Merge pull request galaxyproject#15185 from jmchilton/typathon_types_1

Small mypy improvements.

lib/galaxy/security/__init__.py

@@ -2,11 +2,24 @@
 Galaxy Security
 
 """
+from typing import (
+    List,
+    Optional,
+)
+
+from typing_extensions import Literal
+
 from galaxy.util.bunch import Bunch
 
+ActionModel = Literal["grant", "restrict"]
+
 
 class Action:
-    def __init__(self, action, description, model):
+    action: str
+    description: str
+    model: ActionModel
+
+    def __init__(self, action: str, description: str, model: ActionModel):
         self.action = action
         self.description = description
         self.model = model
@@ -42,14 +55,14 @@ class RBACAgent:
         ),
     )
 
-    def get_action(self, name, default=None):
+    def get_action(self, name: str, default: Optional[Action] = None) -> Optional[Action]:
         """Get a permitted action by its dict key or action name"""
         for k, v in self.permitted_actions.items():
             if k == name or v.action == name:
                 return v
         return default
 
-    def get_actions(self):
+    def get_actions(self) -> List[Action]:
         """Get all permitted actions as a list of Action objects"""
         return list(self.permitted_actions.__dict__.values())
 
@@ -165,5 +178,5 @@ def get_permitted_actions(filter=None):
     if filter is None:
         return RBACAgent.permitted_actions
     tmp_bunch = Bunch()
-    [tmp_bunch.__dict__.__setitem__(k, v) for k, v in RBACAgent.permitted_actions.items() if k.startswith(filter)]
+    [tmp_bunch.dict().__setitem__(k, v) for k, v in RBACAgent.permitted_actions.items() if k.startswith(filter)]
     return tmp_bunch

lib/galaxy/tool_util/verify/asserts/archive.py

@@ -17,7 +17,9 @@ def _extract_from_tar(bytes, fn):
             # so make this consistent for tar
             if ti.isdir():
                 return ""
-            with tar_temp.extractfile(fn) as member_fh:
+            tar_file = tar_temp.extractfile(fn)
+            assert tar_file is not None
+            with tar_file as member_fh:
                 return member_fh.read()
 
 

mypy.ini

@@ -75,8 +75,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-galaxy.tools.bundled.data_source.microbial_import_code]
 check_untyped_defs = False
-[mypy-galaxy.security]
-check_untyped_defs = False
 [mypy-galaxy.datatypes.converters.pileup_to_interval_index_converter]
 check_untyped_defs = False
 [mypy-galaxy.datatypes.converters.bgzip]
@@ -111,8 +109,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-galaxy.tools.bundled.filters.random_lines_two_pass]
 check_untyped_defs = False
-[mypy-galaxy.tool_util.verify.asserts.archive]
-check_untyped_defs = False
 [mypy-galaxy.tool_util.deps.brew_exts]
 check_untyped_defs = False
 [mypy-galaxy.model.item_attrs]

test/unit/data/model/test_model.py

@@ -13,3 +13,8 @@ def test_get_uuid():
 
     rval = model.get_uuid()
     assert isinstance(rval, UUID)
+
+
+def test_permitted_actions():
+    actions = model.Dataset.permitted_actions
+    assert actions and len(actions.values()) == 2