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Source code for tool_shed.webapp.app

import logging
import sys
import time
from typing import Any

from sqlalchemy.orm.scoping import scoped_session

import galaxy.datatypes.registry
import galaxy.tools.data
import tool_shed.repository_registry
import tool_shed.repository_types.registry
import tool_shed.webapp.model
from galaxy import auth
from galaxy.app import SentryClientMixin
from galaxy.config import configure_logging
from galaxy.managers.citations import CitationsManager
from galaxy.managers.users import UserManager
from galaxy.model.base import SharedModelMapping
from galaxy.model.tags import CommunityTagHandler
from galaxy.quota import NoQuotaAgent, QuotaAgent
from galaxy.security import idencoding
from galaxy.structured_app import BasicSharedApp
from galaxy.util.dbkeys import GenomeBuilds
from galaxy.web_stack import application_stack_instance
from tool_shed.grids.repository_grid_filter_manager import RepositoryGridFilterManager
from tool_shed.util.hgweb_config import hgweb_config_manager
from . import config

log = logging.getLogger(__name__)


[docs]class UniverseApplication(BasicSharedApp, SentryClientMixin): """Encapsulates the state of a Universe application"""
[docs] def __init__(self, **kwd) -> None: super().__init__() self[BasicSharedApp] = 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) # Configure Sentry client if configured self.configure_sentry_client() # 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)
[docs] def shutdown(self): pass