Merge pull request #15808 from nsoranzo/mypy_strict_equality

Enable ``strict_equality`` mypy option

lib/galaxy/datatypes/protocols.py

@@ -86,7 +86,7 @@ def get_converted_files_by_type(self, file_type):
     def get_mime(self) -> str:
         ...
 
-    def get_size(self) -> str:
+    def get_size(self) -> int:
         ...
 
     def has_data(self) -> bool:

lib/galaxy/model/__init__.py

@@ -27,6 +27,7 @@
     List,
     NamedTuple,
     Optional,
+    overload,
     Set,
     Tuple,
     Type,
@@ -102,6 +103,7 @@
 from sqlalchemy.orm.collections import attribute_mapped_collection
 from sqlalchemy.sql import exists
 from typing_extensions import (
+    Literal,
     Protocol,
     TypedDict,
 )
@@ -3915,16 +3917,24 @@ def extra_files_path_name(self):
     def _extra_files_rel_path(self):
         return self._extra_files_path or self.extra_files_path_name
 
-    def _calculate_size(self):
+    def _calculate_size(self) -> int:
         if self.external_filename:
             try:
                 return os.path.getsize(self.external_filename)
             except OSError:
                 return 0
-        else:
-            return self.object_store.size(self)
+        assert self.object_store
+        return self.object_store.size(self)
 
-    def get_size(self, nice_size=False, calculate_size=True):
+    @overload
+    def get_size(self, nice_size: Literal[False], calculate_size: bool = True) -> int:
+        ...
+
+    @overload
+    def get_size(self, nice_size: Literal[True], calculate_size: bool = True) -> str:
+        ...
+
+    def get_size(self, nice_size: bool = False, calculate_size: bool = True) -> Union[int, str]:
         """Returns the size of the data on disk"""
         if self.file_size:
             if nice_size:

lib/galaxy/objectstore/__init__.py

@@ -170,7 +170,7 @@ def empty(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt
         raise NotImplementedError()
 
     @abc.abstractmethod
-    def size(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+    def size(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False) -> int:
         """
         Return size of the object identified by `obj`.
 
@@ -850,7 +850,7 @@ def _empty(self, obj, **kwargs):
         """Override `ObjectStore`'s stub by checking file size on disk."""
         return self.size(obj, **kwargs) == 0
 
-    def _size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs) -> int:
         """Override `ObjectStore`'s stub by return file size on disk.
 
         Returns 0 if the object doesn't exist yet or other error.

lib/galaxy/objectstore/cloud.py

@@ -400,8 +400,7 @@ def _get_transfer_progress(self):
     def _get_size_in_cloud(self, rel_path):
         try:
             obj = self.bucket.objects.get(rel_path)
-            if obj:
-                return obj.size
+            return obj.size
         except Exception:
             log.exception("Could not get size of key '%s' from S3", rel_path)
             return -1

lib/galaxy/objectstore/irods.py

@@ -608,7 +608,7 @@ def _empty(self, obj, **kwargs):
         else:
             raise ObjectNotFound(f"objectstore.empty, object does not exist: {obj}, kwargs: {kwargs}")
 
-    def _size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs) -> int:
         ipt_timer = ExecutionTimer()
         rel_path = self._construct_path(obj, **kwargs)
         if self._in_cache(rel_path):

lib/galaxy/objectstore/pithos.py

@@ -309,7 +309,7 @@ def _empty(self, obj, **kwargs):
             raise ObjectNotFound(f"objectstore.empty, object does not exist: {obj}, kwargs: {kwargs}")
         return bool(self._size(obj, **kwargs))
 
-    def _size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs) -> int:
         """
         :returns: The size of the object, or 0 if it doesn't exist (sorry for
             that, not our fault, the ObjectStore interface is like that some

lib/galaxy/objectstore/s3.py

@@ -385,9 +385,8 @@ def _get_transfer_progress(self):
     def _get_size_in_s3(self, rel_path):
         try:
             key = self._bucket.get_key(rel_path)
-            if key:
-                return key.size
-        except S3ResponseError:
+            return key.size
+        except (S3ResponseError, AttributeError):
             log.exception("Could not get size of key '%s' from S3", rel_path)
             return -1
 

lib/galaxy/util/path/__init__.py

@@ -244,7 +244,7 @@ def __path_permission_for_user(path: GenericPath, username: str) -> bool:
     other_permissions = int(oct_mode[-1])
     if (
         other_permissions >= 4
-        or (file_owner == username and owner_permissions >= 4)
+        or (file_owner.pw_name == username and owner_permissions >= 4)
         or (username in group_members and group_permissions >= 4)
     ):
         return True

mypy.ini

@@ -6,6 +6,7 @@ exclude = lib/galaxy/tools/bundled|test/functional
 pretty = True
 no_implicit_reexport = True
 no_implicit_optional = True
+strict_equality = True
 
 # green list - work on growing these please!
 [mypy-galaxy.util.compression_utils]