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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)
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 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)