More type fixes.

lib/galaxy/__init__.py

@@ -3,4 +3,4 @@
 """
 
 from pkgutil import extend_path
-__path__ = extend_path(__path__, __name__)
+__path__ = extend_path(__path__, __name__)  # type: ignore

lib/galaxy/managers/annotatable.py

@@ -20,7 +20,7 @@ def _match_by_user(item, user):
 
 class AnnotatableManagerMixin:
     #: class of AnnotationAssociation (e.g. HistoryAnnotationAssociation)
-    annotation_assoc = None
+    annotation_assoc: type
 
     def annotation(self, item):
         """

lib/galaxy/managers/base.py

@@ -894,9 +894,7 @@ class ModelFilterParser(HasAModelManager):
     # (as the model informs how the filter params are parsed)
     # I have no great idea where this 'belongs', so it's here for now
 
-    #: model class
-    model_class = None
-    subcontainer_model_class = None
+    model_class: type
     parsed_filter = parsed_filter
 
     def __init__(self, app, **kwargs):

lib/galaxy/managers/cloudauthzs.py

@@ -20,9 +20,6 @@ class CloudAuthzManager(sharable.SharableModelManager):
     model_class = model.CloudAuthz
     foreign_key_name = 'cloudauthz'
 
-    def __init__(self, app, *args, **kwargs):
-        super().__init__(app, *args, **kwargs)
-
 
 class CloudAuthzsSerializer(base.ModelSerializer):
     """

lib/galaxy/managers/containers.py

@@ -31,8 +31,8 @@ class ContainerManagerMixin:
     # TODO: terminology is getting a bit convoluted and silly at this point: rename three public below?
     # TODO: this should be an open mapping (not just 2)
     #: the classes that can be contained
-    contained_class = None
-    subcontainer_class = None
+    contained_class: type
+    subcontainer_class: type
     #: how any contents lists produced are ordered - (string) attribute name to sort on or tuple of attribute names
     default_order_by: Optional[str] = None
 

lib/galaxy/managers/datasets.py

@@ -4,6 +4,7 @@
 import glob
 import logging
 import os
+from typing import Type
 
 from galaxy import (
     exceptions,
@@ -232,7 +233,7 @@ class DatasetAssociationManager(base.ModelManager,
     """
     # DA's were meant to be proxies - but were never fully implemented as them
     # Instead, a dataset association HAS a dataset but contains metadata specific to a library (lda) or user (hda)
-    model_class = model.DatasetInstance
+    model_class: Type[model.DatasetInstance] = model.DatasetInstance
 
     # NOTE: model_manager_class should be set in HDA/LDA subclasses
 

lib/galaxy/managers/history_contents.py

@@ -473,7 +473,6 @@ class HistoryContentsFilters(base.ModelFilterParser,
                              tools.ToolFilterMixin):
     # surprisingly (but ominously), this works for both content classes in the union that's filtered
     model_class = model.HistoryDatasetAssociation
-    subcontainer_model_class = model.HistoryDatasetCollectionAssociation
 
     def _parse_orm_filter(self, attr, op, val):
 

lib/galaxy/managers/ratable.py

@@ -2,18 +2,19 @@
 Mixins for Ratable model managers and serializers.
 """
 import logging
+from typing import Type
 
 from sqlalchemy.sql.expression import func
 
+from galaxy.model import ItemRatingAssociation
 from . import base
 
 log = logging.getLogger(__name__)
 
 
 class RatableManagerMixin:
 
-    #: class of RatingAssociation (e.g. HistoryRatingAssociation)
-    rating_assoc = None
+    rating_assoc: Type[ItemRatingAssociation]
 
     def rating(self, item, user, as_int=True):
         """Returns the integer rating given to this item by the user.

lib/galaxy/managers/rbac_secured.py

@@ -21,7 +21,7 @@ class RBACPermission:
     (Libraries, Datasets).
     """
 
-    permissions_class = None
+    permissions_class: type
     permission_failed_error_class = RBACPermissionFailedException
 
     def __init__(self, app):

lib/galaxy/managers/sharable.py

@@ -11,7 +11,7 @@
 """
 import logging
 import re
-from typing import Optional
+from typing import Optional, Type
 
 from sqlalchemy import true
 
@@ -24,6 +24,7 @@
     taggable,
     users
 )
+from galaxy.model import UserShareAssociation
 
 log = logging.getLogger(__name__)
 
@@ -34,7 +35,7 @@ class SharableModelManager(base.ModelManager, secured.OwnableManagerMixin, secur
     # base.DeleteableModelMixin? (all four are deletable)
 
     #: the model used for UserShareAssociations with this model
-    user_share_model = None
+    user_share_model: Type[UserShareAssociation]
 
     #: the single character abbreviation used in username_and_slug: e.g. 'h' for histories: u/user/h/slug
     SINGLE_CHAR_ABBR: Optional[str] = None

lib/galaxy/managers/taggable.py

@@ -5,6 +5,7 @@
 # from galaxy import exceptions as galaxy_exceptions
 
 import logging
+from typing import Type
 
 from sqlalchemy import sql
 
@@ -45,8 +46,7 @@ def _tags_from_strings(item, tag_handler, new_tags_list, user=None):
 
 
 class TaggableManagerMixin:
-    #: class of TagAssociation (e.g. HistoryTagAssociation)
-    tag_assoc = None
+    tag_assoc: Type[model.ItemTagAssociation]
 
     # TODO: most of this can be done by delegating to the GalaxyTagHandler?
     def get_tags(self, item):

lib/galaxy/model/__init__.py

@@ -18,7 +18,7 @@
 from collections import defaultdict
 from datetime import datetime, timedelta
 from string import Template
-from typing import TYPE_CHECKING
+from typing import Optional, TYPE_CHECKING
 from uuid import UUID, uuid4
 
 from boltons.iterutils import remap
@@ -2183,7 +2183,11 @@ def __collection_contents_iter(self, **kwds):
         return self.__filter_contents(HistoryDatasetCollectionAssociation, **kwds)
 
 
-class HistoryUserShareAssociation(RepresentById):
+class UserShareAssociation(RepresentById):
+    user: Optional[User]
+
+
+class HistoryUserShareAssociation(UserShareAssociation):
     def __init__(self):
         self.history = None
         self.user = None
@@ -4867,6 +4871,7 @@ class Workflow(Dictifiable, RepresentById):
     input_step_types = ['data_input', 'data_collection_input', 'parameter_input']
 
     def __init__(self, uuid=None):
+        self.id = None
         self.user = None
         self.name = None
         self.has_cycles = None
@@ -5256,7 +5261,7 @@ def copy(self, copied_step):
         return copied_output
 
 
-class StoredWorkflowUserShareAssociation(RepresentById):
+class StoredWorkflowUserShareAssociation(UserShareAssociation):
 
     def __init__(self):
         self.stored_workflow = None
@@ -6187,7 +6192,7 @@ def to_dict(self, view='element'):
         return rval
 
 
-class PageUserShareAssociation(RepresentById):
+class PageUserShareAssociation(UserShareAssociation):
     def __init__(self):
         self.page = None
         self.user = None
@@ -6251,7 +6256,7 @@ def copy(self, visualization=None):
         )
 
 
-class VisualizationUserShareAssociation(RepresentById):
+class VisualizationUserShareAssociation(UserShareAssociation):
     def __init__(self):
         self.visualization = None
         self.user = None

lib/galaxy/model/mapping.py

@@ -1885,7 +1885,7 @@ def simple_mapping(model, **kwds):
 # Set up proxy so that
 #   History.users_shared_with
 # returns a list of users that history is shared with.
-model.History.users_shared_with_dot_users = association_proxy('users_shared_with', 'user')
+model.History.users_shared_with_dot_users = association_proxy('users_shared_with', 'user')  # type: ignore
 
 mapper(model.HistoryUserShareAssociation, model.HistoryUserShareAssociation.table, properties=dict(
     user=relation(model.User, backref='histories_shared_by_others'),
@@ -1934,7 +1934,7 @@ def simple_mapping(model, **kwds):
 
 # Set up proxy so that this syntax is possible:
 # <user_obj>.preferences[pref_name] = pref_value
-model.User.preferences = association_proxy('_preferences', 'value', creator=model.UserPreference)
+model.User.preferences = association_proxy('_preferences', 'value', creator=model.UserPreference)  # type: ignore
 
 mapper(model.Group, model.Group.table, properties=dict(
     users=relation(model.UserGroupAssociation)
@@ -2502,7 +2502,7 @@ def simple_mapping(model, **kwds):
 # Set up proxy so that
 #   StoredWorkflow.users_shared_with
 # returns a list of users that workflow is shared with.
-model.StoredWorkflow.users_shared_with_dot_users = association_proxy('users_shared_with', 'user')
+model.StoredWorkflow.users_shared_with_dot_users = association_proxy('users_shared_with', 'user')  # type: ignore
 
 mapper(model.StoredWorkflowUserShareAssociation, model.StoredWorkflowUserShareAssociation.table, properties=dict(
     user=relation(model.User,
@@ -2661,7 +2661,7 @@ def simple_mapping(model, **kwds):
 # Set up proxy so that
 #   Page.users_shared_with
 # returns a list of users that page is shared with.
-model.Page.users_shared_with_dot_users = association_proxy('users_shared_with', 'user')
+model.Page.users_shared_with_dot_users = association_proxy('users_shared_with', 'user')  # type: ignore
 
 mapper(model.PageUserShareAssociation, model.PageUserShareAssociation.table,
        properties=dict(user=relation(model.User, backref='pages_shared_by_others'),
@@ -2781,14 +2781,14 @@ def rating_mapping(rating_class, **kwds):
     external_output_metadata=relation(model.JobExternalOutputMetadata, lazy=True),
     tasks=relation(model.Task)
 ))
-model.Job.any_output_dataset_deleted = column_property(
+model.Job.any_output_dataset_deleted = column_property(  # type: ignore
     exists([model.HistoryDatasetAssociation],
            and_(model.Job.table.c.id == model.JobToOutputDatasetAssociation.table.c.job_id,
                 model.HistoryDatasetAssociation.table.c.id == model.JobToOutputDatasetAssociation.table.c.dataset_id,
                 model.HistoryDatasetAssociation.table.c.deleted == true())
            )
 )
-model.Job.any_output_dataset_collection_instances_deleted = column_property(
+model.Job.any_output_dataset_collection_instances_deleted = column_property(  # type: ignore
     exists([model.HistoryDatasetCollectionAssociation.table.c.id],
            and_(model.Job.table.c.id == model.JobToOutputDatasetCollectionAssociation.table.c.job_id,
                 model.HistoryDatasetCollectionAssociation.table.c.id == model.JobToOutputDatasetCollectionAssociation.table.c.dataset_collection_id,
@@ -2861,7 +2861,7 @@ def _workflow_invocation_update(self):
     session.execute(stmt)
 
 
-model.WorkflowInvocation.update = _workflow_invocation_update
+model.WorkflowInvocation.update = _workflow_invocation_update  # type: ignore
 
 
 def init(file_path, url, engine_options=None, create_tables=False, map_install_models=False,

lib/galaxy/model/tool_shed_install/__init__.py

@@ -560,7 +560,7 @@ def is_installed(self):
         return self.status == self.installation_status.INSTALLED
 
 
-class ToolVersion(Dictifiable):
+class ToolVersion(Dictifiable, _HasTable):
     dict_element_visible_keys = ['id', 'tool_shed_repository']
 
     def __init__(self, id=None, create_time=None, tool_id=None, tool_shed_repository=None):

lib/galaxy/web/buildapp.py

@@ -5,6 +5,6 @@
 except ImportError:
     # when installed as a library, galaxy-web-apps may not be available - this
     # is fine - we shouldn't be using this entry point anyway.
-    app_factory = None
+    app_factory = None  # type: ignore
 
 __all__ = ('app_factory', )

lib/galaxy/web/framework/helpers/grids.py

@@ -574,10 +574,10 @@ class Grid:
     Specifies the content and format of a grid (data table).
     """
     title = ""
-    model_class = None
+    model_class: Optional[type] = None
     show_item_checkboxes = False
     use_hide_message = True
-    global_actions: List[Dict] = []
+    global_actions: List[GridAction] = []
     columns: List[GridColumn] = []
     operations: List[GridOperation] = []
     standard_filters: List[GridColumnFilter] = []
@@ -591,7 +591,7 @@ class Grid:
     cur_filter_pref_name = ".filter"
     cur_sort_key_pref_name = ".sort_key"
     legend = None
-    info_text = None
+    info_text: Optional[str] = None
 
     def __init__(self):
         # Determine if any multiple row operations are defined

lib/galaxy/web/legacy_framework/grids.py

@@ -539,7 +539,7 @@ class Grid:
     Specifies the content and format of a grid (data table).
     """
     title = ""
-    model_class = None
+    model_class: Optional[type] = None
     show_item_checkboxes = False
     template = "legacy/grid_base.mako"
     async_template = "legacy/grid_base_async.mako"

lib/galaxy/web_stack/handlers.py

@@ -7,7 +7,8 @@
 import logging
 import os
 import random
-from collections import namedtuple
+from enum import Enum
+from typing import Set, Tuple
 
 from sqlalchemy.orm import object_session
 
@@ -19,12 +20,18 @@
 
 log = logging.getLogger(__name__)
 
-_handler_assignment_methods = (
-    'MEM_SELF', 'DB_SELF', 'DB_PREASSIGN', 'DB_TRANSACTION_ISOLATION', 'DB_SKIP_LOCKED', 'UWSGI_MULE_MESSAGE'
-)
-HANDLER_ASSIGNMENT_METHODS = namedtuple('JOB_HANDLER_ASSIGNMENT_METHODS', _handler_assignment_methods)(
-    *[x.lower().replace('_', '-') for x in _handler_assignment_methods]
-)
+
+class HANDLER_ASSIGNMENT_METHODS(str, Enum):
+    MEM_SELF = 'mem-self'
+    DB_SELF = 'db-self'
+    DB_PREASSIGN = 'db-preassign'
+    DB_TRANSACTION_ISOLATION = 'db-transaction-isolation'
+    DB_SKIP_LOCKED = 'db-skip-locked'
+    UWSGI_MULE_MESSAGE = 'uwsgi-mule-message'
+
+    @classmethod
+    def has_value(cls, value):
+        return value in cls._value2member_map_
 
 
 class HandlerAssignmentSkip(Exception):
@@ -34,8 +41,8 @@ class HandlerAssignmentSkip(Exception):
 
 class ConfiguresHandlers:
     DEFAULT_HANDLER_TAG = '_default_'
-    DEFAULT_BASE_HANDLER_POOLS = ()
-    UNSUPPORTED_HANDLER_ASSIGNMENT_METHODS = ()
+    DEFAULT_BASE_HANDLER_POOLS: Tuple[str, ...] = ()
+    UNSUPPORTED_HANDLER_ASSIGNMENT_METHODS: Set[str] = set()
 
     def add_handler(self, handler_id, tags):
         if handler_id not in self.handlers:
@@ -112,9 +119,9 @@ def _init_handler_assignment_methods(self, handling_config_dict=None):
         if handling_config_dict:
             for method in handling_config_dict.get("assign", []):
                 method = method.lower()
-                assert method in HANDLER_ASSIGNMENT_METHODS, \
+                assert HANDLER_ASSIGNMENT_METHODS.has_value(method), \
                     "Invalid job handler assignment method '{}', must be one of: {}".format(
-                        method, ', '.join(HANDLER_ASSIGNMENT_METHODS))
+                        method, ', '.join([h.value for h in HANDLER_ASSIGNMENT_METHODS]))
                 try:
                     self.handler_assignment_methods.append(method)
                 except AttributeError:

lib/galaxy/webapps/galaxy/api/__init__.py

@@ -2,6 +2,7 @@
 This module *does not* contain API routes. It exclusively contains dependencies to be used in FastAPI routes
 """
 from typing import (
+    cast,
     Optional,
 )
 
@@ -28,7 +29,7 @@
 
 
 def get_app() -> UniverseApplication:
-    return galaxy_app.app
+    return cast(UniverseApplication, galaxy_app.app)
 
 
 def get_job_manager(app: UniverseApplication = Depends(get_app)) -> JobManager:

lib/galaxy/webapps/galaxy/api/jobs.py

@@ -80,7 +80,7 @@ def show(self, id: EncodedDatabaseIdField, trans: SessionRequestContext = Depend
         """
         id = trans.app.security.decode_id(id)
         job = self.job_manager.get_accessible_job(trans, id)
-        return view_show_job(trans, job, full)
+        return view_show_job(trans, job, bool(full))
 
 
 class JobController(BaseAPIController, UsesVisualizationMixin):