Work on types for SA 2.0.

lib/galaxy/app.py

@@ -267,7 +267,7 @@ def __init__(self, fsmon=False, **kwargs) -> None:
         self.vault = self._register_singleton(Vault, VaultFactory.from_app(self))  # type: ignore[type-abstract]
         self._configure_object_store(fsmon=True)
         self._register_singleton(BaseObjectStore, self.object_store)
-        galaxy.model.Dataset.object_store = self.object_store  # type:ignore[assignment]
+        galaxy.model.setup_global_object_store_for_models(self.object_store)
 
     def configure_fluent_log(self):
         if self.config.fluent_log:

lib/galaxy/managers/object_store_instances.py

@@ -26,6 +26,7 @@
 from galaxy.model import (
     User,
     UserObjectStore,
+    OBJECT_STORE_TEMPLATE_CONFIGURATION_VARIABLES_TYPE,
 )
 from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.objectstore import (
@@ -125,19 +126,21 @@ def _upgrade_instance(
         template = catalog.find_template_by(persisted_object_store.object_store_template_id, payload.template_version)
         persisted_object_store.object_store_template_version = template.version
         persisted_object_store.object_store_template_definition = template.model_dump()
-        old_variables = persisted_object_store.object_store_template_variables
+        old_variables = persisted_object_store.object_store_template_variables or {}
         updated_variables = payload.variables
-        actual_variables = {}
+        actual_variables: OBJECT_STORE_TEMPLATE_CONFIGURATION_VARIABLES_TYPE = {}
         for variable in template.variables or []:
             variable_name = variable.name
             old_value = old_variables.get(variable_name)
-            actual_variables[variable_name] = updated_variables.get(variable_name, old_value)
+            updated_value = updated_variables.get(variable_name, old_value)
+            if updated_value:
+                actual_variables[variable_name] = updated_value
 
         persisted_object_store.object_store_template_variables = actual_variables
-        old_secrets = persisted_object_store.object_store_template_secrets
+        old_secrets = persisted_object_store.object_store_template_secrets or []
         new_secrets = payload.secrets
 
-        recorded_secrets = persisted_object_store.object_store_template_secrets
+        recorded_secrets = persisted_object_store.object_store_template_secrets or []
 
         user_vault = trans.user_vault
         upgraded_template_secrets = []
@@ -299,7 +302,8 @@ def recover_secrets(user_object_store: UserObjectStore, vault: Vault) -> Dict[st
     # ones recorded as written in the persisted object, the ones
     # expected in the catalog, or the ones expected in the definition
     # persisted.
-    for secret in user_object_store.object_store_template_secrets:
+    persisted_secret_names = user_object_store.object_store_template_secrets or []
+    for secret in persisted_secret_names:
         vault_key = user_vault_key(user_object_store, secret)
         secret_value = user_vault.read_secret(vault_key)
         assert secret_value

lib/galaxy/model/__init__.py

@@ -213,6 +213,11 @@
 
 STR_TO_STR_DICT = Dict[str, str]
 
+OBJECT_STORE_TEMPLATE_CONFIGURATION_VALUE_TYPE = Union[str, bool, int]
+OBJECT_STORE_TEMPLATE_CONFIGURATION_VARIABLES_TYPE = Dict[str, OBJECT_STORE_TEMPLATE_CONFIGURATION_VALUE_TYPE]
+OBJECT_STORE_TEMPLATE_CONFIGURATION_SECRET_NAMES_TYPE = List[str]
+OBJECT_STORE_TEMPLATE_DEFINITION_TYPE = Dict[str, Any]
+
 
 class TransformAction(TypedDict):
     action: str
@@ -224,6 +229,9 @@ class TransformAction(TypedDict):
     type_annotation_map={
         Optional[STR_TO_STR_DICT]: JSONType,
         Optional[TRANSFORM_ACTIONS]: MutableJSONType,
+        Optional[OBJECT_STORE_TEMPLATE_CONFIGURATION_VARIABLES_TYPE]: JSONType,
+        Optional[OBJECT_STORE_TEMPLATE_CONFIGURATION_SECRET_NAMES_TYPE]: JSONType,
+        Optional[OBJECT_STORE_TEMPLATE_DEFINITION_TYPE]: JSONType,
     },
 )
 
@@ -3991,6 +3999,10 @@ def flush(self):
                 sa_session.commit()
 
 
+def setup_global_object_store_for_models(object_store):
+    Dataset.object_store = object_store  # type:ignore[assignment]
+
+
 class Dataset(Base, StorableObject, Serializable):
     __tablename__ = "dataset"
 
@@ -10973,18 +10985,22 @@ class UserObjectStore(Base, RepresentById):
     # the id/version and not record the definition... as the templates change
     # over time this choice has some big consequences despite being easy to swap
     # implementations.
-    object_store_template_definition: Mapped[Optional[bytes]] = mapped_column(JSONType)
+    object_store_template_definition: Mapped[Optional[OBJECT_STORE_TEMPLATE_DEFINITION_TYPE]] = mapped_column(JSONType)
     # Big JSON blob of the variable name -> value mapping defined for the store's
     # variables by the user.
-    object_store_template_variables: Mapped[Optional[bytes]] = mapped_column(JSONType)
+    object_store_template_variables: Mapped[Optional[OBJECT_STORE_TEMPLATE_CONFIGURATION_VARIABLES_TYPE]] = (
+        mapped_column(JSONType)
+    )
     # Track a list of secrets that were defined for this object store at creation
-    object_store_template_secrets: Mapped[Optional[bytes]] = mapped_column(JSONType)
+    object_store_template_secrets: Mapped[Optional[OBJECT_STORE_TEMPLATE_CONFIGURATION_SECRET_NAMES_TYPE]] = (
+        mapped_column(JSONType)
+    )
 
     user = relationship("User", back_populates="object_stores")
 
     @property
     def template(self) -> ObjectStoreTemplate:
-        return ObjectStoreTemplate(**self.object_store_template_definition)
+        return ObjectStoreTemplate(**self.object_store_template_definition or {})
 
     def object_store_configuration(self, secrets: Dict[str, Any]) -> ObjectStoreConfiguration:
         user = self.user
@@ -10993,9 +11009,10 @@ def object_store_configuration(self, secrets: Dict[str, Any]) -> ObjectStoreConf
             "email": user.email,
             "id": user.id,
         }
+        variables: OBJECT_STORE_TEMPLATE_CONFIGURATION_VARIABLES_TYPE = self.object_store_template_variables or {}
         return template_to_configuration(
             self.template,
-            variables=self.object_store_template_variables,
+            variables=variables,
             secrets=secrets,
             user_details=user_details,
         )

lib/galaxy/model/mapping.py

@@ -32,7 +32,6 @@ def init(
     create_tables=False,
     map_install_models=False,
     database_query_profiling_proxy=False,
-    object_store=None,
     trace_logger=None,
     use_pbkdf2=True,
     slow_query_log_threshold=0,
@@ -60,7 +59,7 @@ def init(
             install_mapping.create_database_objects(engine)
 
     # Configure model, build ModelMapping
-    return configure_model_mapping(file_path, object_store, use_pbkdf2, engine, map_install_models, thread_local_log)
+    return configure_model_mapping(file_path, use_pbkdf2, engine, map_install_models, thread_local_log)
 
 
 def create_additional_database_objects(engine):
@@ -105,11 +104,12 @@ def init_models_from_config(
         config.database_engine_options,
         map_install_models=map_install_models,
         database_query_profiling_proxy=config.database_query_profiling_proxy,
-        object_store=object_store,
         trace_logger=trace_logger,
         use_pbkdf2=config.get_bool("use_pbkdf2", True),
         slow_query_log_threshold=config.slow_query_log_threshold,
         thread_local_log=config.thread_local_log,
         log_query_counts=config.database_log_query_counts,
     )
+    if object_store:
+        model.Dataset.setup_global_object_store_for_models(object_store)
     return model