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Source code for galaxy.structured_app

"""Typed description of Galaxy's app object."""

import abc
from typing import (
    Any,
    Optional,
    TYPE_CHECKING,
)

from kombu import Connection
from typing_extensions import Protocol

from galaxy.auth import AuthManager
from galaxy.datatypes.registry import Registry
from galaxy.di import Container
from galaxy.files import ConfiguredFileSources
from galaxy.job_metrics import JobMetrics
from galaxy.managers.dbkeys import GenomeBuilds
from galaxy.model.base import (
    ModelMapping,
    SharedModelMapping,
)
from galaxy.model.mapping import GalaxyModelMapping
from galaxy.model.security import (
    GalaxyRBACAgent,
    HostAgent,
)
from galaxy.model.tags import GalaxyTagHandler
from galaxy.objectstore import BaseObjectStore
from galaxy.quota import QuotaAgent
from galaxy.security.idencoding import IdEncodingHelper
from galaxy.security.vault import Vault
from galaxy.tool_shed.cache import ToolShedRepositoryCache
from galaxy.tool_util.data import ToolDataTableManager
from galaxy.tool_util.deps.containers import ContainerFinder
from galaxy.tool_util.deps.views import DependencyResolversView
from galaxy.tool_util.verify import test_data
from galaxy.util.tool_shed.tool_shed_registry import Registry as ToolShedRegistry
from galaxy.web_stack import ApplicationStack
from galaxy.webhooks import WebhooksRegistry
from galaxy.workflow.trs_proxy import TrsProxy

if TYPE_CHECKING:
    from galaxy.config_watchers import ConfigWatchers
    from galaxy.jobs import JobConfiguration
    from galaxy.managers.collections import DatasetCollectionManager
    from galaxy.managers.hdas import HDAManager
    from galaxy.managers.histories import HistoryManager
    from galaxy.managers.workflows import WorkflowsManager
    from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
    from galaxy.tools import ToolBox
    from galaxy.tools.cache import ToolCache
    from galaxy.tools.error_reports import ErrorReports
    from galaxy.visualization.genomes import Genomes


[docs]class BasicSharedApp(Container): """Stripped down version of the ``app`` shared between Galaxy and ToolShed. Code that is shared between Galaxy and the Tool Shed should be annotated as using BasicSharedApp instead of StructuredApp below. """ name: str config: Any # 'galaxy.config.BaseAppConfiguration' datatypes_registry: Registry application_stack: ApplicationStack model: SharedModelMapping security: IdEncodingHelper auth_manager: AuthManager security_agent: Any quota_agent: QuotaAgent @property def toolbox(self) -> "ToolBox": raise NotImplementedError()
[docs]class MinimalToolApp(Protocol): is_webapp: bool name: str # Leave config as Any: in a full Galaxy app this is a GalaxyAppConfiguration object, but this is mostly dynamically # generated, and here we want to also allow other kinds of configuration objects (e.g. a Bunch). config: Any datatypes_registry: Registry object_store: BaseObjectStore tool_data_tables: "ToolDataTableManager" file_sources: ConfiguredFileSources security: IdEncodingHelper
[docs]class MinimalApp(BasicSharedApp): is_webapp: bool # is_webapp will be set to true when building WSGI app tag_handler: GalaxyTagHandler model: GalaxyModelMapping install_model: ModelMapping security_agent: GalaxyRBACAgent host_security_agent: HostAgent server_starttime: int
[docs]class MinimalManagerApp(MinimalApp): # Minimal App that is sufficient to run Celery tasks file_sources: ConfiguredFileSources genome_builds: GenomeBuilds dataset_collection_manager: "DatasetCollectionManager" tool_data_tables: "ToolDataTableManager" history_manager: "HistoryManager" hda_manager: "HDAManager" workflow_manager: "WorkflowsManager" workflow_contents_manager: Any # 'galaxy.managers.workflows.WorkflowContentsManager' library_folder_manager: Any # 'galaxy.managers.folders.FolderManager' library_manager: Any # 'galaxy.managers.libraries.LibraryManager' role_manager: Any # 'galaxy.managers.roles.RoleManager' installed_repository_manager: "InstalledRepositoryManager" user_manager: Any job_config: "JobConfiguration" job_manager: Any # galaxy.jobs.manager.JobManager job_metrics: JobMetrics dynamic_tool_manager: Any # 'galaxy.managers.tools.DynamicToolManager' genomes: "Genomes" error_reports: "ErrorReports" notification_manager: Any # 'galaxy.managers.notification.NotificationManager' object_store: BaseObjectStore tool_shed_registry: ToolShedRegistry @property @abc.abstractmethod def is_job_handler(self) -> bool: ...
[docs] def wait_for_toolbox_reload(self, old_toolbox: "ToolBox") -> None: ...
[docs]class StructuredApp(MinimalManagerApp): """Interface defining typed description of the Galaxy UniverseApplication. Ideally nothing that depends on StructuredApp should require StructuredApp so we can have a clean import dag. This will require setting up a lot more distinction between interfaces and implementations in Galaxy though. In the meantime, for imports that would bring in StructuredApp if properly type (cyclical imports), we're just setting the class attributes to Any. """ amqp_internal_connection_obj: Optional[Connection] dependency_resolvers_view: DependencyResolversView container_finder: ContainerFinder tool_dependency_dir: Optional[str] test_data_resolver: test_data.TestDataResolver trs_proxy: TrsProxy vault: Vault webhooks_registry: WebhooksRegistry queue_worker: Any # 'galaxy.queue_worker.GalaxyQueueWorker' data_provider_registry: Any # 'galaxy.visualization.data_providers.registry.DataProviderRegistry' tool_data_tables: ToolDataTableManager tool_cache: "ToolCache" tool_shed_repository_cache: Optional[ToolShedRepositoryCache] watchers: "ConfigWatchers" workflow_scheduling_manager: Any # 'galaxy.workflow.scheduling_manager.WorkflowSchedulingManager' interactivetool_manager: Any api_keys_manager: Any # 'galaxy.managers.api_keys.ApiKeyManager' visualizations_registry: Any # 'galaxy.visualization.plugins.registry.VisualizationsRegistry'