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Commit d1d26e6

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fix: Use JSON for stdio, similiar to the HTTP Transport and use EJSON deserialize when necessary MCP-207 (#571)
1 parent 3dbbc76 commit d1d26e6

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13 files changed

+65
-146
lines changed

13 files changed

+65
-146
lines changed

‎src/tools/args.ts‎

Lines changed: 13 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,5 @@
11
import { z, type ZodString } from "zod";
2+
import { EJSON } from "bson";
23

34
const NO_UNICODE_REGEX = /^[\x20-\x7E]*$/;
45
export const NO_UNICODE_ERROR = "String cannot contain special characters or Unicode symbols";
@@ -68,3 +69,15 @@ export const AtlasArgs = {
6869
password: (): z.ZodString =>
6970
z.string().min(1, "Password is required").max(100, "Password must be 100 characters or less"),
7071
};
72+
73+
function toEJSON<T extends object | undefined>(value: T): T {
74+
if (!value) {
75+
return value;
76+
}
77+
78+
return EJSON.deserialize(value, { relaxed: false }) as T;
79+
}
80+
81+
export function zEJSON(): z.AnyZodObject {
82+
return z.object({}).passthrough().transform(toEJSON) as unknown as z.AnyZodObject;
83+
}

‎src/tools/mongodb/create/insertMany.ts‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,14 +2,15 @@ import { z } from "zod";
22
import type { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
33
import { DbOperationArgs, MongoDBToolBase } from "../mongodbTool.js";
44
import type { ToolArgs, OperationType } from "../../tool.js";
5+
import { zEJSON } from "../../args.js";
56

67
export class InsertManyTool extends MongoDBToolBase {
78
public name = "insert-many";
89
protected description = "Insert an array of documents into a MongoDB collection";
910
protected argsShape = {
1011
...DbOperationArgs,
1112
documents: z
12-
.array(z.object({}).passthrough().describe("An individual MongoDB document"))
13+
.array(zEJSON().describe("An individual MongoDB document"))
1314
.describe(
1415
"The array of documents to insert, matching the syntax of the document argument of db.collection.insertMany()"
1516
),

‎src/tools/mongodb/delete/deleteMany.ts‎

Lines changed: 2 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,18 +1,16 @@
1-
import { z } from "zod";
21
import type { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
32
import { DbOperationArgs, MongoDBToolBase } from "../mongodbTool.js";
43
import type { ToolArgs, OperationType } from "../../tool.js";
54
import { checkIndexUsage } from "../../../helpers/indexCheck.js";
65
import { EJSON } from "bson";
6+
import { zEJSON } from "../../args.js";
77

88
export class DeleteManyTool extends MongoDBToolBase {
99
public name = "delete-many";
1010
protected description = "Removes all documents that match the filter from a MongoDB collection";
1111
protected argsShape = {
1212
...DbOperationArgs,
13-
filter: z
14-
.object({})
15-
.passthrough()
13+
filter: zEJSON()
1614
.optional()
1715
.describe(
1816
"The query filter, specifying the deletion criteria. Matches the syntax of the filter argument of db.collection.deleteMany()"

‎src/tools/mongodb/read/aggregate.ts‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,9 +6,10 @@ import { formatUntrustedData } from "../../tool.js";
66
import { checkIndexUsage } from "../../../helpers/indexCheck.js";
77
import { EJSON } from "bson";
88
import { ErrorCodes, MongoDBError } from "../../../common/errors.js";
9+
import { zEJSON } from "../../args.js";
910

1011
export const AggregateArgs = {
11-
pipeline: z.array(z.object({}).passthrough()).describe("An array of aggregation stages to execute"),
12+
pipeline: z.array(zEJSON()).describe("An array of aggregation stages to execute"),
1213
};
1314

1415
export class AggregateTool extends MongoDBToolBase {

‎src/tools/mongodb/read/count.ts‎

Lines changed: 2 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,11 @@
11
import type { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
22
import { DbOperationArgs, MongoDBToolBase } from "../mongodbTool.js";
33
import type { ToolArgs, OperationType } from "../../tool.js";
4-
import { z } from "zod";
54
import { checkIndexUsage } from "../../../helpers/indexCheck.js";
5+
import { zEJSON } from "../../args.js";
66

77
export const CountArgs = {
8-
query: z
9-
.object({})
10-
.passthrough()
8+
query: zEJSON()
119
.optional()
1210
.describe(
1311
"A filter/query parameter. Allows users to filter the documents to count. Matches the syntax of the filter argument of db.collection.count()."

‎src/tools/mongodb/read/find.ts‎

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -6,11 +6,10 @@ import { formatUntrustedData } from "../../tool.js";
66
import type { SortDirection } from "mongodb";
77
import { checkIndexUsage } from "../../../helpers/indexCheck.js";
88
import { EJSON } from "bson";
9+
import { zEJSON } from "../../args.js";
910

1011
export const FindArgs = {
11-
filter: z
12-
.object({})
13-
.passthrough()
12+
filter: zEJSON()
1413
.optional()
1514
.describe("The query filter, matching the syntax of the query argument of db.collection.find()"),
1615
projection: z

‎src/tools/mongodb/update/updateMany.ts‎

Lines changed: 5 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -3,23 +3,21 @@ import type { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
33
import { DbOperationArgs, MongoDBToolBase } from "../mongodbTool.js";
44
import type { ToolArgs, OperationType } from "../../tool.js";
55
import { checkIndexUsage } from "../../../helpers/indexCheck.js";
6+
import { zEJSON } from "../../args.js";
67

78
export class UpdateManyTool extends MongoDBToolBase {
89
public name = "update-many";
910
protected description = "Updates all documents that match the specified filter for a collection";
1011
protected argsShape = {
1112
...DbOperationArgs,
12-
filter: z
13-
.object({})
14-
.passthrough()
13+
filter: zEJSON()
1514
.optional()
1615
.describe(
1716
"The selection criteria for the update, matching the syntax of the filter argument of db.collection.updateOne()"
1817
),
19-
update: z
20-
.object({})
21-
.passthrough()
22-
.describe("An update document describing the modifications to apply using update operator expressions"),
18+
update: zEJSON().describe(
19+
"An update document describing the modifications to apply using update operator expressions"
20+
),
2321
upsert: z
2422
.boolean()
2523
.optional()

‎src/transports/stdio.ts‎

Lines changed: 1 addition & 49 deletions
Original file line numberDiff line numberDiff line change
@@ -1,55 +1,8 @@
1-
import { EJSON } from "bson";
2-
import type { JSONRPCMessage } from "@modelcontextprotocol/sdk/types.js";
3-
import { JSONRPCMessageSchema } from "@modelcontextprotocol/sdk/types.js";
41
import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
52
import { LogId } from "../common/logger.js";
63
import type { Server } from "../server.js";
74
import { TransportRunnerBase, type TransportRunnerConfig } from "./base.js";
85

9-
// This is almost a copy of ReadBuffer from @modelcontextprotocol/sdk
10-
// but it uses EJSON.parse instead of JSON.parse to handle BSON types
11-
export class EJsonReadBuffer {
12-
private _buffer?: Buffer;
13-
14-
append(chunk: Buffer): void {
15-
this._buffer = this._buffer ? Buffer.concat([this._buffer, chunk]) : chunk;
16-
}
17-
18-
readMessage(): JSONRPCMessage | null {
19-
if (!this._buffer) {
20-
return null;
21-
}
22-
23-
const index = this._buffer.indexOf("\n");
24-
if (index === -1) {
25-
return null;
26-
}
27-
28-
const line = this._buffer.toString("utf8", 0, index).replace(/\r$/, "");
29-
this._buffer = this._buffer.subarray(index + 1);
30-
31-
// This is using EJSON.parse instead of JSON.parse to handle BSON types
32-
return JSONRPCMessageSchema.parse(EJSON.parse(line));
33-
}
34-
35-
clear(): void {
36-
this._buffer = undefined;
37-
}
38-
}
39-
40-
// This is a hacky workaround for https://github.com/mongodb-js/mongodb-mcp-server/issues/211
41-
// The underlying issue is that StdioServerTransport uses JSON.parse to deserialize
42-
// messages, but that doesn't handle bson types, such as ObjectId when serialized as EJSON.
43-
//
44-
// This function creates a StdioServerTransport and replaces the internal readBuffer with EJsonReadBuffer
45-
// that uses EJson.parse instead.
46-
export function createStdioTransport(): StdioServerTransport {
47-
const server = new StdioServerTransport();
48-
server["_readBuffer"] = new EJsonReadBuffer();
49-
50-
return server;
51-
}
52-
536
export class StdioRunner extends TransportRunnerBase {
547
private server: Server | undefined;
558

@@ -60,8 +13,7 @@ export class StdioRunner extends TransportRunnerBase {
6013
async start(): Promise<void> {
6114
try {
6215
this.server = await this.setupServer();
63-
64-
const transport = createStdioTransport();
16+
const transport = new StdioServerTransport();
6517

6618
await this.server.connect(transport);
6719
} catch (error: unknown) {

‎tests/integration/indexCheck.test.ts‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -80,7 +80,7 @@ describe("IndexCheck integration tests", () => {
8080
arguments: {
8181
database: integration.randomDbName(),
8282
collection: "find-test-collection",
83-
filter: { _id: docs[0]?._id }, // Uses _id index (IDHACK)
83+
filter: { _id: {$oid: docs[0]?._id} }, // Uses _id index (IDHACK)
8484
},
8585
});
8686

‎tests/integration/tools/mongodb/create/insertMany.test.ts‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -76,7 +76,7 @@ describeWithMongoDB("insertMany tool", (integration) => {
7676
arguments: {
7777
database: integration.randomDbName(),
7878
collection: "coll1",
79-
documents: [{ prop1: "value1", _id: insertedIds[0] }],
79+
documents: [{ prop1: "value1", _id: {$oid: insertedIds[0]} }],
8080
},
8181
});
8282

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