gn-integration-tests

Integration and end-to-end tests for the GeneNetwork stack (gn2, gn3, gn-auth).

Tests run against a live deployment (CD or production) — no mocking, no local stack required for the smoke suite.

Quick start

pip install -e .          # or: pip install requests pytest
pytest -m "smoke"         # run all smoke tests (no credentials needed)

By default tests target CD (cd.genenetwork.org / auth-cd.genenetwork.org). Override with environment variables:

Variable	Default	Description
`GN2_BASE_URL`	`https://cd.genenetwork.org`	genenetwork2 root
`GN3_BASE_URL`	`https://cd.genenetwork.org/api3`	gn3 API proxy path
`GN_AUTH_BASE_URL`	`https://auth-cd.genenetwork.org`	gn-auth server

To target production:

GN2_BASE_URL=https://genenetwork.org \
GN3_BASE_URL=https://genenetwork.org/api3 \
GN_AUTH_BASE_URL=https://auth.genenetwork.org \
pytest -m "smoke"

The three variables work for any deployment — CD, production, or a personal/feature instance. To run against an arbitrary stack, just point the variables at it:

GN2_BASE_URL=https://gn2-fred.genenetwork.org \
GN3_BASE_URL=https://gn2-fred.genenetwork.org/api3 \
GN_AUTH_BASE_URL=https://gn2-fred-auth.genenetwork.org \
pytest -m "smoke"

No test-code changes are needed — all URL configuration lives in conftest.py.

Test marks

Mark	Description
`smoke`	Public endpoints, no credentials, fast
`gn2`	Tests targeting genenetwork2
`gn3`	Tests targeting the gn3 REST API
`gn_auth`	Tests targeting gn-auth
`auth_flow`	Requires valid test-user credentials (see below)

Run a specific service:

pytest -m "gn_auth and smoke"
pytest -m "gn3 and smoke"
pytest -m "gn2 and smoke"

Auth-flow tests (Phase 2)

Set the following environment variables to enable credential-backed tests:

export GN_TEST_EMAIL=testuser@example.com
export GN_TEST_PASSWORD=secret
export GN_OAUTH2_CLIENT_ID=<uuid>
export GN_OAUTH2_CLIENT_SECRET=<secret>
pytest -m "auth_flow"

Without these variables the auth_flow tests are automatically skipped.

CI integration (planned)

Each component repo's CI triggers only its relevant mark after a successful per-repo build:

genenetwork2 CI → pytest -m gn2
genenetwork3 CI → pytest -m gn3
gn-auth CI → pytest -m gn_auth

Target: cd.genenetwork.org before merges; nightly against production.

URL structure notes

nginx on the deployment host rewrites /api3/<path> → /api/<path> before proxying to gn3, and gn-auth lives on a separate subdomain:

https://cd.genenetwork.org/          → gn2
https://cd.genenetwork.org/api3/     → gn3 (/api3/foo → gn3's /api/foo)
https://auth-cd.genenetwork.org/     → gn-auth

https://genenetwork.org/             → gn2  (production)
https://genenetwork.org/api3/        → gn3  (production)
https://auth.genenetwork.org/        → gn-auth (production)