How to use the ephemeris.run_data_managers.DataManagers function in ephemeris

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github galaxyproject / ephemeris / tests / test_run_data_managers.py View on Github external
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)
github galaxyproject / ephemeris / tests / test_run_data_managers.py View on Github external
{'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)