feat(server): add data migration system

.github/helm/affine/charts/graphql/templates/migration.yaml

@@ -16,7 +16,7 @@ spec:
       containers:
       - name: {{ .Chart.Name }}
         image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
-        command: ["yarn", "prisma", "migrate", "deploy"]
+        command: ["yarn", "predeploy"]
         env:
           - name: NODE_ENV
             value: "{{ .Values.env }}"

packages/backend/server/migrations/20231027090128_data_migration/migration.sql

@@ -0,0 +1,9 @@
+-- CreateTable
+CREATE TABLE "_data_migrations" (
+    "id" VARCHAR(36) NOT NULL,
+    "name" VARCHAR NOT NULL,
+    "started_at" TIMESTAMPTZ(6) NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    "finished_at" TIMESTAMPTZ(6),
+
+    CONSTRAINT "_data_migrations_pkey" PRIMARY KEY ("id")
+);

packages/backend/server/package.json

@@ -13,7 +13,9 @@
     "dev": "nodemon ./src/index.ts",
     "test": "ava --concurrency 1 --serial",
     "test:coverage": "c8 ava --concurrency 1 --serial",
-    "postinstall": "prisma generate"
+    "postinstall": "prisma generate",
+    "data-migration": "node --loader ts-node/esm.mjs --es-module-specifier-resolution node ./src/data/app.ts",
+    "predeploy": "yarn prisma migrate deploy && node --es-module-specifier-resolution node ./dist/data/app.js run"
   },
   "dependencies": {
     "@apollo/server": "^4.9.4",
@@ -59,6 +61,7 @@
     "keyv": "^4.5.4",
     "lodash-es": "^4.17.21",
     "nanoid": "^5.0.1",
+    "nest-commander": "^3.12.0",
     "nestjs-throttler-storage-redis": "^0.4.1",
     "next-auth": "^4.23.2",
     "nodemailer": "^6.9.6",

packages/backend/server/schema.prisma

@@ -164,3 +164,12 @@ model NewFeaturesWaitingList {
 
   @@map("new_features_waiting_list")
 }
+
+model DataMigration {
+  id         String    @id @default(uuid()) @db.VarChar(36)
+  name       String    @db.VarChar
+  startedAt  DateTime  @default(now()) @map("started_at") @db.Timestamptz(6)
+  finishedAt DateTime? @map("finished_at") @db.Timestamptz(6)
+
+  @@map("_data_migrations")
+}

packages/backend/server/src/data/app.ts

@@ -0,0 +1,18 @@
+import { Logger, Module } from '@nestjs/common';
+import { CommandFactory } from 'nest-commander';
+
+import { PrismaModule } from '../prisma';
+import { CreateCommand, NameQuestion } from './commands/create';
+import { RevertCommand, RunCommand } from './commands/run';
+
+@Module({
+  imports: [PrismaModule],
+  providers: [NameQuestion, CreateCommand, RunCommand, RevertCommand],
+})
+class AppModule {}
+
+async function bootstrap() {
+  await CommandFactory.run(AppModule, new Logger());
+}
+
+await bootstrap();

packages/backend/server/src/data/commands/create.ts

@@ -0,0 +1,73 @@
+import { writeFileSync } from 'node:fs';
+import { join } from 'node:path';
+import { fileURLToPath } from 'node:url';
+
+import { Logger } from '@nestjs/common';
+import { camelCase, snakeCase, upperFirst } from 'lodash-es';
+import {
+  Command,
+  CommandRunner,
+  InquirerService,
+  Question,
+  QuestionSet,
+} from 'nest-commander';
+
+@QuestionSet({ name: 'name-questions' })
+export class NameQuestion {
+  @Question({
+    name: 'name',
+    message: 'Name of the data migration script:',
+  })
+  parseName(val: string) {
+    return val.trim();
+  }
+}
+
+@Command({
+  name: 'create',
+  arguments: '[name]',
+  description: 'create a data migration script',
+})
+export class CreateCommand extends CommandRunner {
+  logger = new Logger(CreateCommand.name);
+  constructor(private readonly inquirer: InquirerService) {
+    super();
+  }
+
+  override async run(inputs: string[]): Promise<void> {
+    let name = inputs[0];
+
+    if (!name) {
+      name = (
+        await this.inquirer.ask<{ name: string }>('name-questions', undefined)
+      ).name;
+    }
+
+    const timestamp = Date.now();
+    const content = this.createScript(upperFirst(camelCase(name)) + timestamp);
+    const fileName = `${timestamp}-${snakeCase(name)}.ts`;
+    const filePath = join(
+      fileURLToPath(import.meta.url),
+      '../../migrations',
+      fileName
+    );
+
+    this.logger.log(`Creating ${fileName}...`);
+    writeFileSync(filePath, content);
+    this.logger.log('Done');
+  }
+
+  private createScript(name: string) {
+    const contents = ["import { PrismaService } from '../../prisma';", ''];
+    contents.push(`export class ${name} {`);
+    contents.push('  // do the migration');
+    contents.push('  static async up(db: PrismaService) {}');
+    contents.push('');
+    contents.push('  // revert the migration');
+    contents.push('  static async down(db: PrismaService) {}');
+
+    contents.push('}');
+
+    return contents.join('\n');
+  }
+}

packages/backend/server/src/data/commands/run.ts

@@ -0,0 +1,149 @@
+import { readdirSync } from 'node:fs';
+import { join } from 'node:path';
+import { fileURLToPath } from 'node:url';
+
+import { Logger } from '@nestjs/common';
+import { Command, CommandRunner } from 'nest-commander';
+
+import { PrismaService } from '../../prisma';
+
+interface Migration {
+  file: string;
+  name: string;
+  up: (db: PrismaService) => Promise<void>;
+  down: (db: PrismaService) => Promise<void>;
+}
+
+async function collectMigrations(): Promise<Migration[]> {
+  const folder = join(fileURLToPath(import.meta.url), '../../migrations');
+
+  const migrationFiles = readdirSync(folder)
+    .filter(desc => desc.endsWith('.ts') && desc !== 'index.ts')
+    .map(desc => join(folder, desc));
+
+  const migrations: Migration[] = await Promise.all(
+    migrationFiles.map(async file => {
+      return import(file).then(mod => {
+        const migration = mod[Object.keys(mod)[0]];
+
+        return {
+          file,
+          name: migration.name,
+          up: migration.up,
+          down: migration.down,
+        };
+      });
+    })
+  );
+
+  return migrations;
+}
+@Command({
+  name: 'run',
+  description: 'Run all pending data migrations',
+})
+export class RunCommand extends CommandRunner {
+  logger = new Logger(RunCommand.name);
+  constructor(private readonly db: PrismaService) {
+    super();
+  }
+
+  override async run(): Promise<void> {
+    const migrations = await collectMigrations();
+    const done: Migration[] = [];
+    for (const migration of migrations) {
+      const exists = await this.db.dataMigration.count({
+        where: {
+          name: migration.name,
+        },
+      });
+
+      if (exists) {
+        continue;
+      }
+
+      try {
+        this.logger.log(`Running ${migration.name}...`);
+        const record = await this.db.dataMigration.create({
+          data: {
+            name: migration.name,
+            startedAt: new Date(),
+          },
+        });
+        await migration.up(this.db);
+        await this.db.dataMigration.update({
+          where: {
+            id: record.id,
+          },
+          data: {
+            finishedAt: new Date(),
+          },
+        });
+        done.push(migration);
+      } catch (e) {
+        this.logger.error('Failed to run data migration', e);
+      }
+    }
+
+    this.logger.log(`Done ${done.length} migrations`);
+    done.forEach(migration => {
+      this.logger.log(`  ✔ ${migration.name}`);
+    });
+  }
+}
+
+@Command({
+  name: 'revert',
+  arguments: '[name]',
+  description: 'Revert one data migration with given name',
+})
+export class RevertCommand extends CommandRunner {
+  logger = new Logger(RevertCommand.name);
+
+  constructor(private readonly db: PrismaService) {
+    super();
+  }
+
+  override async run(inputs: string[]): Promise<void> {
+    const name = inputs[0];
+    if (!name) {
+      throw new Error('A migration name is required');
+    }
+
+    const migrations = await collectMigrations();
+
+    const migration = migrations.find(m => m.name === name);
+
+    if (!migration) {
+      this.logger.error('Available migration names:');
+      migrations.forEach(m => {
+        this.logger.error(`  - ${m.name}`);
+      });
+      throw new Error(`Unknown migration name: ${name}.`);
+    }
+
+    const record = await this.db.dataMigration.findFirst({
+      where: {
+        name: migration.name,
+      },
+    });
+
+    if (!record) {
+      throw new Error(`Migration ${name} has not been executed.`);
+    }
+
+    try {
+      this.logger.log(`Reverting ${name}...`);
+      await migration.down(this.db);
+      this.logger.log('Done reverting');
+    } catch (e) {
+      this.logger.error(`Failed to revert data migration ${name}`, e);
+    }
+
+    await this.db.dataMigration.delete({
+      where: {
+        id: record.id,
+      },
+    });
+  }
+}

packages/backend/server/src/data/migrations/1698398506533-guid.ts

@@ -0,0 +1,117 @@
+import { applyUpdate, Doc, encodeStateAsUpdate } from 'yjs';
+
+import { PrismaService } from '../../prisma';
+import { DocID } from '../../utils/doc';
+
+export class Guid1698398506533 {
+  // do the migration
+  static async up(db: PrismaService) {
+    let turn = 0;
+    let lastTurnCount = 100;
+    while (lastTurnCount === 100) {
+      const docs = await db.snapshot.findMany({
+        select: {
+          workspaceId: true,
+          id: true,
+        },
+        skip: turn * 100,
+        take: 100,
+        orderBy: {
+          createdAt: 'asc',
+        },
+      });
+
+      lastTurnCount = docs.length;
+      for (const doc of docs) {
+        const docId = new DocID(doc.id, doc.workspaceId);
+
+        // NOTE:
+        // `doc.id` could be 'space:xxx' or 'xxx'
+        // `docId.guid` is always 'xxx'
+        // what we want achieve is:
+        //   if both 'space:xxx' and 'xxx' exist, merge 'space:xxx' to 'xxx' and delete it
+        //   else just modify 'space:xxx' to 'xxx'
+
+        if (docId && !docId.isWorkspace && docId.guid !== doc.id) {
+          const existingUpdate = await db.snapshot.findFirst({
+            where: {
+              id: docId.guid,
+              workspaceId: doc.workspaceId,
+            },
+            select: {
+              blob: true,
+            },
+          });
+
+          // we have missing update with wrong id used before and need to be recovered
+          if (existingUpdate) {
+            const toBeMergeUpdate = await db.snapshot.findFirst({
+              // id 'space:xxx'
+              where: {
+                id: doc.id,
+                workspaceId: doc.workspaceId,
+              },
+              select: {
+                blob: true,
+              },
+            });
+
+            // no conflict
+            // actually unreachable path
+            if (!toBeMergeUpdate) {
+              continue;
+            }
+
+            // recover
+            const yDoc = new Doc();
+            applyUpdate(yDoc, toBeMergeUpdate.blob);
+            applyUpdate(yDoc, existingUpdate.blob);
+            const update = encodeStateAsUpdate(yDoc);
+
+            await db.$transaction([
+              // we already have 'xxx', delete 'space:xxx'
+              db.snapshot.deleteMany({
+                where: {
+                  id: doc.id,
+                  workspaceId: doc.workspaceId,
+                },
+              }),
+              db.snapshot.update({
+                where: {
+                  id_workspaceId: {
+                    id: docId.guid,
+                    workspaceId: doc.workspaceId,
+                  },
+                },
+                data: {
+                  blob: Buffer.from(update),
+                },
+              }),
+            ]);
+          } else {
+            // there is no updates need to be merged
+            // just modify the id the required one
+            await db.snapshot.update({
+              where: {
+                id_workspaceId: {
+                  id: doc.id,
+                  workspaceId: doc.workspaceId,
+                },
+              },
+              data: {
+                id: docId.guid,
+              },
+            });
+          }
+        }
+      }
+
+      turn++;
+    }
+  }
+
+  // revert the migration
+  static async down() {
+    //
+  }
+}

packages/backend/server/src/middleware/exception-logger.ts

@@ -30,7 +30,7 @@ export class ExceptionLogger implements ExceptionFilter {
       new Error(
         `${requestId ? `requestId-${requestId}: ` : ''}${exception.message}${
           shouldVerboseLog ? '\n' + exception.stack : ''
-        }}`,
+        }`,
         { cause: exception }
       )
     );

packages/backend/server/src/modules/doc/manager.ts

@@ -2,7 +2,6 @@ import {
   Inject,
   Injectable,
   Logger,
-  OnApplicationBootstrap,
   OnModuleDestroy,
   OnModuleInit,
 } from '@nestjs/common';
@@ -14,7 +13,6 @@ import { Config } from '../../config';
 import { Metrics } from '../../metrics/metrics';
 import { PrismaService } from '../../prisma';
 import { mergeUpdatesInApplyWay as jwstMergeUpdates } from '../../storage';
-import { DocID } from '../../utils/doc';
 
 function compare(yBinary: Buffer, jwstBinary: Buffer, strict = false): boolean {
   if (yBinary.equals(jwstBinary)) {
@@ -44,9 +42,7 @@ const MAX_SEQ_NUM = 0x3fffffff; // u31
  * along side all the updates that have not been applies to that snapshot(timestamp).
  */
 @Injectable()
-export class DocManager
-  implements OnModuleInit, OnModuleDestroy, OnApplicationBootstrap
-{
+export class DocManager implements OnModuleInit, OnModuleDestroy {
   protected logger = new Logger(DocManager.name);
   private job: NodeJS.Timeout | null = null;
   private seqMap = new Map<string, number>();
@@ -60,12 +56,6 @@ export class DocManager
     protected readonly metrics: Metrics
   ) {}
 
-  async onApplicationBootstrap() {
-    if (!this.config.node.test) {
-      await this.refreshDocGuid();
-    }
-  }
-
   onModuleInit() {
     if (this.automation) {
       this.logger.log('Use Database');
@@ -421,56 +411,4 @@ export class DocManager
       return last + 1;
     }
   }
-
-  /**
-   * deal with old records that has wrong guid format
-   * correct guid with `${non-wsId}:${variant}:${subId}` to `${subId}`
-   *
-   * @TODO delete in next release
-   * @deprecated
-   */
-  private async refreshDocGuid() {
-    let turn = 0;
-    let lastTurnCount = 100;
-    while (lastTurnCount === 100) {
-      const docs = await this.db.snapshot.findMany({
-        select: {
-          workspaceId: true,
-          id: true,
-        },
-        skip: turn * 100,
-        take: 100,
-        orderBy: {
-          createdAt: 'asc',
-        },
-      });
-
-      lastTurnCount = docs.length;
-      for (const doc of docs) {
-        const docId = new DocID(doc.id, doc.workspaceId);
-
-        if (docId && !docId.isWorkspace && docId.guid !== doc.id) {
-          await this.db.snapshot.deleteMany({
-            where: {
-              id: docId.guid,
-              workspaceId: doc.workspaceId,
-            },
-          });
-          await this.db.snapshot.update({
-            where: {
-              id_workspaceId: {
-                id: doc.id,
-                workspaceId: doc.workspaceId,
-              },
-            },
-            data: {
-              id: docId.guid,
-            },
-          });
-        }
-      }
-
-      turn++;
-    }
-  }
 }

yarn.lock

@@ -722,6 +722,7 @@ __metadata:
     keyv: "npm:^4.5.4"
     lodash-es: "npm:^4.17.21"
     nanoid: "npm:^5.0.1"
+    nest-commander: "npm:^3.12.0"
     nestjs-throttler-storage-redis: "npm:^0.4.1"
     next-auth: "npm:^4.23.2"
     nodemailer: "npm:^6.9.6"
@@ -5273,6 +5274,17 @@ __metadata:
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+"@fig/complete-commander@npm:^2.0.1":
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+  linkType: hard
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@@ -5337,6 +5349,18 @@ __metadata:
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+"@golevelup/nestjs-discovery@npm:4.0.0":
+  version: 4.0.0
+  resolution: "@golevelup/nestjs-discovery@npm:4.0.0"
+  dependencies:
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+  peerDependencies:
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+  languageName: node
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   resolution: "@google-cloud/opentelemetry-cloud-monitoring-exporter@npm:0.17.0"
@@ -17266,6 +17290,13 @@ __metadata:
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+  languageName: node
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+
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   resolution: "commander@npm:11.1.0"
@@ -17681,6 +17712,18 @@ __metadata:
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+"cosmiconfig@npm:8.2.0":
+  version: 8.2.0
+  resolution: "cosmiconfig@npm:8.2.0"
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+    js-yaml: "npm:^4.1.0"
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@@ -22888,6 +22931,29 @@ __metadata:
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+"inquirer@npm:8.2.5":
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+    figures: "npm:^3.0.0"
+    lodash: "npm:^4.17.21"
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+    strip-ansi: "npm:^6.0.0"
+    through: "npm:^2.3.6"
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@@ -26962,6 +27028,23 @@ __metadata:
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+"nest-commander@npm:^3.12.0":
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+    "@golevelup/nestjs-discovery": "npm:4.0.0"
+    commander: "npm:11.0.0"
+    cosmiconfig: "npm:8.2.0"
+    inquirer: "npm:8.2.5"
+  peerDependencies:
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+    "@nestjs/core": ^8.0.0 || ^9.0.0 || ^10.0.0
+    "@types/inquirer": ^8.1.3
+  checksum: 29554f1cef113e0b0fa05a958c81b63613a046c682a2da7f7856b3f03f1e0b4792d76637fa1e47cdac4db98862dba34bbae46b964db71ad72f5bb9fff72ef530
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@@ -29154,7 +29237,7 @@ __metadata:
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