refactor: Prisma から Atlas + kysely-codegen への移行 by coji · Pull Request #101 · coji/upflow

coji · 2025-12-24T14:44:26Z

Summary

Prisma を削除し、Atlas (マイグレーション) + kysely-codegen (型生成) に移行
Kysely はそのまま使用 (ランタイムクエリ)

Changes

追加

atlas.hcl - Atlas 設定ファイル
db/schema.sql - Declarative スキーマ定義
db/migrations/ - Atlas マイグレーション
db/seed.ts - シードデータ (prisma/seed.ts から移動)

削除

prisma/ ディレクトリ全体
app/services/prisma.server.ts
@prisma/client, prisma, prisma-kysely 依存関係

変更

型名を複数形に統一 (Organization → Organizations など)
Dockerfile: Atlas CLI インストール追加、Prisma 削除
start.sh: prisma migrate deploy → atlas migrate apply

New Commands

pnpm setup         # マイグレーション適用 + seed
pnpm db:generate   # 型を再生成
pnpm db:migrate    # スキーマ変更からマイグレーション生成
pnpm db:apply      # マイグレーション適用

Test plan

pnpm validate 通過
Fly.io へのデプロイ確認

🤖 Generated with Claude Code

Summary by CodeRabbit

Chores
- Migrated database tooling from Prisma to Atlas + Kysely; updated startup and Docker flow to use Atlas migrations and new DB tooling.
- Added a local DB schema and migrations for easier local development and one‑step setup.
- Updated dev tooling and dependencies to support the new DB stack.
Refactor
- Standardized data type names and cleaned up component interface formatting (no UI behavior changes).

_{✏️ Tip: You can customize this high-level summary in your review settings.}

- Add db/schema.sql with declarative schema definition - Add db/migrations/ with initial migration - Add db/seed.ts (moved from prisma/seed.ts) - Add atlas.hcl configuration 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Remove @prisma/client, prisma, prisma-kysely - Add kysely-codegen for type generation - Update scripts: setup, db:generate, db:migrate, db:apply 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Remove prisma/schema.prisma - Remove prisma/migrations/ - Remove prisma/seed.ts (moved to db/) - Remove app/services/prisma.server.ts 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Types now use plural names (Organizations, Repositories, etc.) - Generated with --camel-case option 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- DB.Organization -> DB.Organizations - DB.Repository -> DB.Repositories - DB.PullRequest -> DB.PullRequests - DB.Integration -> DB.Integrations - DB.ExportSetting -> DB.ExportSettings - DB.OrganizationSetting -> DB.OrganizationSettings 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Install Atlas CLI in Dockerfile - Remove Prisma-related steps - Update start.sh to use atlas migrate apply - Add automatic baseline setting for existing databases 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

coderabbitai · 2025-12-24T14:44:39Z

Caution

Review failed

The pull request is closed.

📝 Walkthrough

Walkthrough

Replaces Prisma with an Atlas + Kysely DB stack: removes Prisma schema, migrations and client; adds Atlas config, SQL schema and migrations; updates generated DB types (singular → plural), adjusts many function/component type signatures, and updates Docker, CI, start scripts, and package tooling.

Changes

Cohort / File(s)	Summary
Docker, CI & startup `Dockerfile`, `.github/workflows/.../deploy.yml`, `start.sh`, `package.json`	Remove Prisma install/generation; add Atlas install/usage and Kysely/codegen scripts; replace Prisma migrate calls with Atlas commands; adjust multi-stage Docker artifact references to production-deps; update tooling deps.
Atlas config & SQL migrations `atlas.hcl`, `db/schema.sql`, `db/migrations/20251224122040_initial.sql`	Add Atlas environment "local", introduce new SQL schema and initial migration defining tenants, users, orgs, sessions, accounts, members, integrations, repositories, pull_requests, export/org settings, indexes and FKs.
Prisma artifacts removed `prisma/schema.prisma`, `prisma/migrations/...` (all listed migration dirs), `prisma/migrations/migration_lock.toml`	Delete entire Prisma schema, generators, and all Prisma migration files and migration_lock.
DB types & service layer `app/services/type.ts`, `app/services/prisma.server.ts`	Replace singular type aliases with pluralized interfaces (Accounts, Organizations, Repositories, etc.); update DB mapping; remove exported PrismaClient.
API / server signatures (singular → plural) `app/routes/*` (multiple files, e.g., `_dashboard+/`, `admin+/`, `resources+/`)	Update many function, handler and component prop types from `DB.<Singular>`/`Selectable<DB.<Singular>>` to pluralized `DB.<Plurals>`; minor formatting; one query adds `.orderBy('number','desc')`; update allowed fields for updateOrganizationSetting to include `excludedUsers`.
Batch & provider code `batch/`, `batch/provider/`, `batch/provider/github/*`	Update batch/provider function signatures and local collection types to use pluralized DB types (Integrations, Repositories, PullRequests); no logic changes.
Components — formatting only `app/components/AppSortableHeader.tsx`, `app/components/ui/heading.tsx`, `app/components/ui/stack.tsx`, `app/routes/resources+/organization/route.tsx`	Reformat interface/extends clauses across lines; no semantic or runtime changes.
DB codegen / tooling adjustments `package.json`, `.github/...`	Add kysely-codegen and adjust scripts: db:generate, db:migrate, db:apply; remove prisma-related deps and scripts.

Estimated code review effort

🎯 5 (Critical) | ⏱️ ~120 minutes

Possibly related PRs

feat: add excluded users setting and recalculate feature #100 — touches organization settings schema and types (adds/uses excludedUsers) and provider/export logic; strongly related to schema/type changes here.
Feat/better auth #94 — previously modified Prisma DB layer and client usage; strongly related due to removal of Prisma artifacts in this PR.

Poem

🐰 From burrow of Prisma I bound,
Atlas maps now spread the ground,
Types went plural, migrations sing,
Kysely sprouts its tidy Spring,
I hop with joy — new seeds abound! 🌱🥕

Pre-merge checks and finishing touches

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	You can run `@coderabbitai generate docstrings` to improve docstring coverage.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately describes the primary change: migrating from Prisma to Atlas + kysely-codegen for database management.

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CLAUDE.md

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- Remove prisma generate steps (no longer needed) - Replace prisma migrate reset with Atlas-based pnpm setup - Add Atlas CLI installation step for Vitest job 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

coderabbitai

Actionable comments posted: 0

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

batch/provider/github/provider.ts (1)
18-24: Incorrect invariant error messages.

Lines 22-23 check repository.repo and repository.owner but both error messages say "private token not specified". These should reflect what's actually being validated.
🔎 Proposed fix
-    invariant(repository.repo, 'private token not specified')
-    invariant(repository.owner, 'private token not specified')
+    invariant(repository.repo, 'repository repo not specified')
+    invariant(repository.owner, 'repository owner not specified')
     invariant(integration.privateToken, 'private token not specified')

🧹 Nitpick comments (7)

db/schema.sql (2)
16-25: Consider adding updated_at column for consistency.

The organizations table lacks an updated_at column while most other tables include it for audit purposes. This may cause issues if you need to track when organizations are modified.
🔎 Proposed fix
 CREATE TABLE IF NOT EXISTS "organizations" (
     "id" TEXT NOT NULL PRIMARY KEY,
     "name" TEXT NOT NULL,
     "slug" TEXT,
     "logo" TEXT,
     "created_at" DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    "updated_at" DATETIME NOT NULL,
     "metadata" TEXT
 );
131-132: Redundant index on organization_id.

Line 131 creates a unique index on organization_id, which inherently provides indexing for lookups. The additional non-unique index on line 132 is redundant and wastes storage.
🔎 Proposed fix
 CREATE UNIQUE INDEX "integrations_organization_id_key" ON "integrations"("organization_id");
-CREATE INDEX "integrations_organization_id_idx" ON "integrations"("organization_id");
db/migrations/20251224122040_initial.sql (5)
38-39: Consider adding foreign key constraints for active_organization_id and impersonated_by.

These columns appear to reference organizations.id and users.id respectively, but lack FK constraints. This could lead to orphaned references if the referenced records are deleted.

If soft references are intentional (e.g., to preserve session history), consider this acceptable. Otherwise:
🔎 Proposed fix
   `impersonated_by` text NULL,
   `active_organization_id` text NULL,
   PRIMARY KEY (`id`),
-  CONSTRAINT `sessions_user_id_fkey` FOREIGN KEY (`user_id`) REFERENCES `users` (`id`) ON UPDATE CASCADE ON DELETE CASCADE
+  CONSTRAINT `sessions_user_id_fkey` FOREIGN KEY (`user_id`) REFERENCES `users` (`id`) ON UPDATE CASCADE ON DELETE CASCADE,
+  CONSTRAINT `sessions_impersonated_by_fkey` FOREIGN KEY (`impersonated_by`) REFERENCES `users` (`id`) ON UPDATE CASCADE ON DELETE SET NULL,
+  CONSTRAINT `sessions_active_organization_id_fkey` FOREIGN KEY (`active_organization_id`) REFERENCES `organizations` (`id`) ON UPDATE CASCADE ON DELETE SET NULL
136-139: Redundant index: integrations_organization_id_idx is unnecessary.

The unique index integrations_organization_id_key (line 137) already provides efficient lookups on organization_id. The additional non-unique index (line 139) is redundant and wastes storage.
🔎 Proposed fix
 -- Create index "integrations_organization_id_key" to table: "integrations"
 CREATE UNIQUE INDEX `integrations_organization_id_key` ON `integrations` (`organization_id`);
--- Create index "integrations_organization_id_idx" to table: "integrations"
-CREATE INDEX `integrations_organization_id_idx` ON `integrations` (`organization_id`);
161-163: repo column appears redundant with repository_id FK.

The repo text column seems to duplicate data available via the repository_id foreign key (which links to repositories.repo). This could lead to data inconsistency if not kept in sync.

If this is intentional denormalization for query performance or preserving historical values, consider adding a comment in the schema. Otherwise, consider removing it.

73-83: Consider adding unique constraint on members(organization_id, user_id).

Without a unique constraint on the combination, a user could have multiple membership records for the same organization, which is likely unintended.
🔎 Proposed fix
 -- Create "members" table
 CREATE TABLE `members` (
   `id` text NOT NULL,
   `organization_id` text NOT NULL,
   `user_id` text NOT NULL,
   `role` text NOT NULL,
   `created_at` datetime NOT NULL,
   PRIMARY KEY (`id`),
   CONSTRAINT `members_user_id_fkey` FOREIGN KEY (`user_id`) REFERENCES `users` (`id`) ON UPDATE CASCADE ON DELETE CASCADE,
   CONSTRAINT `members_organization_id_fkey` FOREIGN KEY (`organization_id`) REFERENCES `organizations` (`id`) ON UPDATE CASCADE ON DELETE CASCADE
 );
+-- Create index "members_organization_id_user_id_key" to table: "members"
+CREATE UNIQUE INDEX `members_organization_id_user_id_key` ON `members` (`organization_id`, `user_id`);
45-62: Consider adding unique constraints on accounts table.

OAuth account tables typically need unique constraints to prevent duplicates:

(provider_id, account_id) - ensures each provider account links to only one user

Optionally (user_id, provider_id) - if users can only have one account per provider
🔎 Proposed fix
 );
+-- Create index "accounts_provider_id_account_id_key" to table: "accounts"
+CREATE UNIQUE INDEX `accounts_provider_id_account_id_key` ON `accounts` (`provider_id`, `account_id`);

📜 Review details

Configuration used: defaults

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between 62aec87 and 58aa04a.

⛔ Files ignored due to path filters (2)

db/migrations/atlas.sum is excluded by !**/*.sum
pnpm-lock.yaml is excluded by !**/pnpm-lock.yaml

📒 Files selected for processing (51)

Dockerfile
app/components/AppSortableHeader.tsx
app/components/ui/heading.tsx
app/components/ui/stack.tsx
app/routes/_dashboard+/$organization._index/functions/queries.ts
app/routes/_dashboard+/$organization.ongoing/functions/queries.ts
app/routes/admin+/$organization.members/queries.server.ts
app/routes/admin+/$organization.repositories.$repository.$pull/queries.server.ts
app/routes/admin+/$organization.repositories.$repository._index/queries.server.ts
app/routes/admin+/$organization.repositories.$repository.delete/functions/mutations.ts
app/routes/admin+/$organization.repositories.$repository.delete/functions/queries.ts
app/routes/admin+/$organization.repositories.$repository.settings/functions/mutations.ts
app/routes/admin+/$organization.repositories.$repository.settings/functions/queries.ts
app/routes/admin+/$organization.repositories._index/queries.server.ts
app/routes/admin+/$organization.repositories.add/functions/mutations.ts
app/routes/admin+/$organization.repositories.add/functions/queries.ts
app/routes/admin+/$organization.settings/forms/delete-organization.tsx
app/routes/admin+/$organization.settings/forms/export-settings.tsx
app/routes/admin+/$organization.settings/forms/integration-settings.tsx
app/routes/admin+/$organization.settings/forms/organization-settings.tsx
app/routes/admin+/$organization.settings/functions/mutations.server.ts
app/routes/admin+/$organization.settings/functions/queries.server.ts
app/routes/admin+/create/mutations.server.ts
app/routes/resources+/organization/route.tsx
app/services/prisma.server.ts
app/services/type.ts
atlas.hcl
batch/bizlogic/export-spreadsheet.ts
batch/db/mutations.ts
batch/db/queries.ts
batch/provider/github/provider.ts
batch/provider/github/pullrequest.ts
batch/provider/index.ts
db/migrations/20251224122040_initial.sql
db/schema.sql
db/seed.ts
package.json
prisma/migrations/20230804131847_init/migration.sql
prisma/migrations/20230818024457_change_number_to_int/migration.sql
prisma/migrations/20240129044150_snake_case_table_and_column_name/migration.sql
prisma/migrations/20240129070258_add_team_repository/migration.sql
prisma/migrations/20240420114246_fix_repository_unique_key/migration.sql
prisma/migrations/20240421004556_migrate_datetime_from_unix_to_iso/migration.sql
prisma/migrations/20250207031843_add_company_github_user/migration.sql
prisma/migrations/20250408033427_better_auth/migration.sql
prisma/migrations/20250408101920_migrate_company_to_organization_phase1/migration.sql
prisma/migrations/20250408102129_migrate_company_to_organization_phase3_cleanup/migration.sql
prisma/migrations/20251216104437_add_excluded_users_to_organization_settings/migration.sql
prisma/migrations/migration_lock.toml
prisma/schema.prisma
start.sh

💤 Files with no reviewable changes (14)

prisma/migrations/20240129070258_add_team_repository/migration.sql
prisma/migrations/20250408033427_better_auth/migration.sql
prisma/migrations/20250408102129_migrate_company_to_organization_phase3_cleanup/migration.sql
prisma/migrations/20251216104437_add_excluded_users_to_organization_settings/migration.sql
prisma/migrations/20250207031843_add_company_github_user/migration.sql
prisma/migrations/20230818024457_change_number_to_int/migration.sql
prisma/migrations/20240420114246_fix_repository_unique_key/migration.sql
app/services/prisma.server.ts
prisma/schema.prisma
prisma/migrations/20230804131847_init/migration.sql
prisma/migrations/migration_lock.toml
prisma/migrations/20240421004556_migrate_datetime_from_unix_to_iso/migration.sql
prisma/migrations/20240129044150_snake_case_table_and_column_name/migration.sql
prisma/migrations/20250408101920_migrate_company_to_organization_phase1/migration.sql

🧰 Additional context used

📓 Path-based instructions (6)

app/routes/**/*.{ts,tsx}

📄 CodeRabbit inference engine (CLAUDE.md)

Use file-based routing with remix-flat-routes convention: use _layout.tsx for layout routes, _index.tsx for index routes, $param for dynamic segments, and nested route folders like $organization.settings/

Files:

app/routes/admin+/$organization.settings/forms/integration-settings.tsx
app/routes/admin+/$organization.repositories.add/functions/mutations.ts
app/routes/admin+/$organization.repositories.$repository.delete/functions/queries.ts
app/routes/admin+/$organization.settings/forms/delete-organization.tsx
app/routes/admin+/$organization.repositories._index/queries.server.ts
app/routes/admin+/$organization.repositories.$repository.delete/functions/mutations.ts
app/routes/_dashboard+/$organization._index/functions/queries.ts
app/routes/admin+/$organization.settings/forms/organization-settings.tsx
app/routes/admin+/create/mutations.server.ts
app/routes/admin+/$organization.settings/functions/queries.server.ts
app/routes/admin+/$organization.repositories.$repository._index/queries.server.ts
app/routes/admin+/$organization.repositories.add/functions/queries.ts
app/routes/admin+/$organization.members/queries.server.ts
app/routes/admin+/$organization.repositories.$repository.settings/functions/mutations.ts
app/routes/admin+/$organization.repositories.$repository.settings/functions/queries.ts
app/routes/admin+/$organization.repositories.$repository.$pull/queries.server.ts
app/routes/_dashboard+/$organization.ongoing/functions/queries.ts
app/routes/resources+/organization/route.tsx
app/routes/admin+/$organization.settings/forms/export-settings.tsx
app/routes/admin+/$organization.settings/functions/mutations.server.ts

**/*.{ts,tsx}

📄 CodeRabbit inference engine (CLAUDE.md)

Use ~/ path alias prefix for imports from project root (e.g., import { db } from '~/app/services/db.server')

Files:

app/routes/admin+/$organization.settings/forms/integration-settings.tsx
app/routes/admin+/$organization.repositories.add/functions/mutations.ts
app/routes/admin+/$organization.repositories.$repository.delete/functions/queries.ts
batch/provider/index.ts
app/routes/admin+/$organization.settings/forms/delete-organization.tsx
app/routes/admin+/$organization.repositories._index/queries.server.ts
app/routes/admin+/$organization.repositories.$repository.delete/functions/mutations.ts
app/routes/_dashboard+/$organization._index/functions/queries.ts
app/components/ui/heading.tsx
app/routes/admin+/$organization.settings/forms/organization-settings.tsx
app/routes/admin+/create/mutations.server.ts
app/routes/admin+/$organization.settings/functions/queries.server.ts
batch/provider/github/pullrequest.ts
app/routes/admin+/$organization.repositories.$repository._index/queries.server.ts
app/routes/admin+/$organization.repositories.add/functions/queries.ts
batch/provider/github/provider.ts
batch/db/mutations.ts
app/routes/admin+/$organization.members/queries.server.ts
app/routes/admin+/$organization.repositories.$repository.settings/functions/mutations.ts
batch/db/queries.ts
app/routes/admin+/$organization.repositories.$repository.settings/functions/queries.ts
batch/bizlogic/export-spreadsheet.ts
app/routes/admin+/$organization.repositories.$repository.$pull/queries.server.ts
app/components/AppSortableHeader.tsx
app/routes/_dashboard+/$organization.ongoing/functions/queries.ts
app/routes/resources+/organization/route.tsx
app/services/type.ts
app/routes/admin+/$organization.settings/forms/export-settings.tsx
app/components/ui/stack.tsx
app/routes/admin+/$organization.settings/functions/mutations.server.ts

batch/**/*.ts

📄 CodeRabbit inference engine (CLAUDE.md)

Organize batch processing CLI jobs in batch/ directory with separate files for commands (fetch, report, upsert) and provider integrations (GitHub API)

Files:

batch/provider/index.ts
batch/provider/github/pullrequest.ts
batch/provider/github/provider.ts
batch/db/mutations.ts
batch/db/queries.ts
batch/bizlogic/export-spreadsheet.ts

**/*.server.{ts,tsx}

📄 CodeRabbit inference engine (CLAUDE.md)

Use Kysely for runtime database queries with type-safe generated types from Prisma schema (located in app/services/type.ts)

Files:

app/routes/admin+/$organization.repositories._index/queries.server.ts
app/routes/admin+/create/mutations.server.ts
app/routes/admin+/$organization.settings/functions/queries.server.ts
app/routes/admin+/$organization.repositories.$repository._index/queries.server.ts
app/routes/admin+/$organization.members/queries.server.ts
app/routes/admin+/$organization.repositories.$repository.$pull/queries.server.ts
app/routes/admin+/$organization.settings/functions/mutations.server.ts

app/components/**/*.{ts,tsx}

📄 CodeRabbit inference engine (CLAUDE.md)

Use shadcn/ui components with new-york style and Tailwind CSS v4 for the UI

Files:

app/components/ui/heading.tsx
app/components/AppSortableHeader.tsx
app/components/ui/stack.tsx

app/services/**/*.{ts,tsx}

📄 CodeRabbit inference engine (CLAUDE.md)

Use server-side services organized in app/services/ for database clients (db.server.ts, prisma.server.ts) and type definitions (type.ts from prisma-kysely generation)

Files:

app/services/type.ts

🧠 Learnings (9)

📓 Common learnings

Learnt from: CR
Repo: coji/upflow PR: 0
File: CLAUDE.md:0-0
Timestamp: 2025-12-24T12:15:11.101Z
Learning: Applies to prisma/** : Use Prisma for schema definition, migrations, and seeding via prisma/schema.prisma and prisma/seed.ts

Learnt from: CR
Repo: coji/upflow PR: 0
File: CLAUDE.md:0-0
Timestamp: 2025-12-24T12:15:11.101Z
Learning: Applies to **/*.server.{ts,tsx} : Use Kysely for runtime database queries with type-safe generated types from Prisma schema (located in app/services/type.ts)

Learnt from: CR
Repo: coji/upflow PR: 0
File: CLAUDE.md:0-0
Timestamp: 2025-12-24T12:15:11.101Z
Learning: Applies to app/services/**/*.{ts,tsx} : Use server-side services organized in app/services/ for database clients (db.server.ts, prisma.server.ts) and type definitions (type.ts from prisma-kysely generation)