Opal.jl

Opal.jl is a Julia client for Opal, a data warehouse application for biobanks and epidemiological studies.

Installation

using Pkg
Pkg.add("Opal")

Quick Start

using Opal

# Login to Opal server
opal = opal_login(
    username="administrator",
    password="password",
    url="https://opal-demo.obiba.org"
)

# List available projects
projects = opal_get(opal, "projects")

# Logout when done
opal_logout(opal)

Testing

Opal.jl includes comprehensive unit tests and integration tests.

Running Unit Tests Only

Unit tests do not require a live Opal server and run automatically in CI:

# Run all tests (unit tests only without OPAL_TEST_URL)
julia --project -e 'using Pkg; Pkg.test()'

# Or run the test suite directly
julia --project test/runtests.jl

Running Integration Tests

Integration tests require a live Opal server. Set the OPAL_TEST_URL environment variable to enable them:

# Run all tests including integration tests
OPAL_TEST_URL="https://opal-demo.obiba.org" julia --project -e 'using Pkg; Pkg.test()'

# With custom credentials
OPAL_TEST_URL="https://opal-demo.obiba.org" \
OPAL_TEST_USER="administrator" \
OPAL_TEST_PASSWORD="password" \
julia --project -e 'using Pkg; Pkg.test()'

Environment Variables for Testing

• OPAL_TEST_URL - Opal server URL (required to run integration tests)
• OPAL_TEST_USER - Username for authentication (default: administrator)
• OPAL_TEST_PASSWORD - Password for authentication (default: password)

Running Individual Test Files

# Run specific unit test file
julia --project test/unit/test_utils.jl

# Run specific integration test file (requires OPAL_TEST_URL)
OPAL_TEST_URL="https://opal-demo.obiba.org" julia --project test/integration/test_login_logout.jl

Test Organization

test/
├── runtests.jl           # Main test runner
├── test_helpers.jl       # Shared test helper functions
├── unit/                 # Unit tests (no server required)
│   ├── test_utils.jl     # Utility function tests
│   ├── test_rest.jl      # REST operation tests
│   ├── test_session.jl   # Session management tests
│   ├── test_table.jl     # Table operation tests
│   └── test_resource.jl  # Resource operation tests
└── integration/          # Integration tests (live server required)
    ├── test_login_logout.jl
    ├── test_session.jl
    ├── test_table.jl
    └── test_resource.jl

Development

For development guidelines, code style, and workflow instructions, see AGENTS.md.

License

This project is licensed under the GPL-3.0 license.