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" )