def build_galaxy_app(simple_kwargs) -> GalaxyUniverseApplication: """Build a Galaxy app object from a simple keyword arguments. Construct paste style complex dictionary and use load_app_properties so Galaxy override variables are respected. Also setup "global" references to sqlalchemy database context for Galaxy and install databases. """ log.info("Galaxy database connection: %s", simple_kwargs["database_connection"]) simple_kwargs['global_conf'] = get_webapp_global_conf() simple_kwargs['global_conf'][ '__file__'] = "lib/galaxy/config/sample/galaxy.yml.sample" simple_kwargs = load_app_properties(kwds=simple_kwargs) # Build the Universe Application app = GalaxyUniverseApplication(**simple_kwargs) if not simple_kwargs.get("enable_celery_tasks"): rebind_container_to_task(app) log.info("Embedded Galaxy application started") global galaxy_context global install_context galaxy_context = app.model.context install_context = app.install_model.context # Toolbox indexing happens via the work queue out of band recently, and, # beyond potentially running async after tests execute doesn't execute # without building a uwsgi app (app.is_webapp = False for this test kit). # We need to ensure to build an index for the test galaxy app -- this is # pretty fast with the limited toolset app.reindex_tool_search() return app
def build_galaxy_app(simple_kwargs): """Build a Galaxy app object from a simple keyword arguments. Construct paste style complex dictionary and use load_app_properties so Galaxy override variables are respected. Also setup "global" references to sqlalchemy database context for Galaxy and install databases. """ log.info("Galaxy database connection: %s", simple_kwargs["database_connection"]) simple_kwargs['global_conf'] = get_webapp_global_conf() simple_kwargs['global_conf']['__file__'] = "config/galaxy.ini.sample" simple_kwargs = load_app_properties(kwds=simple_kwargs) # Build the Universe Application app = GalaxyUniverseApplication(**simple_kwargs) log.info("Embedded Galaxy application started") database_contexts.galaxy_context = app.model.context database_contexts.install_context = app.install_model.context return app
tool_config_file=[ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ], tool_sheds_config_file=galaxy_tool_sheds_conf_file, tool_parse_help=False, tool_data_table_config_path=galaxy_tool_data_table_conf_file, update_integrated_tool_panel=False, use_heartbeat=False) # ---- Build Galaxy Application -------------------------------------------------- if not galaxy_database_connection.startswith( 'sqlite://' ) and not install_galaxy_database_connection.startswith('sqlite://'): kwargs['database_engine_option_pool_size'] = '10' kwargs['database_engine_option_max_overflow'] = '20' galaxyapp = GalaxyUniverseApplication(**kwargs) log.info("Embedded Galaxy application started") # ---- Run galaxy webserver ------------------------------------------------------ galaxy_server = None galaxy_global_conf['database_file'] = galaxy_database_connection galaxywebapp = galaxybuildapp.app_factory(galaxy_global_conf, use_translogger=False, static_enabled=True, app=galaxyapp) database_contexts.galaxy_context = galaxyapp.model.context database_contexts.install_context = galaxyapp.install_model.context if galaxy_test_port is not None: galaxy_server = httpserver.serve(galaxywebapp, host=galaxy_test_host,
if not galaxy_database_connection.startswith( 'sqlite://' ): kwargs[ 'database_engine_option_max_overflow' ] = '20' galaxyapp = GalaxyUniverseApplication( allow_user_creation = True, allow_user_deletion = True, admin_users = '*****@*****.**', allow_library_path_paste = True, database_connection = galaxy_database_connection, database_engine_option_pool_size = '10', datatype_converters_config_file = "datatype_converters_conf.xml.sample", file_path = galaxy_file_path, global_conf = global_conf, id_secret = 'changethisinproductiontoo', job_queue_workers = 5, log_destination = "stdout", migrated_tools_config = galaxy_migrated_tool_conf_file, new_file_path = galaxy_tempfiles, running_functional_tests=True, shed_tool_data_table_config = shed_tool_data_table_conf_file, shed_tool_path = galaxy_shed_tool_path, template_path = "templates", tool_data_path = tool_data_path, tool_dependency_dir = galaxy_tool_dependency_dir, tool_path = tool_path, tool_config_file = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ], tool_sheds_config_file = galaxy_tool_sheds_conf_file, tool_parse_help = False, tool_data_table_config_path = galaxy_tool_data_table_conf_file, update_integrated_tool_panel = False, use_heartbeat = False, **kwargs ) log.info( "Embedded Galaxy application started" )