xnat4tests 0.3.6

Command line interface

A test XNAT instance can be launched using the CLI with

$ xnat4tests start

This will spin up an empty XNAT instance that can be accessed using the default admin user account user=’admin’/password=’admin’. To add some sample data to play with you can use the add-data command

$ xnat4tests start
$ xnat4tests add-data 'dummydicom'

or in a single line

$ xnat4tests start --with-data 'dummydicom'

By default, xnat4tests will create a configuration file at $HOME/.xnat4tests/configs/default.yaml. The config file can be adapted to modify the names of the Docker images/containers used, the ports the containers run on, and which directories are mounted into the container. Multiple configurations can be used concurrently by saving the config file to a new location and passing it to the base command, i.e.

$ xnat4tests --config /path/to/my/repo/xnat4tests-config.yaml start

To stop or restart the running container you can use xnat4tests stop and xnat4tests restart commands, respectively.

Python API

If you are developing Python applications you will typically want to use the API to launch the XNAT instance using the xnat4tests.start_xnat function. An XnatPy connection session object can be accessed using xnat4tests.connect and the instanced stopped afterwards using stop_xnat.

# Import xnat4tests functions
from xnat4tests import start_xnat, stop_xnat, connect, Config

config = Config.load("default")

# Launch the instance (NB: it takes quite while for an XNAT instance to start). If an existing
# container with the reserved name is already running it is returned instead
start_xnat(config)

# Connect to the XNAT instance using XnatPy and run some tests
with connect(config) as login:
    PROJECT = 'MY_TEST_PROJECT'
    SUBJECT = 'MYSUBJECT'
    SESSION = 'MYSESSION'

    login.put(f'/data/archive/projects/MY_TEST_PROJECT')

    # Create subject
    xsubject = login.classes.SubjectData(label=SUBJECT,
                                         parent=login.projects[PROJECT])
    # Create session
    login.classes.MrSessionData(label=SESSION, parent=xsubject)

assert [p.name for p in (config.xnat_root_dir / "archive").iterdir()] == [PROJECT]

# Remove the container after you are done (not strictly necessary). To avoid
# having to wait for XNAT to restart each time before you run your tests, you can
# skip this line and start_xnat will attempt to use the instance that is already
# running
stop_xnat(config)

Alternatively, if you are using Pytest then you can set up the connection as a fixture in your conftest.py, e.g.

import tempfile
from pathlib import Path
from xnat4tests import start_xnat, stop_xnat, connect, Config

@pytest.fixture(scope="session")
def xnat_config():
    tmp_dir = Path(tempfile.mkdtemp())
    return Config(
        xnat_root_dir=tmp_dir,
        xnat_port=9999,
        docker_image="myrepo_xnat4tests",
        docker_container="myrepo_xnat4tests",
        build_args={
            "xnat_version": "1.8.5",
            "xnat_cs_plugin_version": "3.2.0",
        },
    )

@pytest.fixture(scope="session")
def xnat_uri(xnat_config):
    xnat4tests.start_xnat(xnat_config)
    xnat4tests.add_data("dummydicom")
    yield xnat_config.xnat_uri
    xnat4tests.stop_xnat(xnat_config)