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

package/CHANGELOG.md

@@ -1,5 +1,19 @@
 # Changelog
 
+## 1.3.0
+
+### Minor Changes
+
+- Check npm on startup and auto-install same-major updates for guided prefix installs. Other layouts log a stale-version warning with a manual upgrade recipe.
+
+- Migrate to MCP TypeScript SDK v2 so advertised tool schemas use JSON Schema 2020-12, unblocking Claude Desktop/Code clients that reject draft-07 `outputSchema`.
+
+## 1.2.0
+
+### Minor Changes
+
+- Add `similar_documents` MCP tool for concept-based similar publication/grant lookup from abstract text (replacing the need to hand-write `similar_documents()` via `execute_dsl`).
+
 ## 1.1.0
 
 ### Minor Changes

package/dist/http-main.js

@@ -4,12 +4,14 @@
  * @module http-main
  */
 import { loadDeploymentConfig } from "./client/deployment-config.js";
+import { maybeWarnStaleHostedVersion } from "./mcp/auto-update.js";
 import { startHostedHttpServer } from "./mcp/http-server.js";
 const deployment = loadDeploymentConfig();
 if (deployment.deploymentMode !== "hosted") {
     console.error("http-main requires DEPLOYMENT_MODE=hosted");
     process.exit(1);
 }
+maybeWarnStaleHostedVersion();
 const { close, ready } = startHostedHttpServer({
     hosted: deployment,
     port: deployment.httpPort,

package/dist/http-main.js.map

@@ -1 +1 @@
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package/dist/main.d.ts

@@ -1,8 +1,3 @@
 #!/usr/bin/env node
-/**
- * MCP server entry point.
- * Starts the Dimensions Analytics MCP server with stdio transport.
- * @module main
- */
 export {};
 //# sourceMappingURL=main.d.ts.map

package/dist/main.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"main.d.ts","sourceRoot":"","sources":["../src/main.ts"],"names":[],"mappings":";AACA;;;;GAIG"}
+{"version":3,"file":"main.d.ts","sourceRoot":"","sources":["../src/main.ts"],"names":[],"mappings":""}

package/dist/main.js

@@ -4,8 +4,10 @@
  * Starts the Dimensions Analytics MCP server with stdio transport.
  * @module main
  */
-import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
+import { StdioServerTransport } from "@modelcontextprotocol/server/stdio";
+import { maybeAutoUpdateAndReexec } from "./mcp/auto-update.js";
 import { createMcpServerAsync } from "./mcp/server.js";
+maybeAutoUpdateAndReexec();
 let close;
 try {
     const { server } = await createMcpServerAsync();

package/dist/main.js.map

@@ -1 +1 @@
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package/dist/mcp/auto-update.d.ts

@@ -0,0 +1,63 @@
+/**
+ * Best-effort version check and prefix-only auto-update for stdio installs.
+ * @module mcp/auto-update
+ */
+export declare const NPM_PACKAGE = "@digital-science-dsl/dimensions-analytics-mcp";
+export declare const UPDATING_DOCS_URL = "https://github.com/digital-science/dimensions-analytics-mcp/blob/main/docs/INSTALLATION.md#updating";
+export declare const DEFAULT_UPDATE_INTERVAL_MS = 86400000;
+export declare const NPM_VIEW_TIMEOUT_MS = 3000;
+export declare const NPM_INSTALL_TIMEOUT_MS = 12000;
+export declare const PREFIX_DIR_NAME = ".dimensions-analytics-mcp";
+export type InstallLayout = "prefix" | "npx" | "global" | "source" | "hosted";
+export type VersionRelation = "same" | "older" | "newer-same-major" | "newer-major" | "incomparable";
+export type UpdateCheckResult = "skipped" | "current" | "warned" | "updated";
+export interface UpdateStamp {
+    readonly checkedAt: number;
+    readonly from?: string;
+    readonly to?: string;
+    readonly skippedReason?: string;
+}
+export interface AutoUpdateIo {
+    readonly now: () => number;
+    readonly env: NodeJS.ProcessEnv;
+    readonly layout: InstallLayout;
+    readonly currentVersion: string;
+    readonly allowInstall: boolean;
+    readonly stampPath: string;
+    readonly readStamp: (path: string) => UpdateStamp | undefined;
+    readonly writeStamp: (path: string, stamp: UpdateStamp) => void;
+    readonly npmView: () => string | undefined;
+    readonly npmInstall: (version: string) => boolean;
+    readonly log: (message: string) => void;
+    readonly reexec: () => void;
+}
+export declare function envFlagOff(value: string | undefined): boolean;
+export declare function resolvePackageRoot(moduleUrl?: string): string;
+export declare function readCurrentVersion(packageRoot: string): string;
+export declare function normalizePath(path: string): string;
+export declare function detectInstallLayout(packageRoot: string, homeDir: string): Exclude<InstallLayout, "hosted">;
+export declare function parseSemver(version: string): {
+    major: number;
+    minor: number;
+    patch: number;
+} | undefined;
+export declare function versionRelation(current: string, latest: string): VersionRelation;
+export declare function upgradeGuidance(layout: InstallLayout, current: string, latest: string, options?: {
+    major?: boolean;
+    installFailed?: boolean;
+}): string;
+export declare function upgradeRecipe(layout: InstallLayout): string;
+export declare function resolveNpmBin(execPath?: string, platform?: NodeJS.Platform, exists?: (path: string) => boolean): string;
+export declare function stampPathFor(layout: InstallLayout, homeDir: string, tmpDir: string): string;
+export declare function readStampFile(path: string): UpdateStamp | undefined;
+export declare function writeStampFile(path: string, stamp: UpdateStamp): void;
+export declare function runUpdateCheck(io: AutoUpdateIo): UpdateCheckResult;
+/**
+ * Stdio entry: may install + re-exec for prefix layouts.
+ */
+export declare function maybeAutoUpdateAndReexec(): void;
+/**
+ * Hosted HTTP entry: version warning only, never install or re-exec.
+ */
+export declare function maybeWarnStaleHostedVersion(): void;
+//# sourceMappingURL=auto-update.d.ts.map

package/dist/mcp/auto-update.d.ts.map

@@ -0,0 +1 @@
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package/dist/mcp/auto-update.js

@@ -0,0 +1,295 @@
+/**
+ * Best-effort version check and prefix-only auto-update for stdio installs.
+ * @module mcp/auto-update
+ */
+import { spawnSync } from "node:child_process";
+import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
+import { homedir, tmpdir } from "node:os";
+import { dirname, join } from "node:path";
+import { fileURLToPath } from "node:url";
+export const NPM_PACKAGE = "@digital-science-dsl/dimensions-analytics-mcp";
+export const UPDATING_DOCS_URL = "https://github.com/digital-science/dimensions-analytics-mcp/blob/main/docs/INSTALLATION.md#updating";
+export const DEFAULT_UPDATE_INTERVAL_MS = 86_400_000;
+export const NPM_VIEW_TIMEOUT_MS = 3_000;
+export const NPM_INSTALL_TIMEOUT_MS = 12_000;
+export const PREFIX_DIR_NAME = ".dimensions-analytics-mcp";
+const REGISTRY = "https://registry.npmjs.org";
+const INSTALL_SH = `bash -c "$(curl -fsSL https://raw.githubusercontent.com/digital-science/dimensions-analytics-mcp/main/scripts/install.sh)"`;
+const INSTALL_PS1 = "irm https://raw.githubusercontent.com/digital-science/dimensions-analytics-mcp/main/scripts/install.ps1 | iex";
+export function envFlagOff(value) {
+    if (value == null)
+        return false;
+    return ["0", "false", "off", "no"].includes(value.trim().toLowerCase());
+}
+export function resolvePackageRoot(moduleUrl = import.meta.url) {
+    return join(dirname(fileURLToPath(moduleUrl)), "..", "..");
+}
+export function readCurrentVersion(packageRoot) {
+    const raw = JSON.parse(readFileSync(join(packageRoot, "package.json"), "utf8"));
+    if (typeof raw.version !== "string" || raw.version.length === 0) {
+        throw new Error(`Missing version in ${join(packageRoot, "package.json")}`);
+    }
+    return raw.version;
+}
+export function normalizePath(path) {
+    return path.replace(/\\/g, "/");
+}
+export function detectInstallLayout(packageRoot, homeDir) {
+    const root = normalizePath(packageRoot);
+    const prefixRoot = normalizePath(join(homeDir, PREFIX_DIR_NAME, "node_modules", "@digital-science-dsl", "dimensions-analytics-mcp"));
+    if (root === prefixRoot || root.startsWith(`${prefixRoot}/`))
+        return "prefix";
+    if (root.includes("/_npx/") || root.includes("/_npx"))
+        return "npx";
+    if (root.includes("/node_modules/@digital-science-dsl/dimensions-analytics-mcp"))
+        return "global";
+    return "source";
+}
+export function parseSemver(version) {
+    const match = version
+        .trim()
+        .replace(/^v/i, "")
+        .match(/^(\d+)\.(\d+)\.(\d+)/);
+    if (!match)
+        return undefined;
+    return { major: Number(match[1]), minor: Number(match[2]), patch: Number(match[3]) };
+}
+export function versionRelation(current, latest) {
+    const a = parseSemver(current);
+    const b = parseSemver(latest);
+    if (!a || !b)
+        return "incomparable";
+    if (a.major === b.major && a.minor === b.minor && a.patch === b.patch)
+        return "same";
+    const cmp = a.major !== b.major
+        ? a.major - b.major
+        : a.minor !== b.minor
+            ? a.minor - b.minor
+            : a.patch - b.patch;
+    if (cmp > 0)
+        return "older";
+    if (b.major > a.major)
+        return "newer-major";
+    return "newer-same-major";
+}
+export function upgradeGuidance(layout, current, latest, options = {}) {
+    const lines = [`Dimensions Analytics MCP ${current} is behind npm ${latest}.`];
+    if (options.major) {
+        lines.push("This is a new major version; auto-update will not apply it.");
+    }
+    if (options.installFailed) {
+        lines.push("Automatic update failed; install the new version manually.");
+    }
+    lines.push(upgradeRecipe(layout));
+    lines.push(`See ${UPDATING_DOCS_URL}`);
+    return lines.join("\n");
+}
+export function upgradeRecipe(layout) {
+    switch (layout) {
+        case "prefix":
+            return [
+                "Update with the installer, then restart your AI app:",
+                `  Mac/Linux: ${INSTALL_SH}`,
+                `  Windows PowerShell: ${INSTALL_PS1}`,
+                `  Or: npm install ${NPM_PACKAGE}@latest --prefix ~/${PREFIX_DIR_NAME}`,
+            ].join("\n");
+        case "npx":
+            return [
+                `Set MCP args to ["-y", "${NPM_PACKAGE}@latest"] (or clear the npx cache) and restart.`,
+                "Without @latest, npx keeps the cached tarball.",
+            ].join("\n");
+        case "global":
+            return `Run: npm install -g ${NPM_PACKAGE}@latest\nThen restart your AI app.`;
+        case "source":
+            return "Run: git pull && pnpm install && pnpm run build";
+        case "hosted":
+            return "Bump the deployed image / npm pin and redeploy. Do not run the stdio installer on the host.";
+    }
+}
+export function resolveNpmBin(execPath = process.execPath, platform = process.platform, exists = existsSync) {
+    const dir = dirname(execPath);
+    const names = platform === "win32" ? ["npm.cmd", "npm.exe", "npm"] : ["npm"];
+    for (const name of names) {
+        const candidate = join(dir, name);
+        if (exists(candidate))
+            return candidate;
+    }
+    return platform === "win32" ? "npm.cmd" : "npm";
+}
+export function stampPathFor(layout, homeDir, tmpDir) {
+    if (layout === "hosted") {
+        return join(tmpDir, "dimensions-analytics-mcp-auto-update.json");
+    }
+    return join(homeDir, PREFIX_DIR_NAME, ".auto-update.json");
+}
+export function readStampFile(path) {
+    try {
+        const raw = JSON.parse(readFileSync(path, "utf8"));
+        if (typeof raw.checkedAt !== "number")
+            return undefined;
+        return {
+            checkedAt: raw.checkedAt,
+            ...(typeof raw.from === "string" ? { from: raw.from } : {}),
+            ...(typeof raw.to === "string" ? { to: raw.to } : {}),
+            ...(typeof raw.skippedReason === "string" ? { skippedReason: raw.skippedReason } : {}),
+        };
+    }
+    catch {
+        return undefined;
+    }
+}
+export function writeStampFile(path, stamp) {
+    mkdirSync(dirname(path), { recursive: true });
+    writeFileSync(path, `${JSON.stringify(stamp)}\n`, "utf8");
+}
+function updateIntervalMs(env) {
+    const raw = env.DIMENSIONS_MCP_AUTO_UPDATE_INTERVAL_MS;
+    if (raw == null || raw.trim() === "")
+        return DEFAULT_UPDATE_INTERVAL_MS;
+    const parsed = Number(raw);
+    return Number.isFinite(parsed) && parsed >= 0 ? parsed : DEFAULT_UPDATE_INTERVAL_MS;
+}
+export function runUpdateCheck(io) {
+    if (io.env.DIMENSIONS_MCP_UPDATED === "1")
+        return "skipped";
+    if (envFlagOff(io.env.DIMENSIONS_MCP_UPDATE_CHECK))
+        return "skipped";
+    const stamp = io.readStamp(io.stampPath);
+    if (stamp && io.now() - stamp.checkedAt < updateIntervalMs(io.env)) {
+        return "skipped";
+    }
+    const latest = io.npmView();
+    if (latest == null) {
+        io.writeStamp(io.stampPath, {
+            checkedAt: io.now(),
+            from: io.currentVersion,
+            skippedReason: "view-failed",
+        });
+        return "current";
+    }
+    const relation = versionRelation(io.currentVersion, latest);
+    if (relation === "same" || relation === "older" || relation === "incomparable") {
+        io.writeStamp(io.stampPath, { checkedAt: io.now(), from: io.currentVersion, to: latest });
+        return "current";
+    }
+    const canInstall = io.allowInstall &&
+        io.layout === "prefix" &&
+        !envFlagOff(io.env.DIMENSIONS_MCP_AUTO_UPDATE) &&
+        relation === "newer-same-major";
+    if (canInstall) {
+        const ok = io.npmInstall(latest);
+        if (ok) {
+            io.writeStamp(io.stampPath, { checkedAt: io.now(), from: io.currentVersion, to: latest });
+            io.reexec();
+            return "updated";
+        }
+        io.log(upgradeGuidance(io.layout, io.currentVersion, latest, {
+            installFailed: true,
+            major: false,
+        }));
+        io.writeStamp(io.stampPath, {
+            checkedAt: io.now(),
+            from: io.currentVersion,
+            to: latest,
+            skippedReason: "install-failed",
+        });
+        return "warned";
+    }
+    io.log(upgradeGuidance(io.layout, io.currentVersion, latest, {
+        major: relation === "newer-major",
+    }));
+    io.writeStamp(io.stampPath, {
+        checkedAt: io.now(),
+        from: io.currentVersion,
+        to: latest,
+        skippedReason: relation === "newer-major" ? "major" : "manual",
+    });
+    return "warned";
+}
+function spawnNpm(args, timeout) {
+    const npmBin = resolveNpmBin();
+    const result = spawnSync(npmBin, args, {
+        encoding: "utf8",
+        timeout,
+        windowsHide: true,
+        shell: process.platform === "win32",
+    });
+    return {
+        status: result.status,
+        stdout: result.stdout ?? "",
+        stderr: result.stderr ?? "",
+    };
+}
+function npmViewLatest() {
+    const result = spawnNpm(["view", NPM_PACKAGE, "version", "--registry", REGISTRY], NPM_VIEW_TIMEOUT_MS);
+    if (result.status !== 0)
+        return undefined;
+    const version = result.stdout.trim().replace(/^"+|"+$/g, "");
+    return parseSemver(version) ? version : undefined;
+}
+function npmInstallVersion(version, prefix) {
+    const result = spawnNpm([
+        "install",
+        `${NPM_PACKAGE}@${version}`,
+        "--prefix",
+        prefix,
+        "--registry",
+        REGISTRY,
+        "--no-fund",
+        "--no-audit",
+    ], NPM_INSTALL_TIMEOUT_MS);
+    return result.status === 0;
+}
+function reexecCurrentProcess() {
+    const result = spawnSync(process.execPath, process.argv.slice(1), {
+        env: { ...process.env, DIMENSIONS_MCP_UPDATED: "1" },
+        stdio: "inherit",
+        windowsHide: true,
+    });
+    process.exit(result.status ?? 1);
+}
+function createIo(options) {
+    const home = homedir();
+    const packageRoot = resolvePackageRoot();
+    const layout = options.layout ?? detectInstallLayout(packageRoot, home);
+    const prefix = join(home, PREFIX_DIR_NAME);
+    return {
+        now: () => Date.now(),
+        env: process.env,
+        layout,
+        currentVersion: readCurrentVersion(packageRoot),
+        allowInstall: options.allowInstall,
+        stampPath: stampPathFor(layout, home, tmpdir()),
+        readStamp: readStampFile,
+        writeStamp: writeStampFile,
+        npmView: npmViewLatest,
+        npmInstall: (version) => npmInstallVersion(version, prefix),
+        log: (message) => console.error(message),
+        reexec: reexecCurrentProcess,
+    };
+}
+/**
+ * Stdio entry: may install + re-exec for prefix layouts.
+ */
+export function maybeAutoUpdateAndReexec() {
+    try {
+        runUpdateCheck(createIo({ allowInstall: true }));
+    }
+    catch (error) {
+        const message = error instanceof Error ? error.message : String(error);
+        console.error(`Dimensions Analytics MCP update check failed: ${message}`);
+    }
+}
+/**
+ * Hosted HTTP entry: version warning only, never install or re-exec.
+ */
+export function maybeWarnStaleHostedVersion() {
+    try {
+        runUpdateCheck(createIo({ allowInstall: false, layout: "hosted" }));
+    }
+    catch (error) {
+        const message = error instanceof Error ? error.message : String(error);
+        console.error(`Dimensions Analytics MCP update check failed: ${message}`);
+    }
+}
+//# sourceMappingURL=auto-update.js.map

package/dist/mcp/auto-update.js.map

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package/dist/mcp/examples/dsl-examples.d.ts

@@ -6,8 +6,8 @@
 export declare const DSL_EXAMPLES_BY_SOURCE_URI = "dimensions://examples/{source}";
 /** Example queries keyed by entity type. */
 export declare const DSL_EXAMPLES_BY_ENTITY: Record<string, readonly string[]>;
-/** General DSL patterns (describe, functions, pagination). */
-export declare const DSL_GENERAL_EXAMPLES: readonly ["describe version", "describe schema", "describe source publications", "extract_concepts(text: \"CRISPR gene editing enables precise DNA modification\")", "classify(text: \"Stem cell therapy for diabetes\", system: \"for\")"];
+/** General DSL patterns (describe, functions, pagination, similarity). */
+export declare const DSL_GENERAL_EXAMPLES: readonly ["describe version", "describe schema", "describe source publications", "extract_concepts(text: \"CRISPR gene editing enables precise DNA modification\")", "classify(text: \"Stem cell therapy for diabetes\", system: \"for\")", "search publications for similar_documents(\"After spinal cord injury, macrophages infiltrate the lesion site\") where year > 2015 return publications[id+title+year] sort by score desc limit 5", "search grants for similar_documents(\"Cancer immunotherapy with checkpoint inhibitors and CAR-T\") where start_year >= 2020 return grants[id+title] sort by score desc limit 5"];
 /** Link to official DSL documentation. */
 export declare const DSL_DOCUMENTATION_URL = "https://docs.dimensions.ai/dsl/";
 /** Source names that have curated per-source example resources. */

package/dist/mcp/examples/dsl-examples.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"dsl-examples.d.ts","sourceRoot":"","sources":["../../../src/mcp/examples/dsl-examples.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,qDAAqD;AACrD,eAAO,MAAM,0BAA0B,mCAAmC,CAAC;AAE3E,4CAA4C;AAC5C,eAAO,MAAM,sBAAsB,EAAE,MAAM,CAAC,MAAM,EAAE,SAAS,MAAM,EAAE,CA8CpE,CAAC;AAEF,0EAA0E;AAC1E,eAAO,MAAM,oBAAoB,kmBAQvB,CAAC;AAEX,0CAA0C;AAC1C,eAAO,MAAM,qBAAqB,oCAAoC,CAAC;AAEvE,mEAAmE;AACnE,eAAO,MAAM,wBAAwB,UAA6C,CAAC;AAEnF;;;;GAIG;AACH,wBAAgB,uBAAuB,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,MAAM,EAAE,GAAG,SAAS,CAErF"}

package/dist/mcp/examples/dsl-examples.js

@@ -10,11 +10,13 @@ export const DSL_EXAMPLES_BY_ENTITY = {
         'search publications for "machine learning" return publications[id+title+doi] limit 10',
         'search publications for "CRISPR" where year >= 2020 return publications[id+title+times_cited+year] sort by times_cited desc limit 25',
         'search publications in title_only for "gene therapy" return publications[basics] limit 10',
+        'search publications for similar_documents("After spinal cord injury, macrophages infiltrate the lesion site") where year > 2015 return publications[id+title+year] sort by score desc limit 5',
         "search publications return publications facet journal limit 20",
     ],
     grants: [
         'search grants for "cancer immunotherapy" return grants limit 10',
         'search grants where funder_org_name = "National Institutes of Health" return grants[basics] limit 10',
+        'search grants for similar_documents("Cancer immunotherapy with checkpoint inhibitors and CAR-T") where start_year >= 2020 return grants[id+title] sort by score desc limit 5',
         "search grants return grants aggregate funding_usd",
     ],
     patents: [
@@ -50,13 +52,15 @@ export const DSL_EXAMPLES_BY_ENTITY = {
         'search research_org_groups for "Ivy League" return research_org_groups[basics] limit 10',
     ],
 };
-/** General DSL patterns (describe, functions, pagination). */
+/** General DSL patterns (describe, functions, pagination, similarity). */
 export const DSL_GENERAL_EXAMPLES = [
     "describe version",
     "describe schema",
     "describe source publications",
     'extract_concepts(text: "CRISPR gene editing enables precise DNA modification")',
     'classify(text: "Stem cell therapy for diabetes", system: "for")',
+    'search publications for similar_documents("After spinal cord injury, macrophages infiltrate the lesion site") where year > 2015 return publications[id+title+year] sort by score desc limit 5',
+    'search grants for similar_documents("Cancer immunotherapy with checkpoint inhibitors and CAR-T") where start_year >= 2020 return grants[id+title] sort by score desc limit 5',
 ];
 /** Link to official DSL documentation. */
 export const DSL_DOCUMENTATION_URL = "https://docs.dimensions.ai/dsl/";

package/dist/mcp/examples/dsl-examples.js.map

@@ -1 +1 @@
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+{"version":3,"file":"dsl-examples.js","sourceRoot":"","sources":["../../../src/mcp/examples/dsl-examples.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,qDAAqD;AACrD,MAAM,CAAC,MAAM,0BAA0B,GAAG,gCAAgC,CAAC;AAE3E,4CAA4C;AAC5C,MAAM,CAAC,MAAM,sBAAsB,GAAsC;IACvE,YAAY,EAAE;QACZ,uFAAuF;QACvF,sIAAsI;QACtI,2FAA2F;QAC3F,+LAA+L;QAC/L,gEAAgE;KACjE;IACD,MAAM,EAAE;QACN,iEAAiE;QACjE,sGAAsG;QACtG,8KAA8K;QAC9K,mDAAmD;KACpD;IACD,OAAO,EAAE;QACP,8DAA8D;QAC9D,qEAAqE;KACtE;IACD,eAAe,EAAE;QACf,uEAAuE;QACvE,gFAAgF;KACjF;IACD,QAAQ,EAAE,CAAC,8DAA8D,CAAC;IAC1E,gBAAgB,EAAE;QAChB,iFAAiF;KAClF;IACD,WAAW,EAAE;QACX,0EAA0E;QAC1E,+EAA+E;KAChF;IACD,aAAa,EAAE;QACb,mEAAmE;QACnE,oFAAoF;KACrF;IACD,OAAO,EAAE;QACP,qEAAqE;QACrE,0EAA0E;KAC3E;IACD,aAAa,EAAE;QACb,yEAAyE;QACzE,8FAA8F;KAC/F;IACD,aAAa,EAAE,CAAC,sEAAsE,CAAC;IACvF,mBAAmB,EAAE;QACnB,yFAAyF;KAC1F;CACF,CAAC;AAEF,0EAA0E;AAC1E,MAAM,CAAC,MAAM,oBAAoB,GAAG;IAClC,kBAAkB;IAClB,iBAAiB;IACjB,8BAA8B;IAC9B,gFAAgF;IAChF,iEAAiE;IACjE,+LAA+L;IAC/L,8KAA8K;CACtK,CAAC;AAEX,0CAA0C;AAC1C,MAAM,CAAC,MAAM,qBAAqB,GAAG,iCAAiC,CAAC;AAEvE,mEAAmE;AACnE,MAAM,CAAC,MAAM,wBAAwB,GAAG,MAAM,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC,IAAI,EAAE,CAAC;AAEnF;;;;GAIG;AACH,MAAM,UAAU,uBAAuB,CAAC,MAAc;IACpD,OAAO,sBAAsB,CAAC,MAAM,CAAC,CAAC;AACxC,CAAC"}

package/dist/mcp/examples/usage-scenarios.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"usage-scenarios.d.ts","sourceRoot":"","sources":["../../../src/mcp/examples/usage-scenarios.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,MAAM,WAAW,aAAa;IAC5B,0BAA0B;IAC1B,EAAE,EAAE,MAAM,CAAC;IACX,6CAA6C;IAC7C,IAAI,EAAE,MAAM,CAAC;IACb,0BAA0B;IAC1B,MAAM,EAAE,MAAM,CAAC;IACf,6CAA6C;IAC7C,IAAI,EAAE,MAAM,CAAC;IACb,4DAA4D;IAC5D,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC9B,sEAAsE;IACtE,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;CACxB;AAED,eAAO,MAAM,eAAe,EAAE,SAAS,aAAa,EAoK1C,CAAC"}
+{"version":3,"file":"usage-scenarios.d.ts","sourceRoot":"","sources":["../../../src/mcp/examples/usage-scenarios.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,MAAM,WAAW,aAAa;IAC5B,0BAA0B;IAC1B,EAAE,EAAE,MAAM,CAAC;IACX,6CAA6C;IAC7C,IAAI,EAAE,MAAM,CAAC;IACb,0BAA0B;IAC1B,MAAM,EAAE,MAAM,CAAC;IACf,6CAA6C;IAC7C,IAAI,EAAE,MAAM,CAAC;IACb,4DAA4D;IAC5D,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC9B,sEAAsE;IACtE,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;CACxB;AAED,eAAO,MAAM,eAAe,EAAE,SAAS,aAAa,EA0M1C,CAAC"}

package/dist/mcp/examples/usage-scenarios.js

@@ -148,6 +148,44 @@ export const USAGE_SCENARIOS = [
         },
         dslContains: ["large language model", "citations_per_year(2018, 2024)"],
     },
+    {
+        id: "similar-documents",
+        goal: "Similar papers from an abstract",
+        prompt: "Find publications similar to this abstract about spinal cord injury macrophages.",
+        tool: "similar_documents",
+        args: {
+            entityType: "publications",
+            text: "After spinal cord injury, macrophages infiltrate the lesion site and contribute to both tissue damage and repair processes.",
+            yearFrom: 2016,
+            limit: 10,
+            fields: ["id", "title", "year"],
+        },
+        dslContains: [
+            "search publications for similar_documents(",
+            "year >= 2016",
+            "sort by score desc",
+            "limit 10",
+        ],
+    },
+    {
+        id: "similar-grants",
+        goal: "Similar grants from a description",
+        prompt: "Find grants similar to this description of CAR-T cancer immunotherapy.",
+        tool: "similar_documents",
+        args: {
+            entityType: "grants",
+            text: "Development of novel cancer immunotherapy approaches using checkpoint inhibitors and CAR-T cell engineering for solid tumors.",
+            yearFrom: 2020,
+            limit: 10,
+            fields: ["id", "title", "funding_usd", "start_year"],
+        },
+        dslContains: [
+            "search grants for similar_documents(",
+            "start_year >= 2020",
+            "sort by score desc",
+            "limit 10",
+        ],
+    },
     {
         id: "build-complex-query",
         goal: "Build a complex query",

package/dist/mcp/examples/usage-scenarios.js.map

@@ -1 +1 @@
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+{"version":3,"file":"usage-scenarios.js","sourceRoot":"","sources":["../../../src/mcp/examples/usage-scenarios.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAiBH,MAAM,CAAC,MAAM,eAAe,GAA6B;IACvD;QACE,EAAE,EAAE,kBAAkB;QACtB,IAAI,EAAE,uBAAuB;QAC7B,MAAM,EAAE,wEAAwE;QAChF,IAAI,EAAE,qBAAqB;QAC3B,IAAI,EAAE;YACJ,KAAK,EAAE,qBAAqB;YAC5B,QAAQ,EAAE,IAAI;YACd,MAAM,EAAE,iBAAiB;YACzB,KAAK,EAAE,EAAE;YACT,MAAM,EAAE,CAAC,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,iBAAiB,CAAC;SAC1D;QACD,WAAW,EAAE;YACX,qBAAqB;YACrB,qBAAqB;YACrB,cAAc;YACd,0BAA0B;YAC1B,UAAU;SACX;KACF;IACD;QACE,EAAE,EAAE,YAAY;QAChB,IAAI,EAAE,sBAAsB;QAC5B,MAAM,EAAE,4EAA4E;QACpF,IAAI,EAAE,eAAe;QACrB,IAAI,EAAE;YACJ,KAAK,EAAE,sBAAsB;YAC7B,aAAa,EAAE,IAAI;YACnB,aAAa,EAAE,2BAA2B;YAC1C,KAAK,EAAE,EAAE;YACT,MAAM,EAAE,CAAC,IAAI,EAAE,OAAO,EAAE,aAAa,EAAE,aAAa,EAAE,YAAY,CAAC;SACpE;QACD,WAAW,EAAE;YACX,eAAe;YACf,sBAAsB;YACtB,oBAAoB;YACpB,+CAA+C;YAC/C,UAAU;SACX;KACF;IACD;QACE,EAAE,EAAE,sBAAsB;QAC1B,IAAI,EAAE,sBAAsB;QAC5B,MAAM,EAAE,2DAA2D;QACnE,IAAI,EAAE,aAAa;QACnB,IAAI,EAAE;YACJ,UAAU,EAAE,cAAc;YAC1B,UAAU,EAAE,aAAa;YACzB,KAAK,EAAE,mBAAmB;YAC1B,KAAK,EAAE,EAAE;SACV;QACD,WAAW,EAAE,CAAC,qBAAqB,EAAE,mBAAmB,EAAE,oBAAoB,CAAC;KAChF;IACD;QACE,EAAE,EAAE,qBAAqB;QACzB,IAAI,EAAE,0BAA0B;QAChC,MAAM,EAAE,sEAAsE;QAC9E,IAAI,EAAE,oBAAoB;QAC1B,IAAI,EAAE;YACJ,KAAK,EAAE,iBAAiB;YACxB,MAAM,EAAE,oBAAoB;YAC5B,KAAK,EAAE,EAAE;YACT,MAAM,EAAE,CAAC,IAAI,EAAE,YAAY,EAAE,WAAW,EAAE,oBAAoB,CAAC;SAChE;QACD,WAAW,EAAE,CAAC,oBAAoB,EAAE,iBAAiB,EAAE,4BAA4B,CAAC;KACrF;IACD;QACE,EAAE,EAAE,YAAY;QAChB,IAAI,EAAE,aAAa;QACnB,MAAM,EAAE,yEAAyE;QACjF,IAAI,EAAE,YAAY;QAClB,IAAI,EAAE;YACJ,GAAG,EAAE,qBAAqB;YAC1B,MAAM,EAAE,CAAC,IAAI,EAAE,OAAO,EAAE,aAAa,EAAE,SAAS,CAAC;SAClD;QACD,WAAW,EAAE,CAAC,qBAAqB,CAAC;KACrC;IACD;QACE,EAAE,EAAE,qBAAqB;QACzB,IAAI,EAAE,yBAAyB;QAC/B,MAAM,EAAE,8CAA8C;QACtD,IAAI,EAAE,qBAAqB;QAC3B,IAAI,EAAE;YACJ,KAAK,EAAE,iBAAiB;YACxB,MAAM,EAAE,iBAAiB;YACzB,KAAK,EAAE,EAAE;YACT,MAAM,EAAE,CAAC,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,iBAAiB,EAAE,SAAS,CAAC;SAC9D;QACD,WAAW,EAAE,CAAC,qBAAqB,EAAE,iBAAiB,EAAE,UAAU,CAAC;KACpE;IACD;QACE,EAAE,EAAE,kBAAkB;QACtB,IAAI,EAAE,oBAAoB;QAC1B,MAAM,EAAE,0DAA0D;QAClE,IAAI,EAAE,qBAAqB;QAC3B,IAAI,EAAE;YACJ,OAAO,EAAE,CAAC,EAAE,KAAK,EAAE,kBAAkB,EAAE,QAAQ,EAAE,GAAG,EAAE,KAAK,EAAE,eAAe,EAAE,CAAC;YAC/E,MAAM,EAAE,iBAAiB;YACzB,KAAK,EAAE,EAAE;YACT,MAAM,EAAE,CAAC,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,iBAAiB,CAAC;SACnD;QACD,WAAW,EAAE,CAAC,oCAAoC,EAAE,qBAAqB,CAAC;KAC3E;IACD;QACE,EAAE,EAAE,2BAA2B;QAC/B,IAAI,EAAE,iBAAiB;QACvB,MAAM,EAAE,uEAAuE;QAC/E,IAAI,EAAE,aAAa;QACnB,IAAI,EAAE;YACJ,UAAU,EAAE,cAAc;YAC1B,UAAU,EAAE,SAAS;YACrB,KAAK,EAAE,kBAAkB;YACzB,QAAQ,EAAE,IAAI;YACd,KAAK,EAAE,EAAE;SACV;QACD,WAAW,EAAE,CAAC,kBAAkB,EAAE,cAAc,EAAE,gBAAgB,CAAC;KACpE;IACD;QACE,EAAE,EAAE,iBAAiB;QACrB,IAAI,EAAE,iBAAiB;QACvB,MAAM,EAAE,kEAAkE;QAC1E,IAAI,EAAE,iBAAiB;QACvB,IAAI,EAAE;YACJ,UAAU,EAAE,QAAQ;YACpB,UAAU,EAAE,aAAa;YACzB,UAAU,EAAE,CAAC,SAAS,CAAC;YACvB,KAAK,EAAE,oBAAoB;YAC3B,MAAM,EAAE,SAAS;YACjB,SAAS,EAAE,MAAM;YACjB,KAAK,EAAE,EAAE;SACV;QACD,WAAW,EAAE,CAAC,eAAe,EAAE,oBAAoB,EAAE,sCAAsC,CAAC;KAC7F;IACD;QACE,EAAE,EAAE,gBAAgB;QACpB,IAAI,EAAE,qBAAqB;QAC3B,MAAM,EAAE,yEAAyE;QACjF,IAAI,EAAE,gBAAgB;QACtB,IAAI,EAAE;YACJ,KAAK,EAAE,sBAAsB;YAC7B,SAAS,EAAE,IAAI;YACf,OAAO,EAAE,IAAI;SACd;QACD,WAAW,EAAE,CAAC,sBAAsB,EAAE,gCAAgC,CAAC;KACxE;IACD;QACE,EAAE,EAAE,mBAAmB;QACvB,IAAI,EAAE,iCAAiC;QACvC,MAAM,EAAE,kFAAkF;QAC1F,IAAI,EAAE,mBAAmB;QACzB,IAAI,EAAE;YACJ,UAAU,EAAE,cAAc;YAC1B,IAAI,EAAE,6HAA6H;YACnI,QAAQ,EAAE,IAAI;YACd,KAAK,EAAE,EAAE;YACT,MAAM,EAAE,CAAC,IAAI,EAAE,OAAO,EAAE,MAAM,CAAC;SAChC;QACD,WAAW,EAAE;YACX,4CAA4C;YAC5C,cAAc;YACd,oBAAoB;YACpB,UAAU;SACX;KACF;IACD;QACE,EAAE,EAAE,gBAAgB;QACpB,IAAI,EAAE,mCAAmC;QACzC,MAAM,EAAE,wEAAwE;QAChF,IAAI,EAAE,mBAAmB;QACzB,IAAI,EAAE;YACJ,UAAU,EAAE,QAAQ;YACpB,IAAI,EAAE,+HAA+H;YACrI,QAAQ,EAAE,IAAI;YACd,KAAK,EAAE,EAAE;YACT,MAAM,EAAE,CAAC,IAAI,EAAE,OAAO,EAAE,aAAa,EAAE,YAAY,CAAC;SACrD;QACD,WAAW,EAAE;YACX,sCAAsC;YACtC,oBAAoB;YACpB,oBAAoB;YACpB,UAAU;SACX;KACF;IACD;QACE,EAAE,EAAE,qBAAqB;QACzB,IAAI,EAAE,uBAAuB;QAC7B,MAAM,EACJ,uGAAuG;QACzG,IAAI,EAAE,aAAa;QACnB,IAAI,EAAE;YACJ,GAAG,EAAE,kLAAkL;SACxL;QACD,WAAW,EAAE;YACX,qBAAqB;YACrB,QAAQ;YACR,cAAc;YACd,cAAc;YACd,cAAc;YACd,UAAU;SACX;KACF;CACO,CAAC"}

package/dist/mcp/http-server.js

@@ -3,8 +3,8 @@
  * @module mcp/http-server
  */
 import { randomUUID } from "node:crypto";
-import { createMcpExpressApp } from "@modelcontextprotocol/sdk/server/express.js";
-import { StreamableHTTPServerTransport } from "@modelcontextprotocol/sdk/server/streamableHttp.js";
+import { createMcpExpressApp } from "@modelcontextprotocol/express";
+import { NodeStreamableHTTPServerTransport } from "@modelcontextprotocol/node";
 import { AuthenticationError } from "../client/errors.js";
 import { parseBearerToken, resolveUserFromApiKey } from "../client/resolve-api-key-user.js";
 import { createMcpServerAsync, warmHostedSchemaCache } from "./server.js";
@@ -47,7 +47,7 @@ export function startHostedHttpServer(options) {
                 mcpSessionId,
                 mcpClient,
             });
-            const transport = new StreamableHTTPServerTransport({
+            const transport = new NodeStreamableHTTPServerTransport({
                 sessionIdGenerator: undefined,
             });
             await server.connect(transport);