Interactive Tools

nova-galaxy allows running Galaxy tools in interactive mode, which is especially useful when tools generate URLs that need to be accessed during runtime.

notebook = Dataset(path="tests/test_files/test_jupyter_notebook.ipynb")
test_tool = Tool(TEST_INT_TOOL_ID)
params = Parameters()
params.add_input("mode|mode_select", "previous")
params.add_input("ipynb", notebook)
params.add_input("run_it", True)
link = test_tool.run_interactive(data_store=store, params=params, check_url=False)

By default, interactive tools are not stopped automatically once the Nova connection is closed. To override this behavior, use the DataStore mark_for_cleanup method. This will cause the tool to stop automatically, once the connection is closed (or with block is exited). You can manually stop these tools by using the Tool stop_all_tools_in_store method.

If you want to get the url of an interactive tool at a later point, you can use the get_url method:

assert test_tool.get_url() is not None