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opencloning-cli

opencloning-cli is the command-line companion to the OpenCloning backend. It provides Alembic-backed schema management, guarded local seeding, stub workflows and admin commands for opencloning-db.

Install

opencloning-cli is a uv workspace member. From the repository root:

uv sync
uv run opencloning-cli --help

Apply schema migrations

Use db migrate to bring the configured database to Alembic head. On an empty database this creates all tables (starts from baseline revision faa1e883e333).

source .env.dev
uv run opencloning-cli db migrate

Equivalent to uv run alembic -c packages/opencloning-db/alembic.ini upgrade head with OPENCLONING_DB_URL set. See opencloning-db/README.md for autogenerate workflow.

Seed local DB state

db seed clears object-storage prefixes, ensures schema at head, truncates application tables, and loads the deterministic demo/test baseline. It only runs when OPENCLONING_TESTING=1.

source .env.dev
OPENCLONING_TESTING=1 uv run opencloning-cli db seed

Use --recreate-schema to drop and recreate the public schema before migrating (for broken mid-dev states).

Admin commands

Admin commands read and write the configured database directly. Load .env.dev first.

source .env.dev
uv run opencloning-cli admin list-users
uv run opencloning-cli admin list-workspaces
uv run opencloning-cli admin assign-user view-only-user@example.com 1 --role editor
uv run opencloning-cli admin set-instance-admin bootstrap@example.com

Local .env.dev sets OIDC_TEST_MODE=1, which accepts test:... bearer tokens. OPENCLONING_TESTING=1 is separate and only required for db seed and db stubs.

Generate DB Stubs

Use db stubs to generate JSON stubs for frontend testing. By default it writes one JSON file per yielded stub request into ./stubs/db (for example, get_primers.json, get_sequences.json, and similar request-specific files).

db stubs writes JSON request/response fixtures for frontend or integration tests. It requires OPENCLONING_TESTING=1 because it calls db seed between cases.

source .env.dev
OPENCLONING_TESTING=1 uv run opencloning-cli db stubs --output-dir ./stubs/db

The command reseeds the database to the default baseline between stub cases and records the yielded stub requests as separate files in the output directory.