How to use the ephemeris.sleep.galaxy_wait function in ephemeris

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github galaxyproject / ephemeris / tests / test_run_data_managers.py View on Github external
"""Install the data_managers on galaxy"""
        container = start_container
        data_managers = [
            dict(name="data_manager_fetch_genome_dbkeys_all_fasta",
                 owner="devteam"),
            dict(name="data_manager_sam_fasta_index_builder",
                 owner="devteam"),
            dict(name="data_manager_bwa_mem_index_builder",
                 owner="devteam")
        ]
        irm = InstallRepositoryManager(container.gi)
        irm.install_repositories(data_managers)
        # Galaxy is restarted because otherwise data tables are not watched.
        container.container.exec_run("supervisorctl restart galaxy:")
        time.sleep(10)  # give time for the services to go down
        galaxy_wait(container.url)
github galaxyproject / ephemeris / tests / docker_for_galaxy.py View on Github external
# But alas, the trappings of a proprietary BSD kernel compel us to do ugly workarounds.

    container = client.containers.run(GALAXY_IMAGE, detach=True, ports={'80/tcp': None}, **kwargs)
    container_id = container.attrs.get('Id')
    print(container_id)

    # This seems weird as we also can just get container.attrs but for some reason
    # the network settings are not loaded in container.attrs. With the get request
    # these attributes are loaded
    container_attributes = client.containers.get(container_id).attrs

    # Venturing into deep nested dictionaries.
    exposed_port = container_attributes.get('NetworkSettings').get('Ports').get('80/tcp')[0].get('HostPort')

    container_url = "http://localhost:{0}".format(exposed_port)
    galaxy_wait(container_url,
                timeout=60)  # We are only going to wait 60 seconds. These are tests, and we are impatient!
    yield GalaxyContainer(url=container_url,
                          container=container,
                          attributes=container_attributes,
                          gi=GalaxyInstance(container_url, key="admin"))
    container.remove(force=True)