
+    const { io, logs, stamps } = fakeIo({ env: { DIMENSIONS_MCP_UPDATED: "1" } });
+    expect(runUpdateCheck(io)).toBe("skipped");
+    expect(logs).toEqual([]);
+    expect(stamps.size).toBe(0);
+  });
+
+  it("skips when DIMENSIONS_MCP_UPDATE_CHECK is off", () => {
+    const { io, logs } = fakeIo({ env: { DIMENSIONS_MCP_UPDATE_CHECK: "0" } });
+    expect(runUpdateCheck(io)).toBe("skipped");
+    expect(logs).toEqual([]);
+  });
+
+  it("skips when the stamp is still fresh", () => {
+    const stampPath = join(HOME, PREFIX_DIR_NAME, ".auto-update.json");
+    const { io, logs } = fakeIo({
+      now: () => 50_000,
+      stamps: new Map([[stampPath, { checkedAt: 40_000 }]]),
+      env: { DIMENSIONS_MCP_AUTO_UPDATE_INTERVAL_MS: String(DEFAULT_UPDATE_INTERVAL_MS) },
+    });
+    expect(runUpdateCheck(io)).toBe("skipped");
+    expect(logs).toEqual([]);
+  });
+
+  it("does not warn when npm view fails", () => {
+    const { io, logs, stamps } = fakeIo({ npmView: () => undefined });
+    expect(runUpdateCheck(io)).toBe("current");
+    expect(logs).toEqual([]);
+    expect([...stamps.values()][0]?.skippedReason).toBe("view-failed");
+  });
+
+  it("does not warn when already on latest", () => {
+    const { io, logs, reexec } = fakeIo({ npmView: () => "1.2.0", currentVersion: "1.2.0" });
+    expect(runUpdateCheck(io)).toBe("current");
+    expect(logs).toEqual([]);
+    expect(reexec).not.toHaveBeenCalled();
+  });
+
+  it("installs and re-execs for prefix same-major updates", () => {
+    const { io, logs, reexec, npmInstall, stamps } = fakeIo();
+    expect(runUpdateCheck(io)).toBe("updated");
+    expect(npmInstall).toHaveBeenCalledWith("1.3.0");
+    expect(reexec).toHaveBeenCalledOnce();
+    expect(logs).toEqual([]);
+    expect([...stamps.values()][0]).toMatchObject({ from: "1.2.0", to: "1.3.0" });
+  });
+
+  it("writes the stamp before re-exec on success", () => {
+    const order: string[] = [];
+    const { io } = fakeIo({
+      writeStamp: () => {
+        order.push("stamp");
+      },
+      reexec: () => {
+        order.push("reexec");
+      },
+    });
+    runUpdateCheck(io);
+    expect(order).toEqual(["stamp", "reexec"]);
+  });
+
+  it("warns and does not install when auto-update is disabled", () => {
+    const { io, logs, reexec, npmInstall } = fakeIo({
+      env: { DIMENSIONS_MCP_AUTO_UPDATE: "0" },
+    });
+    expect(runUpdateCheck(io)).toBe("warned");
+    expect(npmInstall).not.toHaveBeenCalled();
+    expect(reexec).not.toHaveBeenCalled();
+    expect(logs[0]).toContain("install.sh");
+  });
+
+  it("warns on major versions and does not install", () => {
+    const { io, logs, npmInstall, reexec } = fakeIo({ npmView: () => "2.0.0" });
+    expect(runUpdateCheck(io)).toBe("warned");
+    expect(npmInstall).not.toHaveBeenCalled();
+    expect(reexec).not.toHaveBeenCalled();
+    expect(logs[0]).toContain("auto-update will not apply it");
+  });
+
+  it("warns with the npx recipe and never installs", () => {
+    const { io, logs, npmInstall, reexec } = fakeIo({ layout: "npx", allowInstall: true });
+    expect(runUpdateCheck(io)).toBe("warned");
+    expect(npmInstall).not.toHaveBeenCalled();
+    expect(reexec).not.toHaveBeenCalled();
+    expect(logs[0]).toContain("@latest");
+    expect(logs[0]).toContain("npx cache");
+  });
+
+  it("warns with the global recipe", () => {
+    const { io, logs, npmInstall } = fakeIo({ layout: "global" });
+    expect(runUpdateCheck(io)).toBe("warned");
+    expect(npmInstall).not.toHaveBeenCalled();
+    expect(logs[0]).toContain("npm install -g");
+  });
+
+  it("warns with the source recipe", () => {
+    const { io, logs, npmInstall } = fakeIo({ layout: "source" });
+    expect(runUpdateCheck(io)).toBe("warned");
+    expect(npmInstall).not.toHaveBeenCalled();
+    expect(logs[0]).toContain("git pull && pnpm install && pnpm run build");
+  });
+
+  it("hosted layout never installs or re-execs", () => {
+    const { io, logs, npmInstall, reexec } = fakeIo({
+      layout: "hosted",
+      allowInstall: false,
+    });
+    expect(runUpdateCheck(io)).toBe("warned");
+    expect(npmInstall).not.toHaveBeenCalled();
+    expect(reexec).not.toHaveBeenCalled();
+    expect(logs[0]).toContain("deployed image");
+  });
+
+  it("warns when prefix install fails", () => {
+    const { io, logs, reexec, npmInstall } = fakeIo();
+    npmInstall.mockReturnValue(false);
+    expect(runUpdateCheck(io)).toBe("warned");
+    expect(reexec).not.toHaveBeenCalled();
+    expect(logs[0]).toContain("Automatic update failed");
+  });
+});

package/test/middleware/field-aliases.test.ts

@@ -1,4 +1,4 @@
-import type { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
+import type { CallToolResult } from "@modelcontextprotocol/server";
 import { describe, expect, it } from "vitest";
 import {
   buildReverseAliasMap,

package/test/resources/schema.test.ts

@@ -12,7 +12,11 @@ describe("registerSchemaResources", () => {
     const context = { store: testSchemaStore() };
     const resources: Array<{ name: string; uri: string | { uriTemplate?: string } }> = [];
     const server = {
-      resource: (name: string, uri: string | { uriTemplate?: string }, ..._rest: unknown[]) => {
+      registerResource: (
+        name: string,
+        uri: string | { uriTemplate?: string },
+        ..._rest: unknown[]
+      ) => {
         resources.push({ name, uri });
       },
     };

package/test/server.test.ts

@@ -2,9 +2,7 @@
  * Tests for the MCP server factory function and startup lifecycle.
  * @module test/server
  */
-
-import { Client } from "@modelcontextprotocol/sdk/client/index.js";
-import { InMemoryTransport } from "@modelcontextprotocol/sdk/inMemory.js";
+import { Client, InMemoryTransport } from "@modelcontextprotocol/client";
 import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
 import {
   buildServerInstructions,
@@ -63,6 +61,7 @@ describe("createMcpServerAsync", () => {
     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");
   });
@@ -137,9 +136,24 @@ 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");
 
+    const jsonSchema2020 = "https://json-schema.org/draft/2020-12/schema";
+    for (const tool of tools.tools) {
+      const inputSchema = tool.inputSchema as { $schema?: string } | undefined;
+      const outputSchema = tool.outputSchema as { $schema?: string } | undefined;
+      expect(inputSchema?.$schema ?? jsonSchema2020).not.toContain("draft-07");
+      expect(outputSchema?.$schema ?? jsonSchema2020).not.toContain("draft-07");
+    }
+    for (const name of ["search_publications", "execute_dsl", "facet_query"]) {
+      const tool = tools.tools.find((t) => t.name === name);
+      const outputSchema = tool?.outputSchema as { $schema?: string } | undefined;
+      expect(outputSchema, `${name} should advertise outputSchema`).toBeDefined();
+      expect(outputSchema?.$schema).toBe(jsonSchema2020);
+    }
+
     const resources = await client.listResources();
     const uris = resources.resources.map((r) => r.uri);
     expect(uris.some((u) => u.startsWith("dimensions://schema"))).toBe(true);

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 @@
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