Merge pull request #19442 from nsoranzo/type_annot

Type annotations improvements

lib/galaxy/app.py

@@ -349,7 +349,7 @@ def _configure_toolbox(self):
         self.citations_manager = CitationsManager(self)
         self.biotools_metadata_source = get_galaxy_biotools_metadata_source(self.config)
 
-        self.dynamic_tools_manager = DynamicToolManager(self)
+        self.dynamic_tool_manager = DynamicToolManager(self)
         self._toolbox_lock = threading.RLock()
         self._toolbox = tools.ToolBox(self.config.tool_configs, self.config.tool_path, self)
         galaxy_root_dir = os.path.abspath(self.config.root)
@@ -565,7 +565,7 @@ def _shutdown_model(self):
         self.model.engine.dispose()
 
 
-class GalaxyManagerApplication(MinimalManagerApp, MinimalGalaxyApplication, InstallationTarget[tools.ToolBox]):
+class GalaxyManagerApplication(MinimalManagerApp, MinimalGalaxyApplication):
     """Extends the MinimalGalaxyApplication with most managers that are not tied to a web or job handling context."""
 
     model: GalaxyModelMapping
@@ -662,9 +662,6 @@ def __init__(self, configure_logging=True, use_converters=True, use_display_appl
         # We need the datatype registry for running certain tasks that modify HDAs, and to build the registry we need
         # to setup the installed repositories ... this is not ideal
         self._configure_tool_config_files()
-        self.installed_repository_manager = self._register_singleton(
-            InstalledRepositoryManager, InstalledRepositoryManager(self)
-        )
         self.dynamic_tool_manager = self._register_singleton(DynamicToolManager)
         self.trs_proxy = self._register_singleton(TrsProxy, TrsProxy(self.config))
         self._configure_datatypes_registry(
@@ -713,7 +710,7 @@ def is_job_handler(self) -> bool:
         ) or not self.config.track_jobs_in_database
 
 
-class UniverseApplication(StructuredApp, GalaxyManagerApplication):
+class UniverseApplication(StructuredApp, GalaxyManagerApplication, InstallationTarget[tools.ToolBox]):
     """Encapsulates the state of a Universe application"""
 
     model: GalaxyModelMapping
@@ -775,6 +772,9 @@ def __init__(self, **kwargs) -> None:
         self._configure_toolbox()
         # Load Data Manager
         self.data_managers = self._register_singleton(DataManagers)
+        self.installed_repository_manager = self._register_singleton(
+            InstalledRepositoryManager, InstalledRepositoryManager(self)
+        )
         # Load the update repository manager.
         self.update_repository_manager = self._register_singleton(
             UpdateRepositoryManager, UpdateRepositoryManager(self)

lib/galaxy/app_unittest_utils/galaxy_mock.py

@@ -175,7 +175,7 @@ def toolbox(self, toolbox: ToolBox):
     def wait_for_toolbox_reload(self, toolbox):
         # TODO: If the tpm test case passes, does the operation really
         # need to wait.
-        return True
+        return
 
     def reindex_tool_search(self) -> None:
         raise NotImplementedError

lib/galaxy/managers/hdcas.py

@@ -59,7 +59,7 @@ def set_collection_attributes(dataset_element, *payload):
 
 # TODO: to DatasetCollectionInstanceManager
 class HDCAManager(
-    base.ModelManager,
+    base.ModelManager[model.HistoryDatasetCollectionAssociation],
     secured.AccessibleManagerMixin,
     secured.OwnableManagerMixin,
     deletable.PurgableManagerMixin,

lib/galaxy/managers/tools.py

@@ -30,7 +30,7 @@
     from galaxy.managers.base import OrmFilterParsersType
 
 
-class DynamicToolManager(ModelManager):
+class DynamicToolManager(ModelManager[model.DynamicTool]):
     """Manages dynamic tools stored in Galaxy's database."""
 
     model_class = model.DynamicTool

lib/galaxy/managers/workflows.py

@@ -46,7 +46,10 @@
     joinedload,
     subqueryload,
 )
-from typing_extensions import Annotated
+from typing_extensions import (
+    Annotated,
+    TypeAlias,
+)
 
 from galaxy import (
     exceptions,
@@ -1827,7 +1830,7 @@ def __module_from_dict(
             self.add_item_annotation(sa_session, trans.get_user(), step, annotation)
 
         # Stick this in the step temporarily
-        DictConnection = Dict[str, Union[int, str]]
+        DictConnection: TypeAlias = Dict[str, Union[int, str]]
         temp_input_connections: Dict[str, Union[List[DictConnection], DictConnection]] = step_dict.get(
             "input_connections", {}
         )

lib/galaxy/queue_worker.py

@@ -11,6 +11,7 @@
 import threading
 import time
 from inspect import ismodule
+from typing import TYPE_CHECKING
 
 from kombu import (
     Consumer,
@@ -31,6 +32,9 @@
 logging.getLogger("kombu").setLevel(logging.WARNING)
 log = logging.getLogger(__name__)
 
+if TYPE_CHECKING:
+    from galaxy.structured_app import MinimalManagerApp
+
 
 def send_local_control_task(app, task, get_response=False, kwargs=None):
     """
@@ -244,7 +248,7 @@ def rebuild_toolbox_search_index(app, **kwargs):
         log.debug("App is not a webapp, not building a search index")
 
 
-def reload_job_rules(app, **kwargs):
+def reload_job_rules(app: "MinimalManagerApp", **kwargs):
     reload_timer = util.ExecutionTimer()
     for module in job_rule_modules(app):
         rules_module_name = module.__name__
@@ -265,7 +269,7 @@ def reload_tour(app, **kwargs):
     log.debug("Tour reloaded")
 
 
-def __job_rule_module_names(app):
+def __job_rule_module_names(app: "MinimalManagerApp"):
     rules_module_names = {"galaxy.jobs.rules"}
     if app.job_config.dynamic_params is not None:
         module_name = app.job_config.dynamic_params.get("rules_module")
@@ -279,7 +283,7 @@ def __job_rule_module_names(app):
     return rules_module_names
 
 
-def job_rule_modules(app):
+def job_rule_modules(app: "MinimalManagerApp"):
     rules_module_list = []
     for rules_module_name in __job_rule_module_names(app):
         rules_module = sys.modules.get(rules_module_name, None)

lib/galaxy/structured_app.py

@@ -1,6 +1,7 @@
 """Typed description of Galaxy's app object."""
 
 import abc
+import threading
 from typing import (
     Any,
     Optional,
@@ -31,7 +32,6 @@
 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
@@ -46,11 +46,14 @@
     from galaxy.managers.collections import DatasetCollectionManager
     from galaxy.managers.hdas import HDAManager
     from galaxy.managers.histories import HistoryManager
+    from galaxy.managers.tools import DynamicToolManager
     from galaxy.managers.workflows import (
         WorkflowContentsManager,
         WorkflowsManager,
     )
+    from galaxy.tool_shed.galaxy_install.client import DataManagersInterface
     from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
+    from galaxy.tool_util.data import ToolDataTableManager
     from galaxy.tools import ToolBox
     from galaxy.tools.cache import ToolCache
     from galaxy.tools.error_reports import ErrorReports
@@ -117,12 +120,11 @@ class MinimalManagerApp(MinimalApp):
     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'
+    dynamic_tool_manager: "DynamicToolManager"
     genomes: "Genomes"
     error_reports: "ErrorReports"
     notification_manager: Any  # 'galaxy.managers.notification.NotificationManager'
@@ -149,7 +151,9 @@ class StructuredApp(MinimalManagerApp):
     """
 
     amqp_internal_connection_obj: Optional[Connection]
+    data_managers: "DataManagersInterface"
     dependency_resolvers_view: DependencyResolversView
+    installed_repository_manager: "InstalledRepositoryManager"
     container_finder: ContainerFinder
     tool_dependency_dir: Optional[str]
     test_data_resolver: test_data.TestDataResolver
@@ -158,11 +162,11 @@ class StructuredApp(MinimalManagerApp):
     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'
+    _toolbox_lock: threading.RLock

lib/galaxy/tool_shed/galaxy_install/client.py

@@ -2,9 +2,9 @@
 from typing import (
     Any,
     Dict,
-    Generic,
     List,
     Optional,
+    runtime_checkable,
     TYPE_CHECKING,
     TypeVar,
     Union,
@@ -15,15 +15,14 @@
 from galaxy.model.base import ModelMapping
 from galaxy.model.tool_shed_install import HasToolBox
 from galaxy.security.idencoding import IdEncodingHelper
-from galaxy.tool_shed.cache import ToolShedRepositoryCache
 from galaxy.tool_util.data import (
     OutputDataset,
     ToolDataTableManager,
 )
 from galaxy.tool_util.toolbox.base import AbstractToolBox
 
 if TYPE_CHECKING:
-    import galaxy.tool_shed.metadata.installed_repository_manger
+    from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
 
 
 class DataManagerInterface(Protocol):
@@ -48,19 +47,17 @@ def get_manager(self, data_manager_id: str) -> Optional[DataManagerInterface]: .
     def remove_manager(self, manager_ids: Union[str, List[str]]) -> None: ...
 
 
-ToolBoxType = TypeVar("ToolBoxType", bound="AbstractToolBox")
+ToolBoxType = TypeVar("ToolBoxType", bound="AbstractToolBox", contravariant=True)
 
 
-class InstallationTarget(HasToolBox, Generic[ToolBoxType]):
+@runtime_checkable
+class InstallationTarget(HasToolBox, Protocol[ToolBoxType]):
     data_managers: DataManagersInterface
     install_model: ModelMapping
-    model: ModelMapping
     security: IdEncodingHelper
     config: Any
-    installed_repository_manager: "galaxy.tool_shed.metadata.installed_repository_manger.InstalledRepositoryManager"
-    watchers: Any  # TODO: interface...
+    installed_repository_manager: "InstalledRepositoryManager"
     _toolbox_lock: threading.RLock
-    tool_shed_repository_cache: Optional[ToolShedRepositoryCache]
     tool_data_tables: ToolDataTableManager
 
     def wait_for_toolbox_reload(self, old_toolbox: ToolBoxType) -> None: ...

lib/galaxy/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py

@@ -30,7 +30,6 @@
 
 
 class InstalledRepositoryMetadataManager(GalaxyMetadataGenerator):
-    app: InstallationTarget
 
     def __init__(
         self,

lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py

@@ -6,6 +6,7 @@
 import json
 import logging
 import os
+from typing import TYPE_CHECKING
 from urllib.error import HTTPError
 from urllib.parse import (
     urlencode,
@@ -17,7 +18,6 @@
 )
 
 from galaxy.model.base import transaction
-from galaxy.tool_shed.galaxy_install import installed_repository_manager
 from galaxy.tool_shed.galaxy_install.tools import tool_panel_manager
 from galaxy.tool_shed.util import repository_util
 from galaxy.tool_shed.util.container_util import get_components_from_key
@@ -35,11 +35,14 @@
     encoding_util,
 )
 
+if TYPE_CHECKING:
+    from galaxy.tool_shed.galaxy_install.client import InstallationTarget
+
 log = logging.getLogger(__name__)
 
 
 class RepositoryDependencyInstallManager:
-    def __init__(self, app):
+    def __init__(self, app: "InstallationTarget"):
         self.app = app
 
     def build_repository_dependency_relationships(self, repo_info_dicts, tool_shed_repositories):
@@ -270,7 +273,7 @@ def create_repository_dependency_objects(
                                 log.info(
                                     f"Reactivating deactivated tool_shed_repository '{str(repository_db_record.name)}'."
                                 )
-                                irm = installed_repository_manager.InstalledRepositoryManager(self.app)
+                                irm = self.app.installed_repository_manager
                                 irm.activate_repository(repository_db_record)
                                 # No additional updates to the database record are necessary.
                                 can_update_db_record = False

lib/galaxy/tool_shed/metadata/metadata_generator.py

@@ -722,13 +722,12 @@ def _check_elem_for_dep(elems):
             if original_valid_tool_dependencies_dict:
                 # We're generating metadata on an update pulled to a tool shed repository installed
                 # into a Galaxy instance, so handle changes to tool dependencies appropriately.
-                installation_target = cast(InstallationTarget, self.app)
-                irm = installation_target.installed_repository_manager
-                (
-                    updated_tool_dependency_names,
-                    deleted_tool_dependency_names,
-                ) = irm.handle_existing_tool_dependencies_that_changed_in_update(
-                    self.repository, original_valid_tool_dependencies_dict, rvs.valid_tool_dependencies_dict
+                assert isinstance(self.app, InstallationTarget)
+                irm = self.app.installed_repository_manager
+                assert self.repository
+                gx_repository = cast(ToolShedRepository, self.repository)
+                irm.handle_existing_tool_dependencies_that_changed_in_update(
+                    gx_repository, original_valid_tool_dependencies_dict, rvs.valid_tool_dependencies_dict
                 )
             metadata_dict["tool_dependencies"] = rvs.valid_tool_dependencies_dict
         if rvs.invalid_tool_dependencies_dict:

lib/galaxy/tool_shed/unittest_utils/__init__.py

@@ -22,6 +22,7 @@
     DataManagersInterface,
     InstallationTarget,
 )
+from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
 from galaxy.tool_shed.util.repository_util import get_installed_repository
 from galaxy.tool_util.data import (
     OutputDataset,
@@ -221,6 +222,7 @@ def __init__(
         )
         dependency_dir = target_directory / "_dependencies"
         dependency_dir.mkdir()
+        self.installed_repository_manager = InstalledRepositoryManager(self)
 
     @property
     def tool_dependency_dir(self) -> Optional[str]:
@@ -236,3 +238,6 @@ def reload_toolbox(self):
     @property
     def toolbox(self) -> TestToolBox:
         return self._toolbox
+
+    def wait_for_toolbox_reload(self, toolbox):
+        return

lib/galaxy/tool_shed/util/dependency_display.py

@@ -2,7 +2,6 @@
 import os
 
 from galaxy import util
-from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
 from galaxy.tool_shed.util import utility_container_manager
 from galaxy.util import UNKNOWN
 from galaxy.util.tool_shed.common_util import parse_repository_dependency_tuple
@@ -198,7 +197,7 @@ def populate_containers_dict_from_repository_metadata(self, repository):
         them for uninstalled repositories that are being reinstalled.
         """
         if metadata := repository.metadata_:
-            irm = InstalledRepositoryManager(self.app)
+            irm = self.app.installed_repository_manager
             # Handle repository dependencies.
             (
                 installed_repository_dependencies,

lib/galaxy/tool_util/cwl/parser.py

@@ -15,6 +15,7 @@
 from typing import (
     Dict,
     List,
+    Optional,
     overload,
     Union,
 )
@@ -531,7 +532,7 @@ class WorkflowProxy:
     def __init__(self, workflow, workflow_path=None):
         self._workflow = workflow
         self._workflow_path = workflow_path
-        self._step_proxies = None
+        self._step_proxies: Optional[List[Union[SubworkflowStepProxy, ToolStepProxy]]] = None
 
     @property
     def cwl_id(self):
@@ -562,7 +563,7 @@ def get_outputs_for_label(self, label):
 
     def tool_reference_proxies(self):
         """Fetch tool source definitions for all referenced tools."""
-        references = []
+        references: List[ToolProxy] = []
         for step in self.step_proxies():
             references.extend(step.tool_reference_proxies())
         return references