def tool_shed_instance(url, key, email, password): ensure_module() tsi = toolshed.ToolShedInstance(url=url, key=key, email=email, password=password) return tsi
def user_api_key(admin_gi): """Use an admin authenticated account to generate a user API key.""" ensure_module() # TODO: thread-safe users = admin_gi.users all_users = users.get_users() user_id = None for user in all_users: if user["email"] == "*****@*****.**": user_id = user["id"] if user_id is None: # TODO: Allow override with --user_api_key. galaxy_config = admin_gi.config.get_config() use_remote_user = bool(galaxy_config["use_remote_user"]) if not use_remote_user: user_response = users.create_local_user( "planemo", "*****@*****.**", "planemo", ) user_id = user_response["id"] else: user_response = users.create_remote_user( "*****@*****.**", ) user_id = user_response["id"] return users.create_user_apikey(user_id)
def gi(port, key=None): """Return a bioblend ``GalaxyInstance`` for Galaxy on this port.""" ensure_module() if key is None: key = DEFAULT_MASTER_API_KEY return galaxy.GalaxyInstance(url="http://localhost:%d" % int(port), key=key)
def tool_shed_instance(url, key, email, password): ensure_module() tsi = toolshed.ToolShedInstance( url=url, key=key, email=email, password=password ) return tsi
def gi(port, key=None): """Return a bioblend ``GalaxyInstance`` for Galaxy on this port.""" ensure_module() if key is None: key = DEFAULT_MASTER_API_KEY return galaxy.GalaxyInstance( url="http://localhost:%d" % int(port), key=key )
def gi(port=None, url=None, key=None): """Return a bioblend ``GalaxyInstance`` for Galaxy on this port.""" ensure_module() if key is None: key = DEFAULT_ADMIN_API_KEY if port is None: url = url else: url = "http://localhost:%d" % int(port) return galaxy.GalaxyInstance(url=url, key=key)
def user_api_key(admin_gi): """Use an admin authenticated account to generate a user API key.""" ensure_module() # TODO: thread-safe users = admin_gi.users # Allow override with --user_api_key. user_response = users.create_local_user( "planemo", "*****@*****.**", "planemo", ) user_id = user_response["id"] return users.create_user_apikey(user_id)
def gi(self): ensure_module(galaxy) return galaxy.GalaxyInstance( url="http://localhost:%d" % self.port, key=self.master_api_key )
def _gi_for_key(self, key): ensure_module(galaxy) return galaxy.GalaxyInstance( url="http://localhost:%d" % self.port, key=key )
def gi(self): ensure_module(galaxy) return galaxy.GalaxyInstance(url="http://localhost:%d" % self.port, key=self.master_api_key)