How to use ephemeris - 10 common examples

def test_install_data_managers(self, start_container):  # noqa: F811 Prevent start_container unused warning.
        """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)

"""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)

# 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)

def test_invalid_keys_in_repo_list(self, caplog, start_container):  # noqa: F811 Prevent start_container unused warning.
        container = start_container
        irm = InstallRepositoryManager(container.gi)
        caplog.set_level(logging.WARNING)
        irm.install_repositories([
            dict(name="bwa",
                 owner="devteam",
                 tool_panel_section_name="NGS: Alignment",
                 sesame_ouvre_toi="Invalid key")
        ], log=logging.getLogger())
        assert "'sesame_ouvre_toi' not a valid key. Will be skipped during parsing" in caplog.text

def test_tool_tests(self, caplog, start_container, parallel_tests):  # noqa: F811
        container = start_container
        irm = InstallRepositoryManager(container.gi)
        caplog.set_level(logging.WARNING)
        repos = [{'name': 'collection_element_identifiers', 'owner': 'iuc', 'tool_panel_section_label': "NGS: Alignment"}]
        log = logging.getLogger()
        irm.install_repositories(
            repositories=repos,
            log=log
        )
        fd, test_result_file = tempfile.mkstemp()
        os.close(fd)
        irm.test_tools(test_json=test_result_file, repositories=repos, log=log, parallel_tests=parallel_tests)
        with open(test_result_file) as test_result:
            result = json.load(test_result)
        assert 'tests' in result

def test_run_data_managers_installation_skipped(self, start_container):  # noqa: F811 Prevent start_container unused warning.
        container = start_container
        with open("tests/run_data_managers.yaml.test") as config_file:
            configuration = yaml.safe_load(config_file)
        dm = DataManagers(container.gi, configuration)
        install_results = dm.run()
        assert (len(install_results.successful_jobs) == 0)
        assert (len(install_results.skipped_jobs) == 9)
        assert (len(install_results.failed_jobs) == 0)

{'dbkey_source|dbkey': 'INVALID'},
                        {'dbkey_source|dbkey_name': 'INVALID_KEY'},
                        {'sequence_name': 'INVALID'},
                        {'sequence_id': 'INVALID'},
                        {'reference_source|reference_source_selector': 'ncbi'},
                        {'reference_source|requested_identifier': 'INVALID0123'}
                    ],
                    data_table_reload=[
                        "all_fasta",
                        "__dbkeys__"
                    ]

                )
            ]
        )
        dm = DataManagers(container.gi, configuration)
        with pytest.raises(RuntimeError):
            dm.run()
        assert ("HTTP Error 404" in caplog.text)
        assert ("Not all jobs successful! aborting..." in caplog.text)
        assert ("finished with exit code: 1. Stderr: " in caplog.text)

def test_run_data_managers(self, start_container):  # noqa: F811 Prevent start_container unused warning.
        """Tests an installation using the command line"""
        container = start_container
        sys.argv = ["run-data-managers",
                    "--user", "admin@galaxy.org",
                    "-p", "admin",
                    "-g", container.url,
                    "--config", "tests/run_data_managers.yaml.test"]
        run_data_managers.main()

def test_flatten_repo_info_invalid_key():
    test_repositories = [
        dict(name="bwa",
             owner="devteam",
             tool_panel_section_label="NGS: Alignment",
             tool_shed_url="toolshed.g2.bx.psu.edu",
             sesame_ouvre_toi="This is an invalid key")
    ]
    flattened_repos = flatten_repo_info(test_repositories)

    assert "sesame_ouvre_toi" not in flattened_repos[0].keys()
    assert "tool_shed_url" in flattened_repos[0].keys()

def test_flatten_repo_info():
    test_repositories = [
        dict(name="bwa",
             owner="devteam",
             tool_panel_section_label="NGS: Alignment",
             revisions=["1", "2"]),
        dict(name="bowtie2",
             owner="devteam",
             tool_panel_section_label="NGS: Alignment",
             changeset_revisions=["3", "4"])
    ]
    flattened_repos = flatten_repo_info(test_repositories)
    assert (flattened_repos == [
        dict(name="bwa",
             owner="devteam",
             tool_panel_section_label="NGS: Alignment",
             changeset_revision="1"),
        dict(name="bwa",
             owner="devteam",
             tool_panel_section_label="NGS: Alignment",
             changeset_revision="2"),
        dict(name="bowtie2",
             owner="devteam",
             tool_panel_section_label="NGS: Alignment")
    ])