Merge pull request #12778 from jmchilton/type_fixes_managers_1

More Python type fixes from deferred data branch.

lib/galaxy/exceptions/__init__.py

@@ -16,15 +16,18 @@ have nothing to do with the web - keep this in mind when defining exception name
 and messages.
 """
 
-from ..exceptions.error_codes import error_codes_by_name
+from ..exceptions.error_codes import (
+    error_codes_by_name,
+    ErrorCode,
+)
 
 
 class MessageException(Exception):
     """Most generic Galaxy exception - indicates merely that some exceptional condition happened."""
     # status code to be set when used with API.
-    status_code = 400
+    status_code: int = 400
     # Error code information embedded into API json responses.
-    err_code = error_codes_by_name['UNKNOWN']
+    err_code: ErrorCode = error_codes_by_name['UNKNOWN']
 
     def __init__(self, err_msg=None, type="info", **extra_error_info):
         self.err_msg = err_msg or self.err_code.default_error_message
@@ -253,7 +256,7 @@ class ServerNotConfiguredForRequest(MessageException):
 class ContainerCLIError(Exception):
     def __init__(self, msg=None, stdout=None, stderr=None, returncode=None,
                  command=None, subprocess_command=None, **kwargs):
-        super().__init__(msg, **kwargs)
+        super().__init__(msg)
         self.stdout = stdout
         self.stderr = stderr
         self.returncode = returncode
@@ -263,24 +266,24 @@ class ContainerCLIError(Exception):
 
 class ContainerNotFound(Exception):
     def __init__(self, msg=None, container_id=None, **kwargs):
-        super().__init__(msg, **kwargs)
+        super().__init__(msg)
         self.container_id = container_id
 
 
 class ContainerImageNotFound(Exception):
     def __init__(self, msg=None, image=None, **kwargs):
-        super().__init__(msg, **kwargs)
+        super().__init__(msg)
         self.image = image
 
 
 class ContainerRunError(Exception):
     def __init__(self, msg=None, image=None, command=None, **kwargs):
-        super().__init__(msg, **kwargs)
+        super().__init__(msg)
         self.image = image
         self.command = command
 
 
 class HandlerAssignmentError(Exception):
     def __init__(self, msg=None, obj=None, **kwargs):
-        super().__init__(msg, **kwargs)
+        super().__init__(msg)
         self.obj = obj

lib/galaxy/managers/datasets.py

@@ -4,7 +4,7 @@ Manager and Serializer for Datasets.
 import glob
 import logging
 import os
-from typing import Type
+from typing import List, Type
 
 from galaxy import (
     exceptions,
@@ -30,6 +30,7 @@ class DatasetManager(base.ModelManager, secured.AccessibleManagerMixin, deletabl
     """
     model_class = model.Dataset
     foreign_key_name = 'dataset'
+    app: MinimalManagerApp
 
     # TODO:?? get + error_if_uploading is common pattern, should upload check be worked into access/owed?
 
@@ -235,6 +236,7 @@ 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: Type[model.DatasetInstance] = model.DatasetInstance
+    app: MinimalManagerApp
 
     # NOTE: model_manager_class should be set in HDA/LDA subclasses
 
@@ -692,6 +694,7 @@ class DatasetAssociationDeserializer(base.ModelDeserializer, deletable.PurgableD
         sa_session = self.app.model.context
         sa_session.flush()
         trans = context.get("trans")
+        assert trans, "Logic error in Galaxy, deserialize_datatype not send a transation object"  # TODO: restructure this for stronger typing
         job, *_ = self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(self.app.datatypes_registry.set_external_metadata_tool, trans, incoming={'input1': item}, overwrite=False)  # overwrite is False as per existing behavior
         trans.app.job_manager.enqueue(job, tool=trans.app.datatypes_registry.set_external_metadata_tool)
         return item.datatype
@@ -731,9 +734,9 @@ class DatasetAssociationFilterParser(base.ModelFilterParser, deletable.PurgableF
         datatypes in the comma separated string `class_strs`?
         """
         parse_datatype_fn = self.app.datatypes_registry.get_datatype_class_by_name
-        comparison_classes = []
+        comparison_classes: List[Type] = []
         for class_str in class_strs.split(','):
             datatype_class = parse_datatype_fn(class_str)
             if datatype_class:
                 comparison_classes.append(datatype_class)
-        return comparison_classes and isinstance(dataset_assoc.datatype, comparison_classes)
+        return comparison_classes and isinstance(dataset_assoc.datatype, tuple(comparison_classes))

lib/galaxy/managers/hdas.py

@@ -43,6 +43,7 @@ class HDAManager(datasets.DatasetAssociationManager,
 
     tag_assoc = model.HistoryDatasetAssociationTagAssociation
     annotation_assoc = model.HistoryDatasetAssociationAnnotationAssociation
+    app: MinimalManagerApp
 
     # TODO: move what makes sense into DatasetManager
     # TODO: which of these are common with LDDAs and can be pushed down into DatasetAssociationManager?

lib/galaxy/structured_app.py

@@ -13,6 +13,7 @@ from galaxy.model.mapping import GalaxyModelMapping
 from galaxy.model.security import GalaxyRBACAgent
 from galaxy.model.security import HostAgent
 from galaxy.model.tags import GalaxyTagHandler
+from galaxy.objectstore import ObjectStore
 from galaxy.quota import QuotaAgent
 from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.tool_util.deps.views import DependencyResolversView
@@ -49,6 +50,7 @@ class MinimalApp(BasicApp):
     install_model: ModelMapping
     security_agent: GalaxyRBACAgent
     host_security_agent: HostAgent
+    object_store: ObjectStore
 
 
 class MinimalManagerApp(MinimalApp):
@@ -64,6 +66,7 @@ class MinimalManagerApp(MinimalApp):
     role_manager: Any  # 'galaxy.managers.roles.RoleManager'
     installed_repository_manager: Any  # 'galaxy.tool_shed.galaxy_install.installed_repository_manager.InstalledRepositoryManager'
     user_manager: Any
+    job_manager: Any  # galaxy.jobs.manager.JobManager
 
     @property
     def is_job_handler(self) -> bool:

setup.cfg

@@ -249,8 +249,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-galaxy.job_metrics]
 check_untyped_defs = False
-[mypy-galaxy.exceptions]
-check_untyped_defs = False
 [mypy-galaxy.datatypes.display_applications.parameters]
 check_untyped_defs = False
 [mypy-tool_shed.webapp.search.tool_search]
@@ -591,8 +589,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-galaxy.metadata.set_metadata]
 check_untyped_defs = False
-[mypy-galaxy.managers.datasets]
-check_untyped_defs = False
 [mypy-galaxy.managers.lddas]
 check_untyped_defs = False
 [mypy-galaxy.tools.error_reports]