Remove deprecated tool document cache

client/src/api/schema/schema.ts

@@ -24359,7 +24359,9 @@ export interface operations {
                     [name: string]: unknown;
                 };
                 content: {
-                    "application/json": unknown;
+                    "application/json": {
+                        [key: string]: unknown;
+                    };
                 };
             };
             /** @description Request Error */

doc/source/admin/galaxy_options.rst

@@ -1217,22 +1217,6 @@
 :Type: str
 
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``enable_tool_document_cache``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-:Description:
-    This option is deprecated, and the tool document cache will be
-    removed in the next release. Whether to enable the tool document
-    cache. This cache stores expanded XML strings. Enabling the tool
-    cache results in slightly faster startup times. The tool cache is
-    backed by a SQLite database, which cannot be stored on certain
-    network disks. The cache location is configurable with the
-    ``tool_cache_data_dir`` tag in tool config files.
-:Default: ``false``
-:Type: bool
-
-
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 ``tool_search_index_dir``
 ~~~~~~~~~~~~~~~~~~~~~~~~~

lib/galaxy/app.py

@@ -788,7 +788,6 @@ def __init__(self, **kwargs) -> None:
         self.datatypes_registry.load_external_metadata_tool(self.toolbox)
         # Load history import/export tools.
         load_lib_tools(self.toolbox)
-        self.toolbox.persist_cache(register_postfork=True)
         # visualizations registry: associates resources with visualizations, controls how to render
         self.visualizations_registry = self._register_singleton(
             VisualizationsRegistry,

lib/galaxy/app_unittest_utils/galaxy_mock.py

@@ -267,8 +267,6 @@ def __init__(self, **kwargs):
         self.version_major = "19.09"
 
         # set by MockDir
-        self.enable_tool_document_cache = False
-        self.tool_cache_data_dir = os.path.join(self.root, "tool_cache")
         self.external_chown_script = None
         self.check_job_script_integrity = False
         self.check_job_script_integrity_count = 0

lib/galaxy/config/sample/galaxy.yml.sample

@@ -935,15 +935,6 @@ galaxy:
   # generated commands run in sh.
   #default_job_shell: /bin/bash
 
-  # This option is deprecated, and the tool document cache will be
-  # removed in the next release. Whether to enable the tool document
-  # cache. This cache stores expanded XML strings. Enabling the tool
-  # cache results in slightly faster startup times. The tool cache is
-  # backed by a SQLite database, which cannot be stored on certain
-  # network disks. The cache location is configurable with the
-  # ``tool_cache_data_dir`` tag in tool config files.
-  #enable_tool_document_cache: false
-
   # Directory in which the toolbox search index is stored. The value of
   # this option will be resolved with respect to <data_dir>.
   #tool_search_index_dir: tool_search_index

lib/galaxy/config/schemas/config_schema.yml

@@ -882,19 +882,6 @@ mapping:
           should be disabled. Containerized jobs always use /bin/sh - so more maximum
           portability tool authors should assume generated commands run in sh.
 
-      enable_tool_document_cache:
-        type: bool
-        default: false
-        required: false
-        desc: |
-          This option is deprecated, and the tool document cache will be removed
-          in the next release.
-          Whether to enable the tool document cache. This cache stores
-          expanded XML strings. Enabling the tool cache results in slightly faster startup
-          times. The tool cache is backed by a SQLite database, which cannot
-          be stored on certain network disks. The cache location is configurable
-          with the ``tool_cache_data_dir`` tag in tool config files.
-
       tool_search_index_dir:
         type: str
         default: tool_search_index

lib/galaxy/dependencies/pinned-requirements.txt

@@ -185,7 +185,6 @@ social-auth-core==4.6.1
 sortedcontainers==2.4.0
 spython==0.3.14
 sqlalchemy==2.0.40
-sqlitedict==2.1.0
 sqlparse==0.5.3
 starlette==0.46.2
 starlette-context==0.4.0

lib/galaxy/managers/tools.py

@@ -53,10 +53,10 @@ def tool_payload_to_tool(app, tool_dict: Dict[str, Any]) -> Optional[Tool]:
     return tool
 
 
-class DynamicToolManager(ModelManager[model.DynamicTool]):
+class DynamicToolManager(ModelManager[DynamicTool]):
     """Manages dynamic tools stored in Galaxy's database."""
 
-    model_class = model.DynamicTool
+    model_class = DynamicTool
 
     def ensure_can_use_unprivileged_tool(self, user: model.User):
         stmt = select(
@@ -70,7 +70,7 @@ def ensure_can_use_unprivileged_tool(self, user: model.User):
         if not self.session().execute(stmt).scalar():
             raise exceptions.InsufficientPermissionsException("User is not allowed to run unprivileged tools")
 
-    def get_tool_by_id_or_uuid(self, id_or_uuid: Union[int, str]):
+    def get_tool_by_id_or_uuid(self, id_or_uuid: Union[int, str]) -> Union[DynamicTool, None]:
         if isinstance(id_or_uuid, int):
             return self.get_tool_by_id(id_or_uuid)
         else:
@@ -213,9 +213,10 @@ def deactivate_unprivileged_tool(self, user: model.User, dynamic_tool: DynamicTo
         session.execute(update_stmt)
         session.commit()
 
-    def deactivate(self, dynamic_tool):
-        self.update(dynamic_tool, {"active": False})
-        return dynamic_tool
+    def deactivate(self, dynamic_tool: DynamicTool) -> DynamicTool:
+        assert isinstance(dynamic_tool.uuid, UUID)
+        del self.app.toolbox._tools_by_uuid[dynamic_tool.uuid]
+        return self.update(dynamic_tool, {"active": False})
 
 
 class ToolFilterMixin:

lib/galaxy/model/__init__.py

@@ -341,7 +341,7 @@ def get_uuid(uuid: Optional[Union[UUID, str]] = None) -> UUID:
         return uuid
     if not uuid:
         return uuid4()
-    return UUID(str(uuid))
+    return UUID(uuid)
 
 
 def to_json(sa_session, column, keys: List[str]):

lib/galaxy/queue_worker.py

@@ -11,7 +11,10 @@
 import threading
 import time
 from inspect import ismodule
-from typing import TYPE_CHECKING
+from typing import (
+    Optional,
+    TYPE_CHECKING,
+)
 
 from kombu import (
     Consumer,
@@ -33,10 +36,14 @@
 log = logging.getLogger(__name__)
 
 if TYPE_CHECKING:
-    from galaxy.structured_app import MinimalManagerApp
+    from galaxy.app import UniverseApplication
+    from galaxy.structured_app import (
+        MinimalManagerApp,
+        StructuredApp,
+    )
 
 
-def send_local_control_task(app, task, get_response=False, kwargs=None):
+def send_local_control_task(app: "StructuredApp", task: str, get_response: bool = False, kwargs: Optional[dict] = None):
     """
     This sends a message to the process-local control worker, which is useful
     for one-time asynchronous tasks like recalculating user disk usage.
@@ -162,7 +169,7 @@ def reload_tool(app, **kwargs):
         log.error("Reload tool invoked without tool id.")
 
 
-def reload_toolbox(app, save_integrated_tool_panel=True, **kwargs):
+def reload_toolbox(app: "UniverseApplication", save_integrated_tool_panel: bool = True, **kwargs) -> None:
     reload_timer = util.ExecutionTimer()
     log.debug("Executing toolbox reload on '%s'", app.config.server_name)
     reload_count = app.toolbox._reload_count
@@ -174,7 +181,7 @@ def reload_toolbox(app, save_integrated_tool_panel=True, **kwargs):
     log.debug("Toolbox reload %s", reload_timer)
 
 
-def _get_new_toolbox(app, save_integrated_tool_panel=True):
+def _get_new_toolbox(app: "UniverseApplication", save_integrated_tool_panel: bool = True) -> None:
     """
     Generate a new toolbox, by constructing a toolbox from the config files,
     and then adding pre-existing data managers from the old toolbox to the new toolbox.
@@ -190,7 +197,6 @@ def _get_new_toolbox(app, save_integrated_tool_panel=True):
     load_lib_tools(new_toolbox)
     [new_toolbox.register_tool(tool) for tool in new_toolbox.data_manager_tools.values()]
     app._toolbox = new_toolbox
-    app.toolbox.persist_cache()
 
 
 def reload_data_managers(app, **kwargs):

lib/galaxy/tool_shed/galaxy_install/tools/tool_panel_manager.py

@@ -42,7 +42,6 @@ def add_to_shed_tool_config(self, shed_tool_conf_dict: Dict[str, Any], elem_list
             return
         old_toolbox = self.app.toolbox
         shed_tool_conf = shed_tool_conf_dict["config_filename"]
-        tool_cache_data_dir = shed_tool_conf_dict.get("tool_cache_data_dir")
         tool_path = shed_tool_conf_dict["tool_path"]
         config_elems = []
         # Ideally shed_tool_conf.xml would be created before the repo is cloned and added to the DB, but this is called
@@ -83,7 +82,7 @@ def add_to_shed_tool_config(self, shed_tool_conf_dict: Dict[str, Any], elem_list
                 else:
                     config_elems.append(elem_entry)
             # Persist the altered shed_tool_config file.
-            self.config_elems_to_xml_file(config_elems, shed_tool_conf, tool_path, tool_cache_data_dir)
+            self.config_elems_to_xml_file(config_elems, shed_tool_conf, tool_path)
             self.app.wait_for_toolbox_reload(old_toolbox)
         else:
             log.error(error_message)
@@ -135,16 +134,13 @@ def add_to_tool_panel(
             self.app.toolbox.update_shed_config(shed_tool_conf_dict)
             self.add_to_shed_tool_config(shed_tool_conf_dict, elem_list)
 
-    def config_elems_to_xml_file(self, config_elems, config_filename, tool_path, tool_cache_data_dir=None) -> None:
+    def config_elems_to_xml_file(self, config_elems, config_filename, tool_path) -> None:
         """
         Persist the current in-memory list of config_elems to a file named by the
         value of config_filename.
         """
         try:
-            tool_cache_data_dir = f' tool_cache_data_dir="{tool_cache_data_dir}"' if tool_cache_data_dir else ""
-            root = parse_xml_string(
-                f'<?xml version="1.0"?>\n<toolbox tool_path="{tool_path}"{tool_cache_data_dir}></toolbox>'
-            )
+            root = parse_xml_string(f'<?xml version="1.0"?>\n<toolbox tool_path="{tool_path}"></toolbox>')
             for elem in config_elems:
                 root.append(elem)
             with RenamedTemporaryFile(config_filename, mode="w") as fh:

lib/galaxy/tool_shed/unittest_utils/__init__.py

@@ -2,10 +2,12 @@
 from pathlib import Path
 from typing import (
     Any,
+    cast,
     Dict,
     List,
     NamedTuple,
     Optional,
+    TYPE_CHECKING,
     Union,
 )
 
@@ -39,6 +41,10 @@
 )
 from galaxy.util.tool_shed.tool_shed_registry import Registry
 
+if TYPE_CHECKING:
+    from galaxy.tools import Tool
+    from galaxy.util.path import StrPath
+
 
 class ToolShedTarget(NamedTuple):
     url: str
@@ -83,7 +89,7 @@ class TestTool:
     params_with_missing_data_table_entry: list = []
     params_with_missing_index_file: list = []
 
-    def __init__(self, config_file, tool_shed_repository, guid):
+    def __init__(self, config_file: "StrPath", tool_shed_repository, guid: str) -> None:
         self.config_file = config_file
         self.tool_shed_repository = tool_shed_repository
         self.guid = guid
@@ -100,12 +106,14 @@ def lineage(self):
 
 
 class TestToolBox(AbstractToolBox):
-    def create_tool(self, config_file, tool_cache_data_dir=None, **kwds):
-        tool = TestTool(config_file, kwds["tool_shed_repository"], kwds["guid"])
+    def create_tool(self, config_file: "StrPath", **kwds) -> "Tool":
+        tool = cast("Tool", TestTool(config_file, kwds["tool_shed_repository"], kwds["guid"]))
         tool._lineage = self._lineage_map.register(tool)  # cleanup?
         return tool
 
-    def _get_tool_shed_repository(self, tool_shed, name, owner, installed_changeset_revision):
+    def _get_tool_shed_repository(
+        self, tool_shed: str, name: str, owner: str, installed_changeset_revision: Optional[str]
+    ):
         return get_installed_repository(
             self.app,
             tool_shed=tool_shed,

lib/galaxy/tool_shed/util/repository_util.py

@@ -247,14 +247,14 @@ def get_absolute_path_to_file_in_repository(repo_files_dir, file_name):
 
 def get_installed_repository(
     app: "InstallationTarget",
-    tool_shed=None,
-    name=None,
-    owner=None,
-    changeset_revision=None,
-    installed_changeset_revision=None,
-    repository_id=None,
-    from_cache=False,
-):
+    tool_shed: Optional[str] = None,
+    name: Optional[str] = None,
+    owner: Optional[str] = None,
+    changeset_revision: Optional[str] = None,
+    installed_changeset_revision: Optional[str] = None,
+    repository_id: Optional[int] = None,
+    from_cache: bool = False,
+) -> ToolShedRepository:
     """
     Return a tool shed repository database record defined by the combination of a toolshed, repository name,
     repository owner and either current or originally installed changeset_revision.

lib/galaxy/tool_util/parser/interface.py

@@ -400,7 +400,7 @@ def parse_creator(self):
         return []
 
     @property
-    def macro_paths(self):
+    def macro_paths(self) -> List[str]:
         return []
 
     @property

lib/galaxy/tool_util/parser/xml.py

@@ -90,6 +90,7 @@
 )
 
 if TYPE_CHECKING:
+    from galaxy.util.path import StrPath
     from .output_objects import ToolOutputBase
 
 log = logging.getLogger(__name__)
@@ -158,7 +159,9 @@ class XmlToolSource(ToolSource):
 
     language = "xml"
 
-    def __init__(self, xml_tree: ElementTree, source_path=None, macro_paths=None):
+    def __init__(
+        self, xml_tree: ElementTree, source_path: Optional["StrPath"] = None, macro_paths: Optional[List[str]] = None
+    ) -> None:
         self.xml_tree = xml_tree
         self.root = self.xml_tree.getroot()
         self._source_path = source_path
@@ -683,7 +686,7 @@ def parse_help(self) -> Optional[HelpContent]:
         return HelpContent(format=help_format, content=content)
 
     @property
-    def macro_paths(self):
+    def macro_paths(self) -> List[str]:
         return self._macro_paths
 
     @property