Merge pull request #15069 from jmchilton/mypy_unchecked_1

Address some of the new mypy notes about unchecked annotations.

lib/galaxy/tool_util/data/__init__.py

@@ -32,6 +32,7 @@ from typing import (
 )
 
 import requests
+from typing_extensions import TypedDict
 
 from galaxy import util
 from galaxy.exceptions import MessageException
@@ -102,9 +103,30 @@ class ToolDataPathFiles:
             return os.path.exists(path)
 
 
+ErrorListT = List[str]
+FileNameInfoT = TypedDict(
+    "FileNameInfoT",
+    {
+        "found": bool,
+        "filename": str,
+        "from_shed_config": bool,
+        "tool_data_path": Optional[StrPath],
+        "config_element": Optional[Element],
+        "tool_shed_repository": Optional[Dict[str, Any]],
+        "errors": ErrorListT,
+    },
+)
+LoadInfoT = Tuple[Tuple[Element, Optional[StrPath]], Dict[str, Any]]
+
+
 class ToolDataTable(Dictifiable):
     type_key: str
     data: List[List[str]]
+    empty_field_value: str
+    empty_field_values: Dict[Optional[str], str]
+    filenames: Dict[str, FileNameInfoT]
+    _load_info: LoadInfoT
+    _merged_load_info: List[Tuple[Type["ToolDataTable"], LoadInfoT]]
 
     @classmethod
     def from_dict(cls, d):
@@ -131,7 +153,7 @@ class ToolDataTable(Dictifiable):
         self.empty_field_values: Dict[str, str] = {}
         self.allow_duplicate_entries = util.asbool(config_element.get("allow_duplicate_entries", True))
         self.here = os.path.dirname(filename) if filename else None
-        self.filenames: Dict[str, Dict[str, Any]] = {}
+        self.filenames: Dict[str, FileNameInfoT] = {}
         self.tool_data_path = tool_data_path
         self.tool_data_path_files = tool_data_path_files
         self.other_config_dict = other_config_dict or {}
@@ -157,7 +179,7 @@ class ToolDataTable(Dictifiable):
             self._loaded_content_version += 1
         return self._loaded_content_version
 
-    def get_empty_field_by_name(self, name):
+    def get_empty_field_by_name(self, name: Optional[str]) -> str:
         return self.empty_field_values.get(name, self.empty_field_value)
 
     def _add_entry(
@@ -355,7 +377,7 @@ class TabularToolDataTable(ToolDataTable):
                         filename = f"{corrected_filename}.sample"
                         found = True
 
-            errors: List[str] = []
+            errors: ErrorListT = []
             if found:
                 self.extend_data_with(filename, errors=errors)
                 self._update_version()
@@ -478,14 +500,14 @@ class TabularToolDataTable(ToolDataTable):
         if "name" not in self.columns:
             self.columns["name"] = self.columns["value"]
 
-    def extend_data_with(self, filename: str, errors: Optional[List[str]] = None) -> None:
+    def extend_data_with(self, filename: str, errors: Optional[ErrorListT] = None) -> None:
         here = os.path.dirname(os.path.abspath(filename))
         self.data.extend(self.parse_file_fields(filename, errors=errors, here=here))
         if not self.allow_duplicate_entries:
             self._deduplicate_data()
 
     def parse_file_fields(
-        self, filename: str, errors: Optional[List[str]] = None, here: str = "__HERE__"
+        self, filename: str, errors: Optional[ErrorListT] = None, here: str = "__HERE__"
     ) -> List[List[str]]:
         """
         Parse separated lines from file and return a list of tuples.

lib/galaxy/tool_util/parser/xml.py

@@ -16,6 +16,7 @@ from galaxy.tool_util.parser.util import (
     DEFAULT_DELTA_FRAC,
 )
 from galaxy.util import (
+    Element,
     ElementTree,
     string_as_bool,
     xml_text,
@@ -56,6 +57,7 @@ class XmlToolSource(ToolSource):
     """Responsible for parsing a tool from classic Galaxy representation."""
 
     language = "xml"
+    root: Element
 
     def __init__(self, xml_tree: ElementTree, source_path=None, macro_paths=None):
         self.xml_tree = xml_tree

lib/galaxy/webapps/galaxy/controllers/admin.py

@@ -1,9 +1,11 @@
 import logging
+from typing import Set
 
 from sqlalchemy import (
     false,
     func,
 )
+from typing_extensions import TypedDict
 
 from galaxy import (
     model,
@@ -17,6 +19,7 @@ from galaxy.exceptions import (
 from galaxy.managers.quotas import QuotaManager
 from galaxy.model import tool_shed_install as install_model
 from galaxy.security.validate_user_input import validate_password
+from galaxy.structured_app import StructuredApp
 from galaxy.util import (
     nice_size,
     pretty_print_time_interval,
@@ -535,6 +538,10 @@ class ToolVersionListGrid(grids.Grid):
         return trans.install_model.context.query(self.model_class)
 
 
+# TODO: Convert admin UI to use the API and drop this.
+DatatypesEntryT = TypedDict("DatatypesEntryT", {"status": str, "keys": list, "data": list, "message": str})
+
+
 class AdminGalaxy(controller.JSAppLauncher):
 
     user_list_grid = UserListGrid()
@@ -564,7 +571,7 @@ class AdminGalaxy(controller.JSAppLauncher):
         "Resend Activation Email", condition=(lambda item: not item.active), allow_multiple=False
     )
 
-    def __init__(self, app):
+    def __init__(self, app: StructuredApp):
         super().__init__(app)
         self.quota_manager: QuotaManager = QuotaManager(app)
 
@@ -594,9 +601,9 @@ class AdminGalaxy(controller.JSAppLauncher):
     @web.expose
     @web.json
     @web.require_admin
-    def data_types_list(self, trans, **kwd):
+    def data_types_list(self, trans, **kwd) -> DatatypesEntryT:
         datatypes = []
-        keys = set()
+        keys: Set[str] = set()
         message = kwd.get("message", "")
         status = kwd.get("status", "done")
         for dtype in sorted(trans.app.datatypes_registry.datatype_elems, key=lambda dt: dt.get("extension")):

lib/galaxy_test/api/test_folder_contents.py

@@ -202,7 +202,7 @@ class TestFolderContentsApi(ApiTestCase):
             self._assert_index_count_is_correct(response, expected_contents_count=1)
 
     @requires_new_library
-    def test_index_permissions_include_deleted(self, history_id):
+    def test_index_permissions_include_deleted(self, history_id) -> None:
         folder_name = "Test Folder Contents Index permissions include deleted"
         folder_id = self._create_folder_in_library(folder_name)
 

test/unit/data/test_galaxy_mapping.py

@@ -239,7 +239,7 @@ class TestMappings(BaseModelTestCase):
         for i in range(elements):
             assert c1[i] == dces[i]
 
-    def test_dataset_instance_order(self):
+    def test_dataset_instance_order(self) -> None:
         u = model.User(email="mary@example.com", password="password")
         h1 = model.History(name="History 1", user=u)
         elements = []

test/unit/workflows/test_modules.py

@@ -257,7 +257,7 @@ class MapOverTestCase(NamedTuple):
     steps: Dict[int, Any]
 
 
-def _construct_steps_for_map_over():
+def _construct_steps_for_map_over() -> List[MapOverTestCase]:
     test_case = MapOverTestCase
     # these are the cartesian product of
     # data_input = ['dataset', 'list', 'list:pair', 'list:list']