How to use the ephemeris.shed_tools.InstallRepositoryManager function in ephemeris

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github galaxyproject / ephemeris / tests / test_run_data_managers.py View on Github external
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)
github galaxyproject / ephemeris / tests / test_shed_tools.py View on Github external
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
github galaxyproject / ephemeris / tests / test_shed_tools.py View on Github external
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
github galaxyproject / planemo / planemo / galaxy / workflows.py View on Github external
def install_shed_repos(runnable, admin_gi, ignore_dependency_problems):
    tools_info = load_shed_repos(runnable)
    if tools_info:
        install_tool_manager = shed_tools.InstallRepositoryManager(admin_gi)
        install_results = install_tool_manager.install_repositories(tools_info)
        if install_results.errored_repositories:
            if ignore_dependency_problems:
                warn(FAILED_REPOSITORIES_MESSAGE)
            else:
                raise Exception(FAILED_REPOSITORIES_MESSAGE)