Fixes after rebase

lib/galaxy/jobs/__init__.py

@@ -298,11 +298,11 @@ class JobConfiguration(ConfiguresHandlers):
 
     runner_plugins: List[dict]
     handlers: dict
-    handler_runner_plugins: Dict[str, List[str]]
+    handler_runner_plugins: Dict[str, str]
     tools: Dict[str, list]
     tool_classes: Dict[str, list]
     resource_groups: Dict[str, list]
-    destinations: Dict[str, list]
+    destinations: Dict[str, tuple]
     resource_parameters: Dict[str, Any]
     DEFAULT_BASE_HANDLER_POOLS = ("job-handlers",)
 
@@ -332,7 +332,7 @@ def __init__(self, app: MinimalManagerApp):
         self.handler_max_grab = None
         self.handler_ready_window_size = JobConfiguration.DEFAULT_HANDLER_READY_WINDOW_SIZE
         self.destinations = {}
-        self.default_destination_id = 'local'
+        self.default_destination_id = None
         self.tools = {}
         self.tool_classes = {}
         self.resource_groups = {}
@@ -601,10 +601,11 @@ def __set_default_job_conf(self):
             self._set_default_handler_assignment_methods()
         else:
             self.app.application_stack.init_job_handling(self)
+        self.handler_ready_window_size = JobConfiguration.DEFAULT_HANDLER_READY_WINDOW_SIZE
         # Set the destination
         self.default_destination_id = "local"
-        self.destinations['local'] = [JobDestination(id='local', runner='local')]
-        log.debug('Done loading job configuration')
+        self.destinations["local"] = [JobDestination(id="local", runner="local")]
+        log.debug("Done loading job configuration")
 
     def get_tool_resource_xml(self, tool_id, tool_type):
         """Given a tool id, return XML elements describing parameters to
@@ -646,9 +647,8 @@ def __parse_resource_parameters(self):
     @staticmethod
     def get_params(config, parent):
         rval = {}
-        for param in parent.findall('param'):
-            key = param.get('id')
-            param_value: Union[str, List[Any]] = []
+        for param in parent.findall("param"):
+            key = param.get("id")
             if key in ["container", "container_override"]:
                 containers = map(requirements.container_from_element, param.findall("container"))
                 param_value = list(map(lambda c: c.to_dict(), containers))
@@ -996,9 +996,6 @@ def __init__(self, job: model.Job, app: MinimalManagerApp, use_persisted_destina
         # the path rewriter needs destination params, so it cannot be set up until after the destination has been
         # resolved
         self._job_io = None
-        self._dataset_path_rewriter = None
-        self.output_paths: List[DatasetPath] = None  # type: ignore[assignment]
-        self.output_hdas_and_paths: Dict[str, Union[List, Tuple]] = None  # type: ignore[assignment]
         self.tool_provided_job_metadata = None
         self.params = None
         if job.params:

lib/galaxy/tool_util/cwl/representation.py

@@ -9,7 +9,7 @@
     Any,
     Dict,
     NamedTuple,
-    Optional
+    Optional,
 )
 
 from galaxy.exceptions import RequestParameterInvalidException

lib/galaxy/tool_util/parser/yaml.py

@@ -1,10 +1,8 @@
 import json
-
-import packaging.version
 from typing import (
     Any,
     Dict,
-    List
+    List,
 )
 
 import packaging.version

mypy.ini

@@ -178,11 +178,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-galaxy.tools.bundled.filters.join]
 check_untyped_defs = False
-[mypy-galaxy.tool_util.output_checker]
-[mypy-galaxy.tools.bundled.data_source.hbvar_filter]
-check_untyped_defs = False
-[mypy-galaxy.tool_util.provided_metadata]
-check_untyped_defs = False
 [mypy-galaxy.tool_util.verify.test_data]
 check_untyped_defs = False
 [mypy-galaxy.tool_util.toolbox.parser]
@@ -271,12 +266,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-galaxy.model.database_utils]
 check_untyped_defs = False
-[mypy-galaxy.job_metrics.instrumenters.env]
-check_untyped_defs = False
-[mypy-galaxy.job_metrics.instrumenters.collectl]
-check_untyped_defs = False
-[mypy-galaxy.job_metrics.instrumenters.cgroup]
-check_untyped_defs = False
 [mypy-galaxy.datatypes.sniff]
 check_untyped_defs = False
 [mypy-galaxy.config.schema]
@@ -357,8 +346,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-galaxy.tool_util.deps]
 check_untyped_defs = False
-[mypy-galaxy.model.tool_shed_install.migrate.check]
-check_untyped_defs = False
 [mypy-galaxy.jobs.runners.util.cli.job.lsf]
 check_untyped_defs = False
 [mypy-galaxy.authnz.managers]
@@ -389,8 +376,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-tool_shed.dependencies.attribute_handlers]
 check_untyped_defs = False
-[mypy-galaxy.tool_shed.galaxy_install.tools.data_manager]
-check_untyped_defs = False
 [mypy-galaxy.tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager]
 check_untyped_defs = False
 [mypy-galaxy.datatypes.triples]