def __init__( self, app ):
self.app = app
if self.app.is_job_handler():
log.debug("Starting job handler")
self.job_handler = handler.JobHandler( app )
self.job_queue = self.job_handler.job_queue
self.job_stop_queue = self.job_handler.job_stop_queue
else:
self.job_handler = NoopHandler()
self.job_queue = self.job_stop_queue = NoopQueue()
self.job_lock = False
def __init__( self, test_directory, mock_model=True ):
# The following line is needed in order to create
# HistoryDatasetAssociations - ideally the model classes would be
# usable without the ORM infrastructure in place.
in_memomry_model = mapping.init( "/tmp", "sqlite:///:memory:", create_tables=True )
self.datatypes_registry = Bunch(
integrated_datatypes_configs='/galaxy/integrated_datatypes_configs.xml',
get_datatype_by_extension=lambda ext: Bunch(),
)
self.config = Bunch(
outputs_to_working_directory=False,
commands_in_new_shell=True,
new_file_path=os.path.join(test_directory, "new_files"),
tool_data_path=os.path.join(test_directory, "tools"),
root=os.path.join(test_directory, "galaxy"),
admin_users="*****@*****.**",
len_file_path=os.path.join( 'tool-data', 'shared', 'ucsc', 'chrom' ),
builds_file_path=os.path.join( 'tool-data', 'shared', 'ucsc', 'builds.txt.sample' ),
migrated_tools_config=os.path.join(test_directory, "migrated_tools_conf.xml"),
)
# Setup some attributes for downstream extension by specific tests.
self.job_config = Bunch(
dynamic_params=None,
)
# Two ways to handle model layer, one is to stub out some objects that
# have an interface similar to real model (mock_model) and can keep
# track of 'persisted' objects in a map. The other is to use a real
# sqlalchemy layer but target an in memory database. Depending on what
# is being tested.
if mock_model:
# Create self.model to mimic app.model.
self.model = Bunch( context=MockContext() )
for module_member_name in dir( galaxy.model ):
module_member = getattr(galaxy.model, module_member_name)
if type( module_member ) == type:
self.model[ module_member_name ] = module_member
else:
self.model = in_memomry_model
self.genome_builds = GenomeBuilds( self )
self.toolbox = None
self.object_store = None
self.security = SecurityHelper(id_secret="testing")
from galaxy.security import GalaxyRBACAgent
self.job_queue = NoopQueue()
self.security_agent = GalaxyRBACAgent( self.model )
self.tool_data_tables = {}
self.dataset_collections_service = None
self.container_finder = NullContainerFinder()
self.name = "galaxy"
def __init__(self, app):
# This runs in the web (main) process pre-fork
self.app = app
self.job_queue = MessageJobQueue(app)
self.job_stop_queue = NoopQueue()
jobs_at_startup = self.app.model.context.query(Job).enable_eagerloads(False) \
.filter((Job.state == Job.states.NEW) & (Job.handler == null())).all()
if jobs_at_startup:
log.info(
'No handler assigned at startup for the following jobs, will dispatch via message: %s',
', '.join([str(j.id) for j in jobs_at_startup]))
for job in jobs_at_startup:
self.job_queue.put(job.id, job.tool_id)
def __init__(self, app):
self.app = app
if (self.app.config.track_jobs_in_database
and self.app.job_config.is_handler(self.app.config.server_name)
) or not self.app.config.track_jobs_in_database:
log.debug("Starting job handler")
self.job_handler = handler.JobHandler(app)
self.job_queue = self.job_handler.job_queue
self.job_stop_queue = self.job_handler.job_stop_queue
else:
self.job_handler = NoopHandler()
self.job_queue = self.job_stop_queue = NoopQueue()
self.job_lock = False
def __init__( self, app ):
self.app = app
self.job_handler = NoopHandler()
if self.app.config.server_name in self.app.config.job_handlers:
self.job_handler = handler.JobHandler( app )
if self.app.config.server_name == self.app.config.job_manager:
job_handler = NoopHandler()
# In the case that webapp == manager == handler, pass jobs in memory
if not self.app.config.track_jobs_in_database:
job_handler = self.job_handler
# Otherwise, even if the manager == one of the handlers, its handler will pick up jobs from the database
self.job_queue = JobManagerQueue( app, job_handler )
self.job_stop_queue = JobManagerStopQueue( app, job_handler )
if self.app.config.enable_beta_job_managers:
from galaxy.jobs.deferred import DeferredJobQueue
self.deferred_job_queue = DeferredJobQueue( app )
else:
self.job_queue = self.job_stop_queue = NoopQueue()
self.job_handler.start()
def __init__(self, config=None, **kwargs):
self.config = config or MockAppConfig(**kwargs)
self.security = self.config.security
self.name = kwargs.get('name', 'galaxy')
self.object_store = objectstore.build_object_store_from_config(self.config)
self.model = mapping.init("/tmp", "sqlite:///:memory:", create_tables=True, object_store=self.object_store)
self.security_agent = self.model.security_agent
self.visualizations_registry = MockVisualizationsRegistry()
self.tag_handler = tags.GalaxyTagManager(self.model.context)
self.quota_agent = quota.QuotaAgent(self.model)
self.init_datatypes()
self.job_config = Bunch(
dynamic_params=None,
)
self.tool_data_tables = {}
self.dataset_collections_service = None
self.container_finder = NullContainerFinder()
self._toolbox_lock = MockLock()
self.genome_builds = GenomeBuilds(self)
self.job_manager = Bunch(job_queue=NoopQueue())
self.application_stack = ApplicationStack()
def __init__(self, *args, **kwargs):
self.job_queue = NoopQueue()
self.job_stop_queue = NoopQueue()