diff --git a/docs/developing-server.md b/docs/developing-server.md
index 1a8509de73..cb38e996c4 100644
--- a/docs/developing-server.md
+++ b/docs/developing-server.md
@@ -74,5 +74,5 @@ Now you should be able to start developing affine with server enabled.
 
 ```sh
 # available at http://localhost:5555
-yarn prisma studio
+yarn affine server prisma studio
 ```
diff --git a/packages/backend/server/package.json b/packages/backend/server/package.json
index 9c78dc604d..196277b3f1 100644
--- a/packages/backend/server/package.json
+++ b/packages/backend/server/package.json
@@ -14,7 +14,7 @@
     "test:copilot": "ava \"tests/**/copilot-*.spec.ts\"",
     "test:coverage": "c8 ava --concurrency 1 --serial",
     "test:copilot:coverage": "c8 ava --timeout=5m \"tests/**/copilot-*.spec.ts\"",
-    "data-migration": "cross-env NODE_ENV=script node ./src/data/index.ts",
+    "data-migration": "cross-env NODE_ENV=script r ./src/data/index.ts",
     "predeploy": "yarn prisma migrate deploy && NODE_ENV=script node --import ./scripts/register.js ./dist/data/index.js run",
     "postinstall": "prisma generate"
   },
@@ -91,6 +91,7 @@
   },
   "devDependencies": {
     "@affine-test/kit": "workspace:*",
+    "@affine-tools/cli": "workspace:*",
     "@affine/server-native": "workspace:*",
     "@nestjs/testing": "^10.4.15",
     "@types/cookie-parser": "^1.4.8",
diff --git a/tools/utils/src/workspace.gen.ts b/tools/utils/src/workspace.gen.ts
index de136e5f1a..00770d7999 100644
--- a/tools/utils/src/workspace.gen.ts
+++ b/tools/utils/src/workspace.gen.ts
@@ -418,7 +418,11 @@ export const PackageList = [
   {
     location: 'packages/backend/server',
     name: '@affine/server',
-    workspaceDependencies: ['tests/kit', 'packages/backend/native'],
+    workspaceDependencies: [
+      'tests/kit',
+      'tools/cli',
+      'packages/backend/native',
+    ],
   },
   {
     location: 'packages/common/debug',
diff --git a/yarn.lock b/yarn.lock
index bb8d7c0897..6aa54caca8 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -753,6 +753,7 @@ __metadata:
   resolution: "@affine/server@workspace:packages/backend/server"
   dependencies:
     "@affine-test/kit": "workspace:*"
+    "@affine-tools/cli": "workspace:*"
     "@affine/server-native": "workspace:*"
     "@apollo/server": "npm:^4.11.2"
     "@aws-sdk/client-s3": "npm:^3.709.0"