Add shim to ensure that manager itself is not reinstantiated, align with existing manager pattern

Author: guerler

lib/galaxy/managers/history_graph.py

@@ -44,6 +44,7 @@
     TruncationInfo,
 )
 from galaxy.security.idencoding import IdEncodingHelper
+from galaxy.structured_app import MinimalManagerApp
 from galaxy.tool_util.toolbox import AbstractToolBox
 
 log = logging.getLogger(__name__)
@@ -54,6 +55,35 @@
 MAX_LIMIT = 1000
 
 
+class HistoryGraphManager:
+    def __init__(self, app: MinimalManagerApp):
+        self.app = app
+
+    def build(
+        self,
+        sa_session: Session,
+        history_id: int,
+        limit: int = 500,
+        include_deleted: bool = False,
+        seed: Optional[str] = None,
+        direction: Literal["backward", "forward", "both"] = "both",
+        depth: int = 5,
+        seed_scope_hid: Optional[int] = None,
+    ) -> HistoryGraphResponse:
+        return HistoryGraphBuilder(
+            sa_session=sa_session,
+            security=self.app.security,
+            toolbox=self.app.toolbox,
+            history_id=history_id,
+            limit=limit,
+            include_deleted=include_deleted,
+            seed=seed,
+            direction=direction,
+            depth=depth,
+            seed_scope_hid=seed_scope_hid,
+        ).build()
+
+
 class HistoryGraphBuilder:
     """Builds a provenance graph from selected history items.
 

lib/galaxy/webapps/galaxy/services/histories.py

@@ -40,7 +40,7 @@
     HistoryManager,
     HistorySerializer,
 )
-from galaxy.managers.history_graph import HistoryGraphBuilder
+from galaxy.managers.history_graph import HistoryGraphManager
 from galaxy.managers.users import UserManager
 from galaxy.model import (
     HistoryDatasetAssociation,
@@ -131,6 +131,7 @@ def __init__(
         deserializer: HistoryDeserializer,
         citations_manager: CitationsManager,
         history_export_manager: HistoryExportManager,
+        history_graph_manager: HistoryGraphManager,
         filters: HistoryFilters,
         short_term_storage_allocator: ShortTermStorageAllocator,
         notification_service: NotificationService,
@@ -142,6 +143,7 @@ def __init__(
         self.deserializer = deserializer
         self.citations_manager = citations_manager
         self.history_export_manager = history_export_manager
+        self.history_graph_manager = history_graph_manager
         self.filters = filters
         self.shareable_service = ShareableHistoryService(self.manager, self.serializer, notification_service)
         self.short_term_storage_allocator = short_term_storage_allocator
@@ -397,19 +399,16 @@ def graph(
     ) -> HistoryGraphResponse:
         history = self.manager.get_accessible(history_id, trans.user, current_history=trans.history)
         seed_scope_hid = self._resolve_seed_scope_hid(trans, history.id, seed_scope) if seed_scope else None
-        builder = HistoryGraphBuilder(
+        return self.history_graph_manager.build(
             sa_session=trans.sa_session,
-            security=self.security,
             history_id=history.id,
             limit=limit,
-            toolbox=trans.app.toolbox,
             include_deleted=include_deleted,
             seed=seed,
             direction=direction,
             depth=depth,
             seed_scope_hid=seed_scope_hid,
         )
-        return builder.build()
 
     def _resolve_seed_scope_hid(self, trans: ProvidesHistoryContext, history_id: int, seed_scope: str) -> int:
         db_id = self.security.decode_id(seed_scope[1:])

test/unit/app/managers/test_HistoryGraphBuilder.py

@@ -10,7 +10,7 @@
 from galaxy.managers.datasets import DatasetManager
 from galaxy.managers.hdas import HDAManager
 from galaxy.managers.histories import HistoryManager
-from galaxy.managers.history_graph import HistoryGraphBuilder
+from galaxy.managers.history_graph import HistoryGraphManager
 from .base import (
     BaseTestCase,
     CreatesCollectionsMixin,
@@ -35,6 +35,8 @@ def set_up_managers(self):
         self.hda_manager = self.app[HDAManager]
         self.history_manager = self.app[HistoryManager]
         self.collection_manager = self.app[DatasetCollectionManager]
+        self.app._toolbox = None  # type: ignore[assignment]
+        self.history_graph_manager = self.app[HistoryGraphManager]
 
     def _build_graph(
         self,
@@ -45,17 +47,15 @@ def _build_graph(
         limit=500,
         seed_scope_hid=None,
     ):
-        builder = HistoryGraphBuilder(
+        return self.history_graph_manager.build(
             sa_session=self.trans.sa_session,
-            security=self.app.security,
             history_id=history.id,
             limit=limit,
             seed=seed,
             direction=direction,
             depth=depth,
             seed_scope_hid=seed_scope_hid,
         )
-        return builder.build()
 
     def _encode(self, prefix, db_id):
         return f"{prefix}{self.app.security.encode_id(db_id)}"
@@ -580,13 +580,11 @@ def test_deleted_items_with_include_deleted(self):
         assert len(graph.nodes) == 0
 
         # With include_deleted: included
-        builder = HistoryGraphBuilder(
+        graph = self.history_graph_manager.build(
             sa_session=self.trans.sa_session,
-            security=self.app.security,
             history_id=history.id,
             include_deleted=True,
         )
-        graph = builder.build()
         assert len(graph.nodes) == 1
 
     def test_expanding_limit_generally_additive(self):
@@ -1015,13 +1013,11 @@ def test_n2_ambiguous_hdca_producer_has_node_but_no_edge(self):
         hdca.implicit_collection_jobs_id = icj.id  # implicit branch
         self.trans.sa_session.flush()
 
-        builder = HistoryGraphBuilder(
+        graph = self.history_graph_manager.build(
             sa_session=self.trans.sa_session,
-            security=self.app.security,
             history_id=history.id,
             limit=500,
         )
-        graph = builder.build()
 
         hdca_enc = self._encode("c", hdca.id)
         node_ids = {n.id for n in graph.nodes}
@@ -1181,15 +1177,15 @@ def set_up_managers(self):
         self.hda_manager = self.app[HDAManager]
         self.history_manager = self.app[HistoryManager]
         self.collection_manager = self.app[DatasetCollectionManager]
+        self.app._toolbox = None  # type: ignore[assignment]
+        self.history_graph_manager = self.app[HistoryGraphManager]
 
     def _build_graph(self, history, **kwargs):
-        builder = HistoryGraphBuilder(
+        return self.history_graph_manager.build(
             sa_session=self.trans.sa_session,
-            security=self.app.security,
             history_id=history.id,
             **kwargs,
         )
-        return builder.build()
 
     def _encode(self, prefix, db_id):
         return f"{prefix}{self.app.security.encode_id(db_id)}"