refactor: move to v2 structure MCP-373 by gagik · Pull Request #1122 · mongodb-js/mongodb-mcp-server

gagik · 2026-04-30T11:54:35Z

Only merge once the last v1 release is complete

It's many PRs merged into one along with many patches on top; I have reviewed every file but it's obviously a lot to expect that, so if you're curious about the major changes, here's the important files:

api-extractor/reports/tools.public.api.md, api-extractor/reports/mongodb-mcp-server.public.api.md - I kept these around purely to have an easier visualization of changes. It provides a good overview of what was removed & updates.
packages/cli - This is the closest to the original index.ts / consumer layer with UserConfig we're used to. Everything around has been decoupled from UserConfig
packages/mongodb-mcp-server - This is an extremely minimal consumer of packages/cli . It also currently has a bunch of re-exporting for the sake of the v2 report comparisons above but this will be removed afterwards.

#1115)

…#1116)

…1124)

Document the breaking changes for the @mongodb-js/mcp-tools-mongodb package extraction, including:

…1148)

- Fix merge conflicts in package.json and src/web.ts - Recreate missing packages/tools-mongodb/package.json and tsconfig.json - Update pnpm-lock.yaml with new dependencies All checks pass.

# Conflicts: # api-extractor/reports/mongodb-mcp-server.public.api.md # api-extractor/reports/tools.public.api.md # api-extractor/reports/web.public.api.md # packages/atlas-telemetry/src/types.ts # src/tools/atlas/tools.ts # src/web.ts

# Conflicts: # src/setup/setupMcpServer.ts # src/setup/setupTelemetry.ts

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addaleax

No major concerns, and I imagine a lot of my comments aren't specific to this PR, but I've still done a full review here

addaleax · 2026-05-21T14:28:02Z

+const NO_UNICODE_REGEX = /^[\x20-\x7E]*$/;
+export const NO_UNICODE_ERROR = "String cannot contain special characters or Unicode symbols";
+
+export const CommonArgs = {
+    string: (): ZodString => z.string().regex(NO_UNICODE_REGEX, NO_UNICODE_ERROR),


Don't really like the naming or the error message here – if I see something like CommonArgs.string(), I would expect that to really correspond to a regular string. Also, saying "cannot contain Unicode symbols" is fairly confusing, since it's really not obvious which actual restriction that corresponds to (it can't be interpreted literally, since strings are by definition sequences of Unicode characters).

Suggested change

const NO_UNICODE_REGEX = /^[\x20-\x7E]*$/;

export const NO_UNICODE_ERROR = "String cannot contain special characters or Unicode symbols";

export const CommonArgs = {

string: (): ZodString => z.string().regex(NO_UNICODE_REGEX, NO_UNICODE_ERROR),

const ASCII_ONLY_NON_CC_REGEX = /^[\x20-\x7E]*$/;

export const ASCII_ONLY_NON_CC_ERROR = "String cannot contain control characters or non-ASCII characters";

export const CommonArgs = {

asciiOnlyString: (): ZodString => z.string().regex(ASCII_ONLY_NON_CC_REGEX, ASCII_ONLY_NON_CC_ERROR),

addaleax · 2026-05-21T14:31:53Z

+                resolve();
+            },
+            { once: true }
+        );


Probably fine, but it's good keeping in mind (esp. since this is a generic utility) that not removing the event listener if the signal does not abort can lead to memory leaks

added cleanup to timeout scenario

addaleax · 2026-05-21T14:36:53Z

@@ -0,0 +1 @@
+{"version":3,"file":"vitest.config.js","sourceRoot":"","sources":["vitest.config.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,eAAe,CAAC;AAE7C,eAAe,YAAY,CAAC;IACxB,IAAI,EAAE;QACF,UAAU,EAAE,CAAC,4BAA4B,CAAC;KAC7C;CACJ,CAAC,CAAC"}


Should these files that are generated from vitest.config.ts be commited?

Nope... accident

addaleax · 2026-05-21T14:48:14Z

+    }
+}
+
+enableFipsIfRequested();


We may want to be careful with ESM and the relative timing of execution here.

This seems to be inspired by similar code in mongosh; mongosh compiles to CJS, and does so in a slightly non-spec-compliant way, where imports get translated to require() calls in place. In "real" ESM (and the presence of import.meta handling in this PR makes me assume that we're targeting ESM now), imported modules evaluate before any code in the calling script runs.

This is a good reminder to also fix this in mongosh: mongodb-js/mongosh#2731

hm yeah. We were already doing this with ESM as our default and I suppose haven't had FIPS users to report anything. I'd like to defer it to a seperate PR if that's fine as this matches current state

addaleax · 2026-05-21T14:48:59Z

+{
+  "name": "mongodb-mcp-server",
+  "description": "MongoDB Model Context Protocol Server",
+  "version": "1.11.0-prerelease.3",


Probably an unnecessary comment, but let's make sure this version is what it should be when we merge this PR?

The way our release workflow is setup, we'll trigger a release when we see an unreleased version. So we should bump it only if we want to also do a release.

addaleax · 2026-05-21T14:51:51Z

+                delete (process.env as Record<string, unknown>)[variable];
+            }
+        },
+    };


useClearEnvironment() restores previous values of environment variables, should this one do the same?

yeah.. generally there's a lot of redundancy here (more obvious now that they're been batched together); I'd love to adopt a hook-based approach across the board eventually. I'd add this for now

addaleax · 2026-05-21T14:55:23Z

+import { z } from "zod";
+import { EJSON } from "bson";
+
+export function toEJSON<T extends object | undefined>(value: T): T {


This does the exact opposite of what it says it does 🙂

Suggested change

export function toEJSON<T extends object | undefined>(value: T): T {

export function fromEJSON<T extends object | undefined>(value: T): T {

I will call this deserializeEJSON to make the Zod chain below easier to read

addaleax · 2026-05-21T14:57:55Z

Should this file be checked in to the repo?

It should be committed (we don't always build this, only on releases as part of generation script) but we could hide it in attributions. This can be done in a different PR though as this matches current state.

It's something worth improving for sure

Hmm I ran into this question for my mcp apps skunkworks too. I copied what the mcp ui package does for now, but I don't like it.

gagik · 2026-05-22T09:21:19Z

Converting this to draft as we want to do a v1 release first before moving to v2.

…es less strict

…o apiClient

gagik and others added 5 commits April 30, 2026 13:09

refactor: move logging to core and logging MCP-480 (#1114)

3fb3bfe

refactor: move UI components into @mongodb-js/mcp-ui package MCP-480 (

421a204

#1115)

refactor: move Atlas Api Client logic into atlas-api-client MCP-480 (…

e3718ca

…#1116)

Merge branch 'main' of github.com:mongodb-js/mongodb-mcp-server into v2

536d0ce

chore: updates

748e68b

github-actions Bot added the type: chore label May 1, 2026

gagik and others added 11 commits May 1, 2026 10:36

chore: fix

5b900a6

refactor: move to telemetry package MCP-480 (#1125)

ea77d28

fix(v2): use native fetch in OIDC curl.mjs fixture (#1143)

fd4ad57

refactor: scaffold @mongodb-js/mcp-tools-atlas-local package MCP-480 (#…

bf2e12d

…1124)

Merge branch 'origin/main' into v2

8f0e459

docs: add MongoDB tools package migration guide

9f43e34

Document the breaking changes for the @mongodb-js/mcp-tools-mongodb package extraction, including:

chore: update lockfile and formatting after merge

ef62490

refactor: split atlas tools into @mongodb-js/mcp-tools-atlas package (#…

c2d50c7

…1148)

fix: resolve merge conflicts and update lockfile

4fc2a65

- Fix merge conflicts in package.json and src/web.ts - Recreate missing packages/tools-mongodb/package.json and tsconfig.json - Update pnpm-lock.yaml with new dependencies All checks pass.

Merge remote-tracking branch 'origin/main' into v2

4e7e28a

# Conflicts: # api-extractor/reports/mongodb-mcp-server.public.api.md # api-extractor/reports/tools.public.api.md # api-extractor/reports/web.public.api.md # packages/atlas-telemetry/src/types.ts # src/tools/atlas/tools.ts # src/web.ts

chore: remove .opencode/worktree.jsonc

393f28d

gagik force-pushed the v2 branch from 4f6a24f to 393f28d Compare May 6, 2026 15:33

gagik added 4 commits May 6, 2026 17:43

chore: adopt changes from d843b35 - remove e2e getRandomUUID test

81fd315

feat: add UpgradeClusterTool adapted to v2 architecture

9518cef

Merge remote-tracking branch 'origin/main' into v2

7385b92

# Conflicts: # src/setup/setupMcpServer.ts # src/setup/setupTelemetry.ts

chore: update lockfile

931edb6

gagik force-pushed the v2 branch 2 times, most recently from 2bc1b03 to fd7d4e6 Compare May 11, 2026 08:31

chore: merge origin/main into v2 - fix knip and conflicts

ea265af

gagik force-pushed the v2 branch from fd7d4e6 to ea265af Compare May 11, 2026 08:36

gagik added 4 commits May 11, 2026 09:43

chore: update gitignore

591e7ca

Merge remote-tracking branch 'origin/main' into v2

664c943

chore: fix conflicts

d0c61b1

chore: update api

e1b981d

Copilot AI reviewed May 20, 2026

View reviewed changes

gagik changed the title ~~WIP: v2 refactor branch~~ refactor: move to v2 structure May 20, 2026

gagik changed the title ~~refactor: move to v2 structure~~ refactor: move to v2 structure MCP-373 May 20, 2026

gagik changed the title ~~refactor: move to v2 structure MCP-373~~ refactor: move to v2 structure MCP-373 May 20, 2026

gagik removed the request for review from cveticm May 20, 2026 15:36

gagik added 2 commits May 21, 2026 08:05

chore: add check, exclude tests from build (make TS-only)

beec151

chore: avoid re-exporting types, parallelize checks

420dc7b

gagik force-pushed the v2 branch from 0a6f077 to a3c4166 Compare May 21, 2026 08:17

github-advanced-security AI found potential problems May 21, 2026

View reviewed changes

Comment thread .github/actions/typescript-build/action.yml Fixed

Comment thread .github/workflows/code-health-fork.yml Fixed

Comment thread .github/workflows/code-health-fork.yml Fixed

gagik force-pushed the v2 branch from bcfadea to 1b9c790 Compare May 21, 2026 08:28

chore: fixup

3cedb1b

gagik force-pushed the v2 branch from 1b9c790 to 3cedb1b Compare May 21, 2026 10:13

nirinchev and others added 2 commits May 21, 2026 12:45

fix: use object for ApiClientError

f91539a

docs: update migration guide

55d695f

addaleax approved these changes May 21, 2026

View reviewed changes

chore: changes from feedback

d813c6f

addaleax approved these changes May 22, 2026

View reviewed changes

chore: proper cleanup

3bba4b2

gagik marked this pull request as draft May 22, 2026 09:21

gagik added 5 commits May 22, 2026 13:23

chore: make connection manager use serverMetadata, make telemetry typ…

0acd04e

…es less strict

chore: remove session store from http runner

171f972

chore: remove metrics from runner

880cb8f

chore: cleanup, create from config helpers, connect server metadata t…

3537d26

…o apiClient

chore: move monitoring server, add hooks

b8fe722

gagik marked this pull request as ready for review May 22, 2026 14:13

gagik added 3 commits May 22, 2026 16:25

Merge branch 'main' of github.com:mongodb-js/mongodb-mcp-server into v2

f8024f3

chore: pnpm i

c4e74f0

chore: reformat

e5194fa

		@@ -0,0 +1 @@
		{"version":3,"file":"vitest.config.js","sourceRoot":"","sources":["vitest.config.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,eAAe,CAAC;AAE7C,eAAe,YAAY,CAAC;IACxB,IAAI,EAAE;QACF,UAAU,EAAE,CAAC,4BAA4B,CAAC;KAC7C;CACJ,CAAC,CAAC"}

	export function toEJSON<T extends object \| undefined>(value: T): T {
	export function fromEJSON<T extends object \| undefined>(value: T): T {

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gagik commented Apr 30, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Only merge once the last v1 release is complete

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gagik May 22, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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gagik commented May 22, 2026

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