def __init__(self, app_name,
security,
model,
tool_data_path,
shed_tool_data_path,
tool_data_tables=None,
registry=None,
hgweb_config_manager=None):
self.name = app_name
self.security = security
self.model = model
self.config = Bunch()
self.config.tool_data_path = tool_data_path
self.config.shed_tool_data_path = shed_tool_data_path
self.temporary_path = tempfile.mkdtemp(prefix='tool_validation_')
self.config.tool_data_table_config = os.path.join(self.temporary_path, 'tool_data_table_conf.xml')
self.config.shed_tool_data_table_config = os.path.join(self.temporary_path, 'shed_tool_data_table_conf.xml')
self.tool_data_tables = tool_data_tables
self.datatypes_registry = registry
self.hgweb_config_manager = hgweb_config_manager
self.config.len_file_path = os.path.join(self.temporary_path, 'chromlen.txt')
# If the builds file path is set to None, tools/__init__.py will load the default.
# Otherwise it will attempt to load a nonexistent file and log an error. This does
# not appear to be an issue with the len_file_path config option.
self.config.builds_file_path = None
self.genome_builds = GenomeBuilds(self)
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",
self.config.database_connection,
create_tables=True,
object_store=self.object_store)
self.security_agent = self.model.security_agent
self.visualizations_registry = MockVisualizationsRegistry()
self.tag_handler = tags.GalaxyTagHandler(self.model.context)
self.quota_agent = quota.DatabaseQuotaAgent(self.model)
self.init_datatypes()
self.job_config = Bunch(dynamic_params=None, destinations={})
self.tool_data_tables = {}
self.dataset_collections_service = None
self.container_finder = NullContainerFinder()
self._toolbox_lock = MockLock()
self.tool_shed_registry = Bunch(tool_sheds={})
self.genome_builds = GenomeBuilds(self)
self.job_manager = NoopManager()
self.application_stack = ApplicationStack()
self.auth_manager = AuthManager(self)
self.user_manager = UserManager(self)
self.execution_timer_factory = Bunch(
get_timer=StructuredExecutionTimer)
def url_for(*args, **kwds):
return "/mock/url"
self.url_for = url_for
def __init__(self, **kwd):
log.debug("python path is: %s", ", ".join(sys.path))
self.name = "tool_shed"
# Read the tool_shed.ini configuration file and check for errors.
self.config = config.Configuration(**kwd)
self.config.check()
configure_logging(self.config)
self.application_stack = application_stack_instance()
# Initialize the Galaxy datatypes registry.
self.datatypes_registry = galaxy.datatypes.registry.Registry()
self.datatypes_registry.load_datatypes(self.config.root,
self.config.datatypes_config)
# Initialize the Tool Shed repository_types registry.
self.repository_types_registry = tool_shed.repository_types.registry.Registry(
)
# Initialize the RepositoryGridFilterManager.
self.repository_grid_filter_manager = RepositoryGridFilterManager()
# Determine the Tool Shed database connection string.
if self.config.database_connection:
db_url = self.config.database_connection
else:
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database
# Initialize the Tool Shed database and check for appropriate schema version.
from galaxy.webapps.tool_shed.model.migrate.check import create_or_verify_database
create_or_verify_database(db_url, self.config.database_engine_options)
# Set up the Tool Shed database engine and ORM.
from galaxy.webapps.tool_shed.model import mapping
self.model = mapping.init(self.config.file_path, db_url,
self.config.database_engine_options)
self.security = idencoding.IdEncodingHelper(
id_secret=self.config.id_secret)
# initialize the Tool Shed tag handler.
self.tag_handler = CommunityTagHandler(self)
# Initialize the Tool Shed tool data tables. Never pass a configuration file here
# because the Tool Shed should always have an empty dictionary!
self.tool_data_tables = galaxy.tools.data.ToolDataTableManager(
self.config.tool_data_path)
self.genome_builds = GenomeBuilds(self)
from galaxy import auth
self.auth_manager = auth.AuthManager(self)
# Citation manager needed to load tools.
from galaxy.managers.citations import CitationsManager
self.citations_manager = CitationsManager(self)
# The Tool Shed makes no use of a Galaxy toolbox, but this attribute is still required.
self.toolbox = tools.ToolBox([], self.config.tool_path, self)
# Initialize the Tool Shed security agent.
self.security_agent = self.model.security_agent
# The Tool Shed makes no use of a quota, but this attribute is still required.
self.quota_agent = galaxy.quota.NoQuotaAgent(self.model)
# Initialize the baseline Tool Shed statistics component.
self.shed_counter = self.model.shed_counter
# Let the Tool Shed's HgwebConfigManager know where the hgweb.config file is located.
self.hgweb_config_manager = self.model.hgweb_config_manager
self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
# Initialize the repository registry.
self.repository_registry = tool_shed.repository_registry.Registry(self)
# used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
self.server_starttime = int(time.time())
log.debug("Tool shed hgweb.config file is: %s",
self.hgweb_config_manager.hgweb_config)
def __init__(self, **kwd):
print >> sys.stderr, "python path is: " + ", ".join(sys.path)
self.name = "tool_shed"
# Read the tool_shed_wsgi.ini configuration file and check for errors.
self.config = config.Configuration(**kwd)
self.config.check()
config.configure_logging(self.config)
# Initialize the Galaxy datatypes registry.
self.datatypes_registry = galaxy.datatypes.registry.Registry()
self.datatypes_registry.load_datatypes(self.config.root,
self.config.datatypes_config)
# Initialize the Tool Shed repository_types registry.
self.repository_types_registry = tool_shed.repository_types.registry.Registry(
)
# Initialize the RepositoryGridFilterManager.
self.repository_grid_filter_manager = RepositoryGridFilterManager()
# Determine the Tool Shed database connection string.
if self.config.database_connection:
db_url = self.config.database_connection
else:
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database
# Initialize the Tool Shed database and check for appropriate schema version.
from galaxy.webapps.tool_shed.model.migrate.check import create_or_verify_database
create_or_verify_database(db_url, self.config.database_engine_options)
# Set up the Tool Shed database engine and ORM.
from galaxy.webapps.tool_shed.model import mapping
self.model = mapping.init(self.config.file_path, db_url,
self.config.database_engine_options)
# Initialize the Tool SHed security helper.
self.security = security.SecurityHelper(
id_secret=self.config.id_secret)
# initialize the Tool Shed tag handler.
self.tag_handler = CommunityTagHandler()
# Initialize the Tool Shed tool data tables. Never pass a configuration file here
# because the Tool Shed should always have an empty dictionary!
self.tool_data_tables = galaxy.tools.data.ToolDataTableManager(
self.config.tool_data_path)
self.genome_builds = GenomeBuilds(self)
# Citation manager needed to load tools.
from galaxy.managers.citations import CitationsManager
self.citations_manager = CitationsManager(self)
# The Tool Shed makes no use of a Galaxy toolbox, but this attribute is still required.
self.toolbox = tools.ToolBox([], self.config.tool_path, self)
# Initialize the Tool Shed security agent.
self.security_agent = self.model.security_agent
# The Tool Shed makes no use of a quota, but this attribute is still required.
self.quota_agent = galaxy.quota.NoQuotaAgent(self.model)
# TODO: Add OpenID support
self.openid_providers = OpenIDProviders()
# Initialize the baseline Tool Shed statistics component.
self.shed_counter = self.model.shed_counter
# Let the Tool Shed's HgwebConfigManager know where the hgweb.config file is located.
self.hgweb_config_manager = self.model.hgweb_config_manager
self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
# Initialize the repository registry.
self.repository_registry = tool_shed.repository_registry.Registry(self)
print >> sys.stderr, "Tool shed hgweb.config file is: ", self.hgweb_config_manager.hgweb_config
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, config=None, **kwargs):
super().__init__()
self[BasicApp] = self
self[MinimalManagerApp] = self
self[StructuredApp] = self
self.config = config or MockAppConfig(**kwargs)
self.security = self.config.security
self[idencoding.IdEncodingHelper] = self.security
self.name = kwargs.get('name', 'galaxy')
self.object_store = objectstore.build_object_store_from_config(
self.config)
self.model = mapping.init("/tmp",
self.config.database_connection,
create_tables=True,
object_store=self.object_store)
self[SharedModelMapping] = self.model
self[GalaxyModelMapping] = self.model
self[scoped_session] = self.model.context
self.security_agent = self.model.security_agent
self.visualizations_registry = MockVisualizationsRegistry()
self.tag_handler = tags.GalaxyTagHandler(self.model.context)
self[tags.GalaxyTagHandler] = self.tag_handler
self.quota_agent = quota.DatabaseQuotaAgent(self.model)
self.init_datatypes()
self.job_config = Bunch(dynamic_params=None,
destinations={},
use_messaging=False,
assign_handler=lambda *args, **kwargs: None)
self.tool_data_tables = {}
self.dataset_collections_service = None
self.container_finder = NullContainerFinder()
self._toolbox_lock = MockLock()
self.tool_shed_registry = Bunch(tool_sheds={})
self.genome_builds = GenomeBuilds(self)
self.job_manager = NoopManager()
self.application_stack = ApplicationStack()
self.auth_manager = AuthManager(self.config)
self.user_manager = UserManager(self)
self.execution_timer_factory = Bunch(
get_timer=StructuredExecutionTimer)
self.is_job_handler = False
rebind_container_to_task(self)
def url_for(*args, **kwds):
return "/mock/url"
self.url_for = url_for
def __init__(
self,
sa_session: SessionlessContext,
tool_app_config: ToolAppConfig,
datatypes_registry: Registry,
object_store: ObjectStore,
tool_data_table_manager: ToolDataTableManager,
file_sources: ConfiguredFileSources,
):
self.model = Bunch(context=sa_session)
self.config = tool_app_config
self.datatypes_registry = datatypes_registry
self.object_store = object_store
self.genome_builds = GenomeBuilds(self)
self.tool_data_tables = tool_data_table_manager
self.file_sources = file_sources
self.biotools_metadata_source = None
def __init__(self, config=None, **kwargs):
super().__init__()
config = config or MockAppConfig(**kwargs)
GalaxyDataTestApp.__init__(self, config=config, **kwargs)
self[BasicSharedApp] = self
self[MinimalManagerApp] = self
self[StructuredApp] = self
self[idencoding.IdEncodingHelper] = self.security
self.name = kwargs.get('name', 'galaxy')
self[SharedModelMapping] = self.model
self[GalaxyModelMapping] = self.model
self[galaxy_scoped_session] = self.model.context
self.visualizations_registry = MockVisualizationsRegistry()
self.tag_handler = tags.GalaxyTagHandler(self.model.context)
self[tags.GalaxyTagHandler] = self.tag_handler
self.quota_agent = quota.DatabaseQuotaAgent(self.model)
self.job_config = Bunch(
dynamic_params=None,
destinations={},
use_messaging=False,
assign_handler=lambda *args, **kwargs: None
)
self.tool_data_tables = ToolDataTableManager(tool_data_path=self.config.tool_data_path)
self.dataset_collections_service = None
self.container_finder = NullContainerFinder()
self._toolbox_lock = MockLock()
self.tool_shed_registry = Bunch(tool_sheds={})
self.genome_builds = GenomeBuilds(self)
self.job_manager = NoopManager()
self.application_stack = ApplicationStack()
self.auth_manager = AuthManager(self.config)
self.user_manager = UserManager(self)
self.execution_timer_factory = Bunch(get_timer=StructuredExecutionTimer)
self.file_sources = Bunch(to_dict=lambda *args, **kwargs: {})
self.interactivetool_manager = Bunch(create_interactivetool=lambda *args, **kwargs: None)
self.is_job_handler = False
self.biotools_metadata_source = None
rebind_container_to_task(self)
def url_for(*args, **kwds):
return "/mock/url"
self.url_for = url_for
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 _configure_genome_builds(self,
data_table_name="__dbkeys__",
load_old_style=True):
self.genome_builds = GenomeBuilds(self,
data_table_name=data_table_name,
load_old_style=load_old_style)
def __init__(self, **kwd) -> None:
super().__init__()
self[BasicApp] = self
log.debug("python path is: %s", ", ".join(sys.path))
self.name = "tool_shed"
# will be overwritten when building WSGI app
self.is_webapp = False
# Read the tool_shed.ini configuration file and check for errors.
self.config: Any = config.Configuration(**kwd)
self.config.check()
configure_logging(self.config)
self.application_stack = application_stack_instance()
# Initialize the Galaxy datatypes registry.
self.datatypes_registry = galaxy.datatypes.registry.Registry()
self.datatypes_registry.load_datatypes(self.config.root,
self.config.datatypes_config)
# Initialize the Tool Shed repository_types registry.
self.repository_types_registry = tool_shed.repository_types.registry.Registry(
)
# Initialize the RepositoryGridFilterManager.
self.repository_grid_filter_manager = RepositoryGridFilterManager()
# Determine the Tool Shed database connection string.
if self.config.database_connection:
db_url = self.config.database_connection
else:
db_url = f"sqlite:///{self.config.database}?isolation_level=IMMEDIATE"
# Initialize the Tool Shed database and check for appropriate schema version.
from tool_shed.webapp.model.migrate.check import create_or_verify_database
create_or_verify_database(db_url, self.config.database_engine_options)
# Set up the Tool Shed database engine and ORM.
from tool_shed.webapp.model import mapping
model: mapping.ToolShedModelMapping = mapping.init(
self.config.file_path, db_url, self.config.database_engine_options)
self.model = model
self.security = idencoding.IdEncodingHelper(
id_secret=self.config.id_secret)
self._register_singleton(idencoding.IdEncodingHelper, self.security)
self._register_singleton(SharedModelMapping, model)
self._register_singleton(mapping.ToolShedModelMapping, model)
self._register_singleton(scoped_session, self.model.context)
self._register_singleton(UserManager, UserManager)
# initialize the Tool Shed tag handler.
self.tag_handler = CommunityTagHandler(self)
# Initialize the Tool Shed tool data tables. Never pass a configuration file here
# because the Tool Shed should always have an empty dictionary!
self.tool_data_tables = galaxy.tools.data.ToolDataTableManager(
self.config.tool_data_path)
self.genome_builds = GenomeBuilds(self)
self.auth_manager = self._register_singleton(
auth.AuthManager, auth.AuthManager(self.config))
# Citation manager needed to load tools.
self.citations_manager = self._register_singleton(
CitationsManager, CitationsManager(self))
self.use_tool_dependency_resolution = False
# Initialize the Tool Shed security agent.
self.security_agent = model.security_agent
# The Tool Shed makes no use of a quota, but this attribute is still required.
self.quota_agent = self._register_singleton(QuotaAgent, NoQuotaAgent())
# Initialize the baseline Tool Shed statistics component.
self.shed_counter = model.shed_counter
# Let the Tool Shed's HgwebConfigManager know where the hgweb.config file is located.
self.hgweb_config_manager = hgweb_config_manager
self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir
# Initialize the repository registry.
self.repository_registry = tool_shed.repository_registry.Registry(self)
# used for cachebusting -- refactor this into a *SINGLE* UniverseApplication base.
self.server_starttime = int(time.time())
log.debug("Tool shed hgweb.config file is: %s",
self.hgweb_config_manager.hgweb_config)
