From bfa60a039dee1d81685f685df991e6ea4c6cb812 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Tue, 9 Nov 2021 18:10:03 +0100
Subject: [PATCH] improve typing of lib/galaxy/tools/wrappers.py

---
 lib/galaxy/datatypes/binary.py                |  14 +-
 lib/galaxy/datatypes/data.py                  |  11 +-
 lib/galaxy/datatypes/registry.py              |   9 +-
 lib/galaxy/model/__init__.py                  |  37 +-
 lib/galaxy/model/metadata.py                  |  11 +-
 lib/galaxy/tools/parameters/basic.py          |   4 +-
 lib/galaxy/tools/parameters/wrapped_json.py   |  13 +-
 lib/galaxy/tools/wrappers.py                  | 386 +++++++++++++-----
 .../visualization/data_providers/genome.py    |   2 +-
 setup.cfg                                     |  12 +-
 test/unit/app/tools/test_wrappers.py          |  17 +-
 11 files changed, 362 insertions(+), 154 deletions(-)

diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py
index 9de3825e558..3d171cf1fe5 100644
--- a/lib/galaxy/datatypes/binary.py
+++ b/lib/galaxy/datatypes/binary.py
@@ -25,6 +25,7 @@ from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP
 from galaxy import util
 from galaxy.datatypes import metadata
 from galaxy.datatypes.data import (
+    Data,
     DatatypeValidation,
     get_file_peek,
 )
@@ -267,7 +268,10 @@ class Bref3(Binary):
 
 class DynamicCompressedArchive(CompressedArchive):
 
-    def matches_any(self, target_datatypes):
+    compressed_format: str
+    uncompressed_datatype_instance: Data
+
+    def matches_any(self, target_datatypes) -> bool:
         """Treat two aspects of compressed datatypes separately.
         """
         compressed_target_datatypes = []
@@ -281,8 +285,12 @@ class DynamicCompressedArchive(CompressedArchive):
 
         # TODO: Add gz and bz2 as proper datatypes and use those instances instead of
         # CompressedArchive() in the following check.
-        return self.uncompressed_datatype_instance.matches_any(uncompressed_target_datatypes) or \
-            CompressedArchive().matches_any(compressed_target_datatypes)
+        if not hasattr(self, "uncompressed_datatype_instance"):
+            raise Exception("Missing 'uncompressed_datatype_instance' attribute.")
+        else:
+            return self.uncompressed_datatype_instance.matches_any(
+                uncompressed_target_datatypes
+            ) or CompressedArchive().matches_any(compressed_target_datatypes)
 
 
 class GzDynamicCompressedArchive(DynamicCompressedArchive):
diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index ae2c9c89b7c..58926ca2e3a 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -6,7 +6,7 @@ import shutil
 import string
 import tempfile
 from inspect import isclass
-from typing import Any, Dict, Optional
+from typing import Any, Dict, List, Optional, Tuple, TYPE_CHECKING
 
 import webob.exc
 from markupsafe import escape
@@ -29,6 +29,9 @@ from . import (
     metadata
 )
 
+if TYPE_CHECKING:
+    from galaxy.model import DatasetInstance
+
 XSS_VULNERABLE_MIME_TYPES = [
     'image/svg+xml',  # Unfiltered by Galaxy and may contain JS that would be executed by some browsers.
     'application/xml',  # Some browsers will evalute SVG embedded JS in such XML documents.
@@ -633,7 +636,9 @@ class Data(metaclass=DataMeta):
         """Returns available converters by type for this dataset"""
         return datatypes_registry.get_converters_by_datatype(original_dataset.ext)
 
-    def find_conversion_destination(self, dataset, accepted_formats, datatypes_registry, **kwd):
+    def find_conversion_destination(
+        self, dataset, accepted_formats: List[str], datatypes_registry, **kwd
+    ) -> Tuple[bool, Optional[str], Optional["DatasetInstance"]]:
         """Returns ( direct_match, converted_ext, existing converted dataset )"""
         return datatypes_registry.find_conversion_destination_for_dataset_by_extensions(dataset, accepted_formats, **kwd)
 
@@ -726,7 +731,7 @@ class Data(metaclass=DataMeta):
     def has_resolution(self):
         return False
 
-    def matches_any(self, target_datatypes):
+    def matches_any(self, target_datatypes: List[Any]) -> bool:
         """
         Check if this datatype is of any of the target_datatypes or is
         a subtype thereof.
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index a2669f872ea..cf13e051355 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -6,7 +6,7 @@ import imp
 import logging
 import os
 from string import Template
-from typing import Dict
+from typing import Dict, List, Optional, Tuple, TYPE_CHECKING
 
 import yaml
 
@@ -28,6 +28,9 @@ from . import (
 )
 from .display_applications.application import DisplayApplication
 
+if TYPE_CHECKING:
+    from galaxy.model import DatasetInstance
+
 
 class ConfigurationError(Exception):
     pass
@@ -885,7 +888,9 @@ class Registry:
             return converters[target_ext]
         return None
 
-    def find_conversion_destination_for_dataset_by_extensions(self, dataset_or_ext, accepted_formats, converter_safe=True):
+    def find_conversion_destination_for_dataset_by_extensions(
+        self, dataset_or_ext, accepted_formats: List[str], converter_safe: bool = True
+    ) -> Tuple[bool, Optional[str], Optional["DatasetInstance"]]:
         """
         returns (direct_match, converted_ext, converted_dataset)
         - direct match is True iff no the data set already has an accepted format
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 29950ebfce1..a141cb910e2 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -27,6 +27,7 @@ from typing import (
     List,
     NamedTuple,
     Optional,
+    Tuple,
     Type,
     TYPE_CHECKING,
     Union,
@@ -143,6 +144,8 @@ AUTO_PROPAGATED_TAGS = ["name"]
 
 
 if TYPE_CHECKING:
+    from galaxy.datatypes.data import Data
+
     class _HasTable:
         table: Table
         __table__: Table
@@ -210,8 +213,9 @@ def set_datatypes_registry(d_registry):
 
 
 class HasTags:
-    dict_collection_visible_keys = ['tags']
-    dict_element_visible_keys = ['tags']
+    dict_collection_visible_keys = ["tags"]
+    dict_element_visible_keys = ["tags"]
+    tags: List["ItemTagAssociation"]
 
     def to_dict(self, *args, **kwargs):
         rval = super().to_dict(*args, **kwargs)
@@ -3449,7 +3453,7 @@ class DatasetHash(Base, Serializable):
         return rval
 
 
-def datatype_for_extension(extension, datatypes_registry=None):
+def datatype_for_extension(extension, datatypes_registry=None) -> "Data":
     if extension is not None:
         extension = extension.lower()
     if datatypes_registry is None:
@@ -3545,12 +3549,12 @@ class DatasetInstance(_HasTable):
                 object_session(self).flush()  # flush here, because hda.flush() won't flush the Dataset object
     state = property(get_dataset_state, set_dataset_state)
 
-    def get_file_name(self):
+    def get_file_name(self) -> str:
         if self.dataset.purged:
             return ""
         return self.dataset.get_file_name()
 
-    def set_file_name(self, filename):
+    def set_file_name(self, filename: str):
         return self.dataset.set_file_name(filename)
     file_name = property(get_file_name, set_file_name)
 
@@ -3568,7 +3572,7 @@ class DatasetInstance(_HasTable):
         return self.dataset.extra_files_path_exists()
 
     @property
-    def datatype(self):
+    def datatype(self) -> "Data":
         return datatype_for_extension(self.extension)
 
     def get_metadata(self):
@@ -3595,7 +3599,7 @@ class DatasetInstance(_HasTable):
                 meta_types.append(meta_type)
         return meta_types
 
-    def get_metadata_file_paths_and_extensions(self):
+    def get_metadata_file_paths_and_extensions(self) -> List[Tuple[str, str]]:
         metadata = self.metadata
         metadata_files = []
         for metadata_name in self.metadata_file_types:
@@ -3802,7 +3806,9 @@ class DatasetInstance(_HasTable):
     def can_convert_to(self, format):
         return format in self.get_converter_types()
 
-    def find_conversion_destination(self, accepted_formats, **kwd):
+    def find_conversion_destination(
+        self, accepted_formats: List[str], **kwd
+    ) -> Tuple[bool, Optional[str], Optional["DatasetInstance"]]:
         """Returns ( target_ext, existing converted dataset )"""
         return self.datatype.find_conversion_destination(self, accepted_formats, _get_datatypes_registry(), **kwd)
 
@@ -5263,7 +5269,9 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
         return [(row[:-2], row.extension, row.Dataset.file_name) for row in q]
 
     @property
-    def element_identifiers_extensions_paths_and_metadata_files(self):
+    def element_identifiers_extensions_paths_and_metadata_files(
+        self,
+    ) -> List[List[Any]]:
         q = self._get_nested_collection_attributes(
             element_attributes=('element_identifier',),
             hda_attributes=('extension',),
@@ -8125,6 +8133,7 @@ class ItemTagAssociation(Dictifiable):
     dict_element_visible_keys = dict_collection_visible_keys
     associated_item_names: List[str] = []
     user_tname: Column
+    user_value = Column(TrimmedString(255), index=True)
 
     def __init_subclass__(cls, **kwargs):
         super().__init_subclass__(**kwargs)
@@ -8151,7 +8160,6 @@ class HistoryTagAssociation(Base, ItemTagAssociation, RepresentById):
     user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    user_value = Column(TrimmedString(255), index=True)
     history = relationship('History', back_populates='tags')
     tag = relationship('Tag')
     user = relationship('User')
@@ -8167,7 +8175,6 @@ class HistoryDatasetAssociationTagAssociation(Base, ItemTagAssociation, Represen
     user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    user_value = Column(TrimmedString(255), index=True)
     history_dataset_association = relationship('HistoryDatasetAssociation', back_populates='tags')
     tag = relationship('Tag')
     user = relationship('User')
@@ -8183,7 +8190,6 @@ class LibraryDatasetDatasetAssociationTagAssociation(Base, ItemTagAssociation, R
     user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    user_value = Column(TrimmedString(255), index=True)
     library_dataset_dataset_association = relationship(
         'LibraryDatasetDatasetAssociation', back_populates='tags')
     tag = relationship('Tag')
@@ -8199,7 +8205,6 @@ class PageTagAssociation(Base, ItemTagAssociation, RepresentById):
     user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    user_value = Column(TrimmedString(255), index=True)
     page = relationship('Page', back_populates='tags')
     tag = relationship('Tag')
     user = relationship('User')
@@ -8214,7 +8219,6 @@ class WorkflowStepTagAssociation(Base, ItemTagAssociation, RepresentById):
     user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    user_value = Column(TrimmedString(255), index=True)
     workflow_step = relationship('WorkflowStep', back_populates='tags')
     tag = relationship('Tag')
     user = relationship('User')
@@ -8229,7 +8233,6 @@ class StoredWorkflowTagAssociation(Base, ItemTagAssociation, RepresentById):
     user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    user_value = Column(TrimmedString(255), index=True)
     stored_workflow = relationship('StoredWorkflow', back_populates='tags')
     tag = relationship('Tag')
     user = relationship('User')
@@ -8244,7 +8247,6 @@ class VisualizationTagAssociation(Base, ItemTagAssociation, RepresentById):
     user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    user_value = Column(TrimmedString(255), index=True)
     visualization = relationship('Visualization', back_populates='tags')
     tag = relationship('Tag')
     user = relationship('User')
@@ -8260,7 +8262,6 @@ class HistoryDatasetCollectionTagAssociation(Base, ItemTagAssociation, Represent
     user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    user_value = Column(TrimmedString(255), index=True)
     dataset_collection = relationship('HistoryDatasetCollectionAssociation', back_populates='tags')
     tag = relationship('Tag')
     user = relationship('User')
@@ -8276,7 +8277,6 @@ class LibraryDatasetCollectionTagAssociation(Base, ItemTagAssociation, Represent
     user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    user_value = Column(TrimmedString(255), index=True)
     dataset_collection = relationship('LibraryDatasetCollectionAssociation', back_populates='tags')
     tag = relationship('Tag')
     user = relationship('User')
@@ -8291,7 +8291,6 @@ class ToolTagAssociation(Base, ItemTagAssociation, RepresentById):
     user_id = Column(Integer, ForeignKey('galaxy_user.id'), index=True)
     user_tname = Column(TrimmedString(255), index=True)
     value = Column(TrimmedString(255), index=True)
-    user_value = Column(TrimmedString(255), index=True)
     tag = relationship('Tag')
     user = relationship('User')
 
diff --git a/lib/galaxy/model/metadata.py b/lib/galaxy/model/metadata.py
index 9d448d6df36..a77048b3f95 100644
--- a/lib/galaxy/model/metadata.py
+++ b/lib/galaxy/model/metadata.py
@@ -13,6 +13,7 @@ import weakref
 from collections import OrderedDict
 from collections.abc import Mapping
 from os.path import abspath
+from typing import Any, Iterator, TYPE_CHECKING, Union
 
 from sqlalchemy.orm import object_session
 from sqlalchemy.orm.attributes import flag_modified
@@ -28,6 +29,10 @@ from galaxy.util import (
 )
 from galaxy.util.json import safe_dumps
 
+if TYPE_CHECKING:
+    from galaxy.model import DatasetInstance
+    from galaxy.model.none_like import NoneDataset
+
 log = logging.getLogger(__name__)
 
 STATEMENTS = "__galaxy_statements__"  # this is the name of the property in a Datatype class where new metadata spec element Statements are stored
@@ -66,7 +71,7 @@ class MetadataCollection(Mapping):
     retrieved, returning default values in cases when metadata is not set.
     """
 
-    def __init__(self, parent):
+    def __init__(self, parent: Union["DatasetInstance", "NoneDataset"]) -> None:
         self.parent = parent
         # initialize dict if needed
         if self.parent._metadata is None:
@@ -88,7 +93,7 @@ class MetadataCollection(Mapping):
     def spec(self):
         return self.parent.datatype.metadata_spec
 
-    def __iter__(self):
+    def __iter__(self) -> Iterator[Any]:
         yield from self.spec.keys()
 
     def __getitem__(self, key):
@@ -142,7 +147,7 @@ class MetadataCollection(Mapping):
         else:
             log.info(f"Attempted to delete invalid key '{name}' from MetadataCollection")
 
-    def element_is_set(self, name):
+    def element_is_set(self, name) -> bool:
         """
         check if the meta data with the given name is set, i.e.
 
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index d085eeb73d4..3425f4d1828 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -256,7 +256,7 @@ class ToolParameter(Dictifiable):
             return str_value
         return "Not available."
 
-    def to_param_dict_string(self, value, other_values=None):
+    def to_param_dict_string(self, value, other_values=None) -> str:
         """Called via __str__ when used in the Cheetah template"""
         if value is None:
             value = ""
@@ -845,6 +845,8 @@ class SelectToolParameter(ToolParameter):
     y,z
     """
 
+    value_label: str
+
     def __init__(self, tool, input_source, context=None):
         input_source = ensure_input_source(input_source)
         super().__init__(tool, input_source)
diff --git a/lib/galaxy/tools/parameters/wrapped_json.py b/lib/galaxy/tools/parameters/wrapped_json.py
index 1e419204437..82c37e8dccb 100644
--- a/lib/galaxy/tools/parameters/wrapped_json.py
+++ b/lib/galaxy/tools/parameters/wrapped_json.py
@@ -1,4 +1,5 @@
 import logging
+from typing import Any, Dict, List, Sequence
 
 import packaging.version
 
@@ -33,8 +34,12 @@ def data_collection_input_to_path(v):
     return v.all_paths
 
 
-def data_collection_input_to_staging_path_and_source_path(v, invalid_chars=('/',), include_collection_name=False):
-    staging_paths = v.get_all_staging_paths(invalid_chars=invalid_chars, include_collection_name=include_collection_name)
+def data_collection_input_to_staging_path_and_source_path(
+    v, invalid_chars: Sequence[str] = ("/",), include_collection_name: bool = False
+) -> List[Dict[str, Any]]:
+    staging_paths = v.get_all_staging_paths(
+        invalid_chars=invalid_chars, include_collection_name=include_collection_name
+    )
     source_paths = v.all_paths
     metadata_files = v.all_metadata_files
     return [
@@ -44,7 +49,9 @@ def data_collection_input_to_staging_path_and_source_path(v, invalid_chars=('/',
          } for staging_path, source_path, metadata_files in zip(staging_paths, source_paths, metadata_files)]
 
 
-def data_input_to_staging_path_and_source_path(v, invalid_chars=('/',)):
+def data_input_to_staging_path_and_source_path(
+    v, invalid_chars: Sequence[str] = ("/",)
+) -> Dict[str, Any]:
     staging_path = v.get_staging_path(invalid_chars=invalid_chars)
     return {
         'staging_path': staging_path,
diff --git a/lib/galaxy/tools/wrappers.py b/lib/galaxy/tools/wrappers.py
index d91aeb189d8..80a575249ef 100644
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -3,8 +3,30 @@ import os
 import shlex
 import tempfile
 from functools import total_ordering
+from typing import (
+    Any,
+    cast,
+    Dict,
+    Iterable,
+    Iterator,
+    KeysView,
+    List,
+    Optional,
+    Sequence,
+    Tuple,
+    TYPE_CHECKING,
+    Union,
+)
 
 from galaxy import exceptions
+from galaxy.model import (
+    DatasetCollection,
+    DatasetCollectionElement,
+    DatasetCollectionInstance,
+    DatasetInstance,
+    HasTags,
+    HistoryDatasetCollectionAssociation,
+)
 from galaxy.model.none_like import NoneDataset
 from galaxy.security.object_wrapper import wrap_with_safe_string
 from galaxy.tools.parameters.wrapped_json import (
@@ -13,6 +35,13 @@ from galaxy.tools.parameters.wrapped_json import (
 )
 from galaxy.util import filesystem_safe_string
 
+if TYPE_CHECKING:
+    from galaxy.tools import Tool
+    from galaxy.tools.parameters.basic import SelectToolParameter, ToolParameter
+    from galaxy.datatypes.registry import Registry
+    from galaxy.jobs import ComputeEnvironment
+    from galaxy.model.metadata import MetadataCollection
+
 log = logging.getLogger(__name__)
 
 # Fields in .log files corresponding to paths, must have one of the following
@@ -27,11 +56,14 @@ class ToolParameterValueWrapper:
     Base class for object that Wraps a Tool Parameter and Value.
     """
 
-    def __bool__(self):
+    value: Union[str, List[str]]
+    input: "ToolParameter"
+
+    def __bool__(self) -> bool:
         return bool(self.value)
     __nonzero__ = __bool__
 
-    def get_display_text(self, quote=True):
+    def get_display_text(self, quote: bool = True) -> str:
         """
         Returns a string containing the value that would be displayed to the user in the tool interface.
         When quote is True (default), the string is escaped for e.g. command-line usage.
@@ -47,21 +79,21 @@ class RawObjectWrapper(ToolParameterValueWrapper):
     Wraps an object so that __str__ returns module_name:class_name.
     """
 
-    def __init__(self, obj):
+    def __init__(self, obj: Any):
         self.obj = obj
 
-    def __bool__(self):
+    def __bool__(self) -> bool:
         return bool(self.obj)  # FIXME: would it be safe/backwards compatible to rename .obj to .value, so that we can just inherit this method?
     __nonzero__ = __bool__
 
-    def __str__(self):
+    def __str__(self) -> str:
         try:
             return f"{self.obj.__module__}:{self.obj.__class__.__name__}"
         except Exception:
             # Most likely None, which lacks __module__.
             return str(self.obj)
 
-    def __getattr__(self, key):
+    def __getattr__(self, key: Any) -> Any:
         return getattr(self.obj, key)
 
 
@@ -71,12 +103,17 @@ class InputValueWrapper(ToolParameterValueWrapper):
     Wraps an input so that __str__ gives the "param_dict" representation.
     """
 
-    def __init__(self, input, value, other_values=None):
+    def __init__(
+        self,
+        input: "ToolParameter",
+        value: str,
+        other_values: Optional[Dict[str, str]] = None,
+    ) -> None:
         self.input = input
         self.value = value
-        self._other_values = other_values or {}
+        self._other_values: Dict[str, str] = other_values or {}
 
-    def _get_cast_value(self, other):
+    def _get_cast_value(self, other: Any) -> Union[str, int, float, bool, None]:
         if self.input.type == 'boolean' and isinstance(other, str):
             return str(self)
         # For backward compatibility, allow `$wrapper != ""` for optional non-text param
@@ -85,44 +122,46 @@ class InputValueWrapper(ToolParameterValueWrapper):
                 return str(self)
             else:
                 return None
-        cast = {
+        cast_table = {
             'text': str,
             'integer': int,
             'float': float,
             'boolean': bool,
         }
-        return cast.get(self.input.type, str)(self)
+        return cast(
+            Union[str, int, float, bool], cast_table.get(self.input.type, str)(self)
+        )
 
-    def __eq__(self, other):
-        return self._get_cast_value(other) == other
+    def __eq__(self, other: Any) -> bool:
+        return bool(self._get_cast_value(other) == other)
 
-    def __ne__(self, other):
+    def __ne__(self, other: Any) -> bool:
         return not self == other
 
-    def __str__(self):
+    def __str__(self) -> str:
         to_param_dict_string = self.input.to_param_dict_string(self.value, self._other_values)
         if isinstance(to_param_dict_string, list):
             return ','.join(to_param_dict_string)
         else:
             return to_param_dict_string
 
-    def __iter__(self):
+    def __iter__(self) -> Iterable[str]:
         to_param_dict_string = self.input.to_param_dict_string(self.value, self._other_values)
         if not isinstance(to_param_dict_string, list):
             return iter([to_param_dict_string])
         else:
             return iter(to_param_dict_string)
 
-    def __getattr__(self, key):
+    def __getattr__(self, key: Any) -> Any:
         return getattr(self.value, key)
 
-    def __gt__(self, other):
-        return self._get_cast_value(other) > other
+    def __gt__(self, other: Any) -> bool:
+        return bool(self._get_cast_value(other) > other)
 
-    def __int__(self):
+    def __int__(self) -> int:
         return int(float(self))
 
-    def __float__(self):
+    def __float__(self) -> float:
         return float(str(self))
 
 
@@ -132,20 +171,28 @@ class SelectToolParameterWrapper(ToolParameterValueWrapper):
     attributes are accessible.
     """
 
+    input: "SelectToolParameter"
+
     class SelectToolParameterFieldWrapper:
         """
         Provide access to any field by name or index for this particular value.
         Only applicable for dynamic_options selects, which have more than simple 'options' defined (name, value, selected).
         """
 
-        def __init__(self, input, value, other_values, compute_environment):
+        def __init__(
+            self,
+            input: "SelectToolParameter",
+            value: Union[str, List[str]],
+            other_values: Optional[Dict[str, str]],
+            compute_environment: Optional["ComputeEnvironment"],
+        ) -> None:
             self._input = input
             self._value = value
             self._other_values = other_values
-            self._fields = {}
+            self._fields: Dict[str, str] = {}
             self._compute_environment = compute_environment
 
-        def __getattr__(self, name):
+        def __getattr__(self, name: str) -> Any:
             if name not in self._fields:
                 self._fields[name] = self._input.options.get_field_by_name_for_value(name, self._value, None, self._other_values)
             values = map(str, self._fields[name])
@@ -158,12 +205,17 @@ class SelectToolParameterWrapper(ToolParameterValueWrapper):
                         new_values.append(rewrite_value)
                     else:
                         new_values.append(value)
-
-                values = new_values
+                return self._input.separator.join(new_values)
 
             return self._input.separator.join(values)
 
-    def __init__(self, input, value, other_values=None, compute_environment=None):
+    def __init__(
+        self,
+        input: "SelectToolParameter",
+        value: Union[str, List[str]],
+        other_values: Optional[Dict[str, str]] = None,
+        compute_environment: Optional["ComputeEnvironment"] = None,
+    ):
         self.input = input
         self.value = value
         self.input.value_label = input.value_to_display_text(value)
@@ -171,30 +223,32 @@ class SelectToolParameterWrapper(ToolParameterValueWrapper):
         self.compute_environment = compute_environment
         self.fields = self.SelectToolParameterFieldWrapper(input, value, other_values, self.compute_environment)
 
-    def __eq__(self, other):
+    def __eq__(self, other: Any) -> bool:
         if isinstance(other, str):
             if other == '' and self.value in (None, []):
                 # Allow $wrapper == '' for select (self.value is None) and multiple select (self.value is []) params
                 return True
             return str(self) == other
         else:
-            return super() == other
+            return super().__eq__(other)
 
-    def __ne__(self, other):
+    def __ne__(self, other: Any) -> bool:
         return not self == other
 
-    def __str__(self):
+    def __str__(self) -> str:
         # Assuming value is never a path - otherwise would need to pass
         # along following argument value_map=self._path_rewriter.
-        return self.input.to_param_dict_string(self.value, other_values=self._other_values)
+        return str(
+            self.input.to_param_dict_string(self.value, other_values=self._other_values)
+        )
 
-    def __add__(self, x):
+    def __add__(self, x: Any) -> str:
         return f'{self}{x}'
 
-    def __getattr__(self, key):
+    def __getattr__(self, key: Any) -> Any:
         return getattr(self.input, key)
 
-    def __iter__(self):
+    def __iter__(self) -> Iterable[str]:
         if not self.input.multiple:
             raise Exception("Tried to iterate over a non-multiple parameter.")
         return self.value.__iter__()
@@ -206,6 +260,8 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
     attributes are accessible.
     """
 
+    false_path: Optional[str]
+
     class MetadataWrapper:
         """
         Wraps a Metadata Collection to return MetadataParameters wrapped
@@ -213,12 +269,16 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
         of a Metadata Collection.
         """
 
-        def __init__(self, dataset, compute_environment=None):
+        def __init__(
+            self,
+            dataset: DatasetInstance,
+            compute_environment: Optional["ComputeEnvironment"] = None,
+        ) -> None:
             self.dataset = dataset
-            self.metadata = dataset.metadata
+            self.metadata: "MetadataCollection" = dataset.metadata
             self.compute_environment = compute_environment
 
-        def __getattr__(self, name):
+        def __getattr__(self, name: str) -> Any:
             rval = self.metadata.get(name, None)
             if name in self.metadata.spec:
                 if rval is None:
@@ -239,33 +299,49 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
                 rval = wrap_with_safe_string(rval)
             return rval
 
-        def __bool__(self):
-            return self.metadata.__nonzero__()
+        def __bool__(self) -> bool:
+            return bool(self.metadata.__nonzero__())
         __nonzero__ = __bool__
 
-        def __iter__(self):
+        def __iter__(self) -> Iterator[Any]:
             return self.metadata.__iter__()
 
-        def element_is_set(self, name):
+        def element_is_set(self, name: str) -> bool:
             return self.metadata.element_is_set(name)
 
-        def get(self, key, default=None):
+        def get(self, key: str, default: Any = None) -> Any:
             try:
                 return getattr(self, key)
             except Exception:
                 return default
 
-        def items(self):
+        def items(self) -> Iterator[Tuple[str, Any]]:
             return iter((k, self.get(k)) for k, v in self.metadata.items())
 
-    def __init__(self, dataset, datatypes_registry=None, tool=None, name=None, compute_environment=None, identifier=None, io_type="input", formats=None):
+    def __init__(
+        self,
+        dataset: Optional[DatasetInstance],
+        datatypes_registry: Optional["Registry"] = None,
+        tool: Optional["Tool"] = None,
+        name: Optional[str] = None,
+        compute_environment: Optional["ComputeEnvironment"] = None,
+        identifier: Optional[str] = None,
+        io_type: str = "input",
+        formats: Optional[List[str]] = None,
+    ) -> None:
         if not dataset:
             try:
                 # TODO: allow this to work when working with grouping
-                ext = tool.inputs[name].extensions[0]
+                ext = tool.inputs[name].extensions[0]  # type: ignore
             except Exception:
-                ext = 'data'
-            self.dataset = wrap_with_safe_string(NoneDataset(datatypes_registry=datatypes_registry, ext=ext), no_wrap_classes=ToolParameterValueWrapper)
+                ext = "data"
+            self.dataset = cast(
+                DatasetInstance,
+                wrap_with_safe_string(
+                    NoneDataset(datatypes_registry=datatypes_registry, ext=ext),
+                    no_wrap_classes=ToolParameterValueWrapper,
+                ),
+            )
         else:
             # Tool wrappers should not normally be accessing .dataset directly,
             # so we will wrap it and keep the original around for file paths
@@ -274,10 +350,11 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
                 direct_match, target_ext, converted_dataset = dataset.find_conversion_destination(formats)
                 if not direct_match and target_ext and converted_dataset:
                     dataset = converted_dataset
-            self.unsanitized = dataset
+            self.unsanitized: DatasetInstance = dataset
             self.dataset = wrap_with_safe_string(dataset, no_wrap_classes=ToolParameterValueWrapper)
+            assert dataset
             self.metadata = self.MetadataWrapper(dataset, compute_environment)
-            if hasattr(dataset, 'tags'):
+            if isinstance(dataset, HasTags):
                 self.groups = {tag.user_value.lower() for tag in dataset.tags if tag.user_tname == 'group'}
             else:
                 # May be a 'FakeDatasetAssociation'
@@ -301,21 +378,27 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
         self._element_identifier = identifier
 
     @property
-    def element_identifier(self):
+    def element_identifier(self) -> str:
         identifier = self._element_identifier
         if identifier is None:
             identifier = self.name
         return identifier
 
     @property
-    def file_ext(self):
-        return getattr(self.unsanitized.datatype, 'file_ext_export_alias', self.dataset.extension)
+    def file_ext(self) -> str:
+        return str(
+            getattr(
+                self.unsanitized.datatype,
+                "file_ext_export_alias",
+                self.dataset.extension,
+            )
+        )
 
     @property
-    def name_and_ext(self):
+    def name_and_ext(self) -> str:
         return f"{self.element_identifier}.{self.file_ext}"
 
-    def get_staging_path(self, invalid_chars=('/',)):
+    def get_staging_path(self, invalid_chars: Sequence[str] = ("/",)) -> str:
         """
         Strip leading dots, unicode null chars, replace `/` with `_`, truncate at 255 characters.
 
@@ -326,18 +409,26 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
         return f"{safe_element_identifier}.{self.file_ext}"
 
     @property
-    def all_metadata_files(self):
+    def all_metadata_files(self) -> List[Tuple[str, str]]:
         return self.unsanitized.get_metadata_file_paths_and_extensions() if self else []
 
-    def serialize(self, invalid_chars=('/',)):
-        return data_input_to_staging_path_and_source_path(self, invalid_chars=invalid_chars) if self else {}
+    def serialize(self, invalid_chars: Sequence[str] = ("/",)) -> Dict[str, Any]:
+        return (
+            data_input_to_staging_path_and_source_path(
+                self, invalid_chars=invalid_chars
+            )
+            if self
+            else {}
+        )
 
     @property
-    def is_collection(self):
+    def is_collection(self) -> bool:
         return False
 
-    def is_of_type(self, *exts):
+    def is_of_type(self, *exts: str) -> bool:
         datatypes = []
+        if not self.datatypes_registry:
+            raise Exception("datatypes_registry is required to use 'is_of_type'.")
         for e in exts:
             datatype = self.datatypes_registry.get_datatype_by_extension(e)
             if datatype is not None:
@@ -346,13 +437,13 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
                 log.warning(f"Datatype class not found for extension '{e}', which is used as parameter of 'is_of_type()' method")
         return self.dataset.datatype.matches_any(datatypes)
 
-    def __str__(self):
+    def __str__(self) -> str:
         if self.false_path is not None:
             return self.false_path
         else:
-            return self.unsanitized.file_name
+            return str(self.unsanitized.file_name)
 
-    def __getattr__(self, key):
+    def __getattr__(self, key: Any) -> Any:
         if self.false_path is not None and key == 'file_name':
             # Path to dataset was rewritten for this job.
             return self.false_path
@@ -385,17 +476,24 @@ class DatasetFilenameWrapper(ToolParameterValueWrapper):
         else:
             return getattr(self.dataset, key)
 
-    def __bool__(self):
+    def __bool__(self) -> bool:
         return bool(self.dataset)
     __nonzero__ = __bool__
 
 
 class HasDatasets:
 
-    def _dataset_wrapper(self, dataset, **kwargs):
+    job_working_directory: Optional[str]
+
+    def __iter__(self) -> Iterator[Any]:
+        pass
+
+    def _dataset_wrapper(
+        self, dataset: DatasetInstance, **kwargs: Any
+    ) -> DatasetFilenameWrapper:
         return DatasetFilenameWrapper(dataset, **kwargs)
 
-    def paths_as_file(self, sep="\n"):
+    def paths_as_file(self, sep: str = "\n") -> str:
         contents = sep.join(map(str, self))
         with tempfile.NamedTemporaryFile(mode='w+', prefix="gx_file_list", dir=self.job_working_directory, delete=False) as fh:
             fh.write(contents)
@@ -403,28 +501,54 @@ class HasDatasets:
         return filepath
 
 
-class DatasetListWrapper(list, ToolParameterValueWrapper, HasDatasets):
-    """
-    """
+class DatasetListWrapper(
+    List[DatasetFilenameWrapper], ToolParameterValueWrapper, HasDatasets
+):
+    """ """
 
-    def __init__(self, job_working_directory, datasets, **kwargs):
-        self._dataset_elements_cache = {}
-        if not isinstance(datasets, list):
+    def __init__(
+        self,
+        job_working_directory: Optional[str],
+        datasets: Union[
+            Sequence[
+                Union[
+                    None,
+                    DatasetInstance,
+                    DatasetCollectionInstance,
+                    DatasetCollectionElement,
+                ]
+            ],
+            DatasetInstance,
+        ],
+        **kwargs: Any,
+    ) -> None:
+        self._dataset_elements_cache: Dict[str, List[DatasetFilenameWrapper]] = {}
+        if not isinstance(datasets, Sequence):
             datasets = [datasets]
 
-        def to_wrapper(dataset):
-            if hasattr(dataset, "dataset_instance"):
-                element = dataset
-                dataset = element.dataset_instance
-                kwargs["identifier"] = element.element_identifier
-            return self._dataset_wrapper(dataset, **kwargs)
+        def to_wrapper(
+            dataset: Union[
+                None,
+                DatasetInstance,
+                DatasetCollectionInstance,
+                DatasetCollectionElement,
+            ]
+        ) -> DatasetFilenameWrapper:
+            if isinstance(dataset, DatasetCollectionElement):
+                dataset2 = dataset.dataset_instance
+                kwargs["identifier"] = dataset.element_identifier
+            else:
+                dataset2 = dataset
+            return self._dataset_wrapper(dataset2, **kwargs)
 
         list.__init__(self, map(to_wrapper, datasets))
         self.job_working_directory = job_working_directory
 
     @staticmethod
-    def to_dataset_instances(dataset_instance_sources):
-        dataset_instances = []
+    def to_dataset_instances(
+        dataset_instance_sources: Any,
+    ) -> List[Union[None, DatasetInstance]]:
+        dataset_instances: List[Optional[DatasetInstance]] = []
         if not isinstance(dataset_instance_sources, list):
             dataset_instance_sources = [dataset_instance_sources]
         for dataset_instance_source in dataset_instance_sources:
@@ -438,7 +562,7 @@ class DatasetListWrapper(list, ToolParameterValueWrapper, HasDatasets):
                 dataset_instances.extend(dataset_instance_source.collection.dataset_elements)
         return dataset_instances
 
-    def get_datasets_for_group(self, group):
+    def get_datasets_for_group(self, group: str) -> List[DatasetFilenameWrapper]:
         group = str(group).lower()
         if not self._dataset_elements_cache.get(group):
             wrappers = []
@@ -448,25 +572,37 @@ class DatasetListWrapper(list, ToolParameterValueWrapper, HasDatasets):
             self._dataset_elements_cache[group] = wrappers
         return self._dataset_elements_cache[group]
 
-    def serialize(self, invalid_chars=('/',)):
+    def serialize(self, invalid_chars: Sequence[str] = ("/",)) -> List[Dict[str, Any]]:
         return [v.serialize(invalid_chars) for v in self]
 
-    def __str__(self):
+    def __str__(self) -> str:
         return ','.join(map(str, self))
 
-    def __bool__(self):
+    def __bool__(self) -> bool:
         # Fail `#if $param` checks in cheetah if optional input is not provided
         return any(self)
     __nonzero__ = __bool__
 
 
 class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
+    name: Optional[str]
+    collection: DatasetCollection
 
-    def __init__(self, job_working_directory, has_collection, datatypes_registry, **kwargs):
+    def __init__(
+        self,
+        job_working_directory: Optional[str],
+        has_collection: Union[
+            None, DatasetCollectionElement, HistoryDatasetCollectionAssociation
+        ],
+        datatypes_registry: "Registry",
+        **kwargs: Any,
+    ) -> None:
         super().__init__()
         self.job_working_directory = job_working_directory
-        self._dataset_elements_cache = {}
-        self._element_identifiers_extensions_paths_and_metadata_files = None
+        self._dataset_elements_cache: Dict[str, List[DatasetFilenameWrapper]] = {}
+        self._element_identifiers_extensions_paths_and_metadata_files: Optional[
+            List[List[Any]]
+        ] = None
         self.datatypes_registry = datatypes_registry
         kwargs['datatypes_registry'] = datatypes_registry
         self.kwargs = kwargs
@@ -477,12 +613,10 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
         else:
             self.__input_supplied = True
 
-        if hasattr(has_collection, "name"):
-            # It is a HistoryDatasetCollectionAssociation
+        if isinstance(has_collection, HistoryDatasetCollectionAssociation):
             collection = has_collection.collection
             self.name = has_collection.name
-        elif hasattr(has_collection, "child_collection"):
-            # It is a DatasetCollectionElement instance referencing another collection
+        elif isinstance(has_collection, DatasetCollectionElement):
             collection = has_collection.child_collection
             self.name = has_collection.element_identifier
         else:
@@ -499,7 +633,11 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
             element_identifier = dataset_collection_element.element_identifier
 
             if dataset_collection_element.is_collection:
-                element_wrapper = DatasetCollectionWrapper(job_working_directory, dataset_collection_element, **kwargs)
+                element_wrapper: Union[
+                    DatasetCollectionWrapper, DatasetFilenameWrapper
+                ] = DatasetCollectionWrapper(
+                    job_working_directory, dataset_collection_element, **kwargs
+                )
             else:
                 element_wrapper = self._dataset_wrapper(element_object, identifier=element_identifier, **kwargs)
 
@@ -509,7 +647,7 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
         self.__element_instances = element_instances
         self.__element_instance_list = element_instance_list
 
-    def get_datasets_for_group(self, group):
+    def get_datasets_for_group(self, group: str) -> List[DatasetFilenameWrapper]:
         group = str(group).lower()
         if not self._dataset_elements_cache.get(group):
             wrappers = []
@@ -519,37 +657,47 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
             self._dataset_elements_cache[group] = wrappers
         return self._dataset_elements_cache[group]
 
-    def keys(self):
+    def keys(self) -> Union[List[str], KeysView[Any]]:
         if not self.__input_supplied:
             return []
         return self.__element_instances.keys()
 
     @property
-    def is_collection(self):
+    def is_collection(self) -> bool:
         return True
 
     @property
-    def element_identifier(self):
+    def element_identifier(self) -> Optional[str]:
         return self.name
 
     @property
-    def all_paths(self):
+    def all_paths(self) -> List[str]:
         return [path for _, _, path, _ in self.element_identifiers_extensions_paths_and_metadata_files]
 
     @property
-    def all_metadata_files(self):
+    def all_metadata_files(self) -> List[List[str]]:
         return [metadata_files for _, _, _, metadata_files in self.element_identifiers_extensions_paths_and_metadata_files]
 
     @property
-    def element_identifiers_extensions_paths_and_metadata_files(self):
+    def element_identifiers_extensions_paths_and_metadata_files(
+        self,
+    ) -> List[List[Any]]:
         if self._element_identifiers_extensions_paths_and_metadata_files is None:
             if self.collection:
-                self._element_identifiers_extensions_paths_and_metadata_files = self.collection.element_identifiers_extensions_paths_and_metadata_files
+                result = (
+                    self.collection.element_identifiers_extensions_paths_and_metadata_files
+                )
+                self._element_identifiers_extensions_paths_and_metadata_files = result
+                return result
             else:
                 return []
         return self._element_identifiers_extensions_paths_and_metadata_files
 
-    def get_all_staging_paths(self, invalid_chars=('/',), include_collection_name=False):
+    def get_all_staging_paths(
+        self,
+        invalid_chars: Sequence[str] = ("/",),
+        include_collection_name: bool = False,
+    ) -> List[str]:
         safe_element_identifiers = []
         for element_identifiers, extension, *_ in self.element_identifiers_extensions_paths_and_metadata_files:
             datatype = self.datatypes_registry.get_datatype_by_extension(extension)
@@ -559,7 +707,7 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
             for element_identifier in element_identifiers:
                 max_len = 254 - len(extension)
                 if include_collection_name:
-                    max_len = max_len - (len(self.name) + 1)
+                    max_len = max_len - (len(self.name or "") + 1)
                     assert max_len >= 1, 'Could not stage element, element identifier is too long'
                 current_element_identifier = filesystem_safe_string(element_identifier, max_len=max_len, invalid_chars=invalid_chars)
                 if include_collection_name and self.name:
@@ -569,14 +717,24 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
             safe_element_identifiers.append(f'{os.path.sep.join(current_element_identifiers)}.{extension}')
         return safe_element_identifiers
 
-    def serialize(self, invalid_chars=('/',), include_collection_name=False):
-        return data_collection_input_to_staging_path_and_source_path(self, invalid_chars=invalid_chars, include_collection_name=include_collection_name)
+    def serialize(
+        self,
+        invalid_chars: Sequence[str] = ("/",),
+        include_collection_name: bool = False,
+    ) -> List[Dict[str, Any]]:
+        return data_collection_input_to_staging_path_and_source_path(
+            self,
+            invalid_chars=invalid_chars,
+            include_collection_name=include_collection_name,
+        )
 
     @property
-    def is_input_supplied(self):
+    def is_input_supplied(self) -> bool:
         return self.__input_supplied
 
-    def __getitem__(self, key):
+    def __getitem__(
+        self, key: Union[str, int]
+    ) -> Union[None, "DatasetCollectionWrapper", DatasetFilenameWrapper]:
         if not self.__input_supplied:
             return None
         if isinstance(key, int):
@@ -584,7 +742,9 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
         else:
             return self.__element_instances[key]
 
-    def __getattr__(self, key):
+    def __getattr__(
+        self, key: str
+    ) -> Union[None, "DatasetCollectionWrapper", DatasetFilenameWrapper]:
         if not self.__input_supplied:
             return None
         try:
@@ -592,12 +752,14 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
         except KeyError:
             raise AttributeError()
 
-    def __iter__(self):
+    def __iter__(
+        self,
+    ) -> Iterator[Union["DatasetCollectionWrapper", DatasetFilenameWrapper]]:
         if not self.__input_supplied:
             return [].__iter__()
         return self.__element_instance_list.__iter__()
 
-    def __bool__(self):
+    def __bool__(self) -> bool:
         # Fail `#if $param` checks in cheetah is optional input
         # not specified or if resulting collection is empty.
         return self.__input_supplied and bool(self.__element_instance_list)
@@ -607,13 +769,15 @@ class DatasetCollectionWrapper(ToolParameterValueWrapper, HasDatasets):
 class ElementIdentifierMapper:
     """Track mapping of dataset collection elements datasets to element identifiers."""
 
-    def __init__(self, input_datasets=None):
+    def __init__(self, input_datasets: Optional[Dict[str, Any]] = None) -> None:
         if input_datasets is not None:
             self.identifier_key_dict = {v: f"{k}|__identifier__" for k, v in input_datasets.items()}
         else:
             self.identifier_key_dict = {}
 
-    def identifier(self, dataset_value, input_values):
+    def identifier(
+        self, dataset_value: str, input_values: Dict[str, str]
+    ) -> Optional[str]:
         identifier_key = self.identifier_key_dict.get(dataset_value, None)
         element_identifier = None
         if identifier_key:
diff --git a/lib/galaxy/visualization/data_providers/genome.py b/lib/galaxy/visualization/data_providers/genome.py
index 0291258bc38..cd6f5d622ba 100644
--- a/lib/galaxy/visualization/data_providers/genome.py
+++ b/lib/galaxy/visualization/data_providers/genome.py
@@ -234,7 +234,7 @@ class GenomeDataProvider(BaseDataProvider):
         """
         # Get column names.
         try:
-            column_names = self.original_dataset.datatype.column_names
+            column_names = self.original_dataset.datatype.column_names  # type: ignore
         except AttributeError:
             try:
                 column_names = list(range(self.original_dataset.metadata.columns))
diff --git a/setup.cfg b/setup.cfg
index d6001d672f8..a85298c1255 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -414,7 +414,17 @@ check_untyped_defs = False
 [mypy-tool_shed.util.metadata_util]
 check_untyped_defs = False
 [mypy-galaxy.tools.wrappers]
-check_untyped_defs = False
+disallow_any_generics = True
+disallow_subclassing_any = True
+disallow_untyped_calls = False
+disallow_untyped_defs = True
+disallow_incomplete_defs = True
+check_untyped_defs = True
+disallow_untyped_decorators = True
+no_implicit_optional = True
+warn_unused_ignores = True
+no_implicit_reexport = True
+strict_equality = True
 [mypy-galaxy.tools.error_reports.plugins.base_git]
 check_untyped_defs = False
 [mypy-galaxy.tool_util.deps.mulled.mulled_build]
diff --git a/test/unit/app/tools/test_wrappers.py b/test/unit/app/tools/test_wrappers.py
index 6a025569b68..fb94a026280 100644
--- a/test/unit/app/tools/test_wrappers.py
+++ b/test/unit/app/tools/test_wrappers.py
@@ -1,11 +1,14 @@
 import os
 import tempfile
+from typing import cast
 from unittest.mock import Mock
 
 import pytest
 
 from galaxy.datatypes.metadata import MetadataSpecCollection
 from galaxy.job_execution.datasets import DatasetPath
+from galaxy.jobs import ComputeEnvironment
+from galaxy.model import DatasetInstance
 from galaxy.tools.parameters.basic import (
     BooleanToolParameter,
     DrillDownSelectToolParameter,
@@ -101,7 +104,7 @@ def test_select_wrapper_multiple(tool):
 @with_mock_tool
 def test_select_wrapper_with_path_rewritting(tool):
     parameter = _setup_blast_tool(tool, multiple=True)
-    compute_environment = MockComputeEnvironment(None)
+    compute_environment = cast(ComputeEnvironment, MockComputeEnvironment(None))
     wrapper = SelectToolParameterWrapper(parameter, ["val1", "val2"], other_values={}, compute_environment=compute_environment)
     assert wrapper.fields.path == "Rewrite<path1>,Rewrite<path2>"
 
@@ -190,7 +193,7 @@ def test_input_value_wrapper_input_value_wrapper_comparison(tool):
 
 
 def test_dataset_wrapper():
-    dataset = MockDataset()
+    dataset = cast(DatasetInstance, MockDataset())
     wrapper = DatasetFilenameWrapper(dataset)
     assert str(wrapper) == MOCK_DATASET_PATH
     assert wrapper.file_name == MOCK_DATASET_PATH
@@ -199,9 +202,9 @@ def test_dataset_wrapper():
 
 
 def test_dataset_wrapper_false_path():
-    dataset = MockDataset()
+    dataset = cast(DatasetInstance, MockDataset())
     new_path = "/new/path/dataset_123.dat"
-    wrapper = DatasetFilenameWrapper(dataset, compute_environment=MockComputeEnvironment(false_path=new_path))
+    wrapper = DatasetFilenameWrapper(dataset, compute_environment=cast(ComputeEnvironment, MockComputeEnvironment(false_path=new_path)))
     assert str(wrapper) == new_path
     assert wrapper.file_name == new_path
 
@@ -223,19 +226,19 @@ class MockComputeEnvironment:
 
 
 def test_dataset_false_extra_files_path():
-    dataset = MockDataset()
+    dataset = cast(DatasetInstance, MockDataset())
 
     wrapper = DatasetFilenameWrapper(dataset)
     assert wrapper.extra_files_path == MOCK_DATASET_EXTRA_FILES_PATH
 
     new_path = "/new/path/dataset_123.dat"
     dataset_path = DatasetPath(123, MOCK_DATASET_PATH, false_path=new_path)
-    wrapper = DatasetFilenameWrapper(dataset, compute_environment=MockComputeEnvironment(dataset_path))
+    wrapper = DatasetFilenameWrapper(dataset, compute_environment=cast(ComputeEnvironment, MockComputeEnvironment(dataset_path)))
     # Setting false_path is not enough to override
     assert wrapper.extra_files_path == MOCK_DATASET_EXTRA_FILES_PATH
 
     new_files_path = "/new/path/dataset_123_files"
-    wrapper = DatasetFilenameWrapper(dataset, compute_environment=MockComputeEnvironment(false_path=new_path, false_extra_files_path=new_files_path))
+    wrapper = DatasetFilenameWrapper(dataset, compute_environment=cast(ComputeEnvironment, MockComputeEnvironment(false_path=new_path, false_extra_files_path=new_files_path)))
     assert wrapper.extra_files_path == new_files_path