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, **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)
