Source code for galaxy.structured_app

"""Typed description of Galaxy's app object."""
from typing import (
    Any,
    Optional,
    TYPE_CHECKING,
    Union,
)

from kombu import Connection

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.model.base import (
    ModelMapping,
    SharedModelMapping,
)
from galaxy.model.mapping import GalaxyModelMapping
from galaxy.model.scoped_session import galaxy_scoped_session
from galaxy.model.security import (
    GalaxyRBACAgent,
    HostAgent,
)
from galaxy.model.store import SessionlessContext
from galaxy.model.tags import GalaxyTagHandler
from galaxy.objectstore import ObjectStore
from galaxy.quota import QuotaAgent
from galaxy.security.idencoding import IdEncodingHelper
from galaxy.security.vault import Vault
from galaxy.tool_util.deps.views import DependencyResolversView
from galaxy.tool_util.verify import test_data
from galaxy.util.dbkeys import GenomeBuilds
from galaxy.web_stack import ApplicationStack
from galaxy.webhooks import WebhooksRegistry
from galaxy.workflow.trs_proxy import TrsProxy

if TYPE_CHECKING:
    from galaxy.jobs import JobConfiguration
    from galaxy.managers.workflows import WorkflowsManager
    from galaxy.tools.data import ToolDataTableManager


[docs]class BasicApp(Container):
    name: str
    config: Any  # 'galaxy.config.BaseAppConfiguration'
    datatypes_registry: Registry


[docs]class BasicSharedApp(BasicApp):
    """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.
    """

    application_stack: ApplicationStack
    model: SharedModelMapping
    security: IdEncodingHelper
    auth_manager: AuthManager
    toolbox: Any  # 'galaxy.tools.ToolBox'
    security_agent: Any
    quota_agent: QuotaAgent


[docs]class MinimalToolApp(BasicApp):
    sa_session: Union[galaxy_scoped_session, SessionlessContext]
    datatypes_registry: Registry
    object_store: ObjectStore
    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
    object_store: ObjectStore


[docs]class MinimalManagerApp(MinimalApp):
    # Minimal App that is sufficient to run Celery tasks
    file_sources: ConfiguredFileSources
    genome_builds: GenomeBuilds
    dataset_collection_manager: Any  # 'galaxy.managers.collections.DatasetCollectionManager'
    history_manager: Any  # 'galaxy.managers.histories.HistoryManager'
    hda_manager: Any  # 'galaxy.managers.hdas.HDAManager'
    workflow_manager: Any  # 'galaxy.managers.workflows.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: Any  # 'galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager'
    user_manager: Any
    job_config: "JobConfiguration"
    job_manager: Any  # galaxy.jobs.manager.JobManager
    job_metrics: "JobMetrics"

    @property
    def is_job_handler(self) -> bool:
        pass


[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.
    """

    is_webapp: bool  # is_webapp will be set to true when building WSGI app
    tag_handler: GalaxyTagHandler
    amqp_internal_connection_obj: Optional[Connection]
    dependency_resolvers_view: DependencyResolversView
    test_data_resolver: test_data.TestDataResolver
    file_sources: ConfiguredFileSources
    genome_builds: GenomeBuilds
    job_metrics: JobMetrics
    model: GalaxyModelMapping
    install_model: ModelMapping
    security_agent: GalaxyRBACAgent
    host_security_agent: HostAgent
    trs_proxy: TrsProxy
    vault: Vault
    webhooks_registry: WebhooksRegistry

    queue_worker: Any  # 'galaxy.queue_worker.GalaxyQueueWorker'
    history_manager: Any  # 'galaxy.managers.histories.HistoryManager'
    hda_manager: Any  # 'galaxy.managers.hdas.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'
    dynamic_tool_manager: Any  # 'galaxy.managers.tools.DynamicToolManager'
    data_provider_registry: Any  # 'galaxy.visualization.data_providers.registry.DataProviderRegistry'
    tool_data_tables: "ToolDataTableManager"
    genomes: Any  # 'galaxy.visualization.genomes.Genomes'
    error_reports: Any  # 'galaxy.tools.error_reports.ErrorReports'
    tool_cache: Any  # 'galaxy.tools.cache.ToolCache'
    tool_shed_repository_cache: Optional[Any]  # 'galaxy.tools.cache.ToolShedRepositoryCache'
    watchers: Any  # 'galaxy.config_watchers.ConfigWatchers'
    installed_repository_manager: Any  # 'galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager'
    workflow_scheduling_manager: Any  # 'galaxy.workflow.scheduling_manager.WorkflowSchedulingManager'
    interactivetool_manager: Any
    job_config: "JobConfiguration"
    job_manager: Any  # galaxy.jobs.manager.JobManager
    user_manager: Any
    api_keys_manager: Any  # 'galaxy.managers.api_keys.ApiKeyManager'
    visualizations_registry: Any  # 'galaxy.visualization.plugins.registry.VisualizationsRegistry'