def install_repository_revision(self, trans, payload, **kwd):
"""
POST /api/tool_shed_repositories/install_repository_revision
Install a specified repository revision from a specified tool shed into Galaxy.
:param key: the current Galaxy admin user's API key
The following parameters are included in the payload.
:param tool_shed_url (required): the base URL of the Tool Shed from which to install the Repository
:param name (required): the name of the Repository
:param owner (required): the owner of the Repository
:param changeset_revision (required): the changeset_revision of the RepositoryMetadata object associated with the Repository
:param new_tool_panel_section_label (optional): label of a new section to be added to the Galaxy tool panel in which to load
tools contained in the Repository. Either this parameter must be an empty string or
the tool_panel_section_id parameter must be an empty string or both must be an empty
string (both cannot be used simultaneously).
:param tool_panel_section_id (optional): id of the Galaxy tool panel section in which to load tools contained in the Repository.
If this parameter is an empty string and the above new_tool_panel_section_label parameter is an
empty string, tools will be loaded outside of any sections in the tool panel. Either this
parameter must be an empty string or the tool_panel_section_id parameter must be an empty string
of both must be an empty string (both cannot be used simultaneously).
:param install_repository_dependencies (optional): Set to True if you want to install repository dependencies defined for the specified
repository being installed. The default setting is False.
:param install_tool_dependencies (optional): Set to True if you want to install tool dependencies defined for the specified repository being
installed. The default setting is False.
:param shed_tool_conf (optional): The shed-related tool panel configuration file configured in the "tool_config_file" setting in the Galaxy config file
(e.g., galaxy.ini). At least one shed-related tool panel config file is required to be configured. Setting
this parameter to a specific file enables you to choose where the specified repository will be installed because
the tool_path attribute of the <toolbox> from the specified file is used as the installation location
(e.g., <toolbox tool_path="database/shed_tools">). If this parameter is not set, a shed-related tool panel
configuration file will be selected automatically.
"""
# Get the information about the repository to be installed from the payload.
tool_shed_url, name, owner, changeset_revision = self.__parse_repository_from_payload(
payload, include_changeset=True)
self.__ensure_can_install_repos(trans)
irm = InstallRepositoryManager(self.app)
installed_tool_shed_repositories = irm.install(tool_shed_url, name,
owner,
changeset_revision,
payload)
def to_dict(tool_shed_repository):
tool_shed_repository_dict = tool_shed_repository.as_dict(
value_mapper=self.__get_value_mapper(trans,
tool_shed_repository))
tool_shed_repository_dict['url'] = url_for(
controller='tool_shed_repositories',
action='show',
id=trans.security.encode_id(tool_shed_repository.id))
return tool_shed_repository_dict
if installed_tool_shed_repositories:
return list(map(to_dict, installed_tool_shed_repositories))
message = "No repositories were installed, possibly because the selected repository has already been installed."
return dict(status="ok", message=message)
class InstallRepositoryManagerTestCase(ToolShedRepoBaseTestCase):
def setUp(self):
super().setUp()
self.irm = InstallRepositoryManager(self.app)
self.app.config.enable_tool_shed_check = False
self.app.update_repository_manager = UpdateRepositoryManager(self.app)
def test_tool_shed_repository_install(self):
hg_util.clone_repository = MagicMock(return_value=(True, None))
self._install_tool_shed_repository(start_status='New', end_status='Installed', changeset_revision='1')
hg_util.clone_repository.assert_called_with(
'github.com/repos/galaxyproject/example',
os.path.abspath(os.path.join('../shed_tools', 'github.com/repos/galaxyproject/example/1/example')),
'1',
)
def test_tool_shed_repository_update(self):
common_util.get_tool_shed_url_from_tool_shed_registry = MagicMock(return_value='https://github.com')
repository_util.get_tool_shed_status_for_installed_repository = MagicMock(return_value={'revision_update': 'false'})
hg_util.pull_repository = MagicMock()
hg_util.update_repository = MagicMock(return_value=(True, None))
self._install_tool_shed_repository(start_status='Installed', end_status='Installed', changeset_revision='2')
assert hg_util.pull_repository.call_args[0][0].endswith('github.com/repos/galaxyproject/example/1/example')
assert hg_util.pull_repository.call_args[0][1] == 'https://github.com/repos/galaxyproject/example'
assert hg_util.pull_repository.call_args[0][2] == '2'
assert hg_util.update_repository.call_args[0][0].endswith('github.com/repos/galaxyproject/example/1/example')
assert hg_util.update_repository.call_args[0][1] == '2'
def _install_tool_shed_repository(self, start_status, end_status, changeset_revision):
repository = self._setup_repository()
repository.status = start_status
repo_info_dict: Dict[str, Any] = {
'example': (
'description', 'github.com/repos/galaxyproject/example', changeset_revision, changeset_revision, 'galaxyproject', [], [],
)
}
self.irm.install_tool_shed_repository(
repository,
repo_info_dict,
'section_key',
self.app.config.tool_configs[0],
'../shed_tools',
False,
False,
reinstalling=False,
)
assert repository.status == end_status
assert repository.changeset_revision == changeset_revision
def setUp(self):
super().setUp()
self.irm = InstallRepositoryManager(self.app)
self.app.config.enable_tool_shed_check = False
self.app.update_repository_manager = UpdateRepositoryManager(self.app)