Merge pull request #13519 from jmchilton/no_implicit_optional

Disable implicit optional types.

lib/galaxy/managers/datasets.py

@@ -7,6 +7,7 @@ import os
 from typing import (
     Dict,
     List,
+    Optional,
     Type,
     TypeVar,
 )
@@ -526,7 +527,7 @@ class _UnflattenedMetadataDatasetAssociationSerializer(base.ModelSerializer[T],
         # because of that: we need to add a few keys that will use the default serializer
         self.serializable_keyset.update(["name", "state", "tool_version", "extension", "visible", "dbkey"])
 
-    def _proxy_to_dataset(self, serializer: base.Serializer = None, proxy_key=None):
+    def _proxy_to_dataset(self, serializer: Optional[base.Serializer] = None, proxy_key: Optional[str] = None):
         # dataset associations are (rough) proxies to datasets - access their serializer using this remapping fn
         # remapping done by either kwarg key: IOW dataset attr key (e.g. uuid)
         # or by kwarg serializer: a function that's passed in (e.g. permissions)

lib/galaxy/model/unittest_utils/data_app.py

@@ -8,6 +8,7 @@ galaxy-data.
 import os
 import shutil
 import tempfile
+from typing import Optional
 
 from galaxy import (
     model,
@@ -76,7 +77,7 @@ class GalaxyDataTestApp:
     model: GalaxyModelMapping
     security_agent: GalaxyRBACAgent
 
-    def __init__(self, config: GalaxyDataTestConfig = None, **kwd):
+    def __init__(self, config: Optional[GalaxyDataTestConfig] = None, **kwd):
         config = config or GalaxyDataTestConfig(**kwd)
         self.config = config
         self.security = config.security

lib/galaxy/tool_util/deps/conda_util.py

@@ -8,7 +8,10 @@ import shlex
 import shutil
 import sys
 import tempfile
-from typing import List
+from typing import (
+    List,
+    Optional,
+)
 
 import packaging.version
 
@@ -305,7 +308,7 @@ class CondaContext(installable.InstallableContext):
             stdout_path = "/dev/null"
         return self.exec_command("clean", clean_args, stdout_path=stdout_path)
 
-    def exec_search(self, args: List[str], json: bool = False, offline: bool = False, platform: str = None):
+    def exec_search(self, args: List[str], json: bool = False, offline: bool = False, platform: Optional[str] = None):
         """
         Search conda channels for a package
 
@@ -513,7 +516,9 @@ def cleanup_failed_install(conda_target, conda_context=None):
     cleanup_failed_install_of_environment(conda_target.install_environment, conda_context=conda_context)
 
 
-def best_search_result(conda_target, conda_context: CondaContext, offline: bool = False, platform: str = None):
+def best_search_result(
+    conda_target, conda_context: CondaContext, offline: bool = False, platform: Optional[str] = None
+):
     """Find best "conda search" result for specified target.
 
     Return ``None`` if no results match.

lib/galaxy/tool_util/linters/tests.py

@@ -1,4 +1,5 @@
 """This module contains a linting functions for tool tests."""
+import typing
 from inspect import (
     Parameter,
     signature,
@@ -118,12 +119,16 @@ def _check_asserts(test_idx, assertions, lint_ctx):
                 if attrib not in assert_function_sig.parameters:
                     lint_ctx.error(f"Test {test_idx}: unknown attribute '{attrib}' for '{a.tag}'", node=a)
                     continue
-                if assert_function_sig.parameters[attrib].annotation is not Parameter.empty:
+                annotation = assert_function_sig.parameters[attrib].annotation
+                annotation = _handle_optionals(annotation)
+                if annotation is not Parameter.empty:
                     try:
-                        assert_function_sig.parameters[attrib].annotation(a.attrib[attrib])
+                        annotation(a.attrib[attrib])
+                    except TypeError:
+                        raise Exception(f"Faild to instantiate {attrib} for {assert_function_name}")
                     except ValueError:
                         lint_ctx.error(
-                            f"Test {test_idx}: attribute '{attrib}' for '{a.tag}' needs to be '{assert_function_sig.parameters[attrib].annotation.__name__}' got '{a.attrib[attrib]}'",
+                            f"Test {test_idx}: attribute '{attrib}' for '{a.tag}' needs to be '{annotation.__name__}' got '{a.attrib[attrib]}'",
                             node=a,
                         )
             # check missing required attributes
@@ -141,6 +146,13 @@ def _check_asserts(test_idx, assertions, lint_ctx):
                     lint_ctx.error(f"Test {test_idx}: '{a.tag}' needs to specify 'n', 'min', or 'max'", node=a)
 
 
+def _handle_optionals(annotation):
+    as_dict = annotation.__dict__
+    if "__origin__" in as_dict and as_dict["__origin__"] == typing.Union:
+        return as_dict["__args__"][0]
+    return annotation
+
+
 def _collect_output_names(tool_xml):
     output_data_names = []
     output_collection_names = []

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

@@ -3,6 +3,7 @@ import re
 import tarfile
 import tempfile
 import zipfile
+from typing import Optional
 
 from galaxy.util import asbool
 from ._util import _assert_presence_number
@@ -55,10 +56,10 @@ def assert_has_archive_member(
     verify_assertions_function,
     children,
     all="false",
-    n: int = None,
+    n: Optional[int] = None,
     delta: int = 0,
-    min: int = None,
-    max: int = None,
+    min: Optional[int] = None,
+    max: Optional[int] = None,
     negate: bool = False,
 ):
     """Recursively checks the specified children assertions against the text of

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

@@ -1,8 +1,15 @@
+from typing import Optional
+
 from ._util import _assert_number
 
 
 def assert_has_size(
-    output_bytes, value: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False
+    output_bytes,
+    value: Optional[int] = None,
+    delta: int = 0,
+    min: Optional[int] = None,
+    max: Optional[int] = None,
+    negate: bool = False,
 ):
     """
     Asserts the specified output has a size of the specified value,

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

@@ -1,4 +1,5 @@
 import re
+from typing import Optional
 
 from ._util import _assert_number
 
@@ -18,7 +19,14 @@ def get_first_line(output, comment):
 
 
 def assert_has_n_columns(
-    output, n: int = None, delta: int = 0, min: int = None, max: int = None, sep="\t", comment="", negate: bool = False
+    output,
+    n: Optional[int] = None,
+    delta: int = 0,
+    min: Optional[int] = None,
+    max: Optional[int] = None,
+    sep="\t",
+    comment="",
+    negate: bool = False,
 ):
     """Asserts the tabular output contains n columns. The optional
     sep argument specifies the column seperator used to determine the

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

@@ -1,4 +1,5 @@
 import re
+from typing import Optional
 
 from ._util import (
     _assert_number,
@@ -7,7 +8,13 @@ from ._util import (
 
 
 def assert_has_text(
-    output, text, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False
+    output,
+    text,
+    n: Optional[int] = None,
+    delta: int = 0,
+    min: Optional[int] = None,
+    max: Optional[int] = None,
+    negate: bool = False,
 ):
     """Asserts specified output contains the substring specified by
     the argument text. The exact number of occurrences can be
@@ -37,7 +44,13 @@ def assert_not_has_text(output, text):
 
 
 def assert_has_line(
-    output, line, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False
+    output,
+    line,
+    n: Optional[int] = None,
+    delta: int = 0,
+    min: Optional[int] = None,
+    max: Optional[int] = None,
+    negate: bool = False,
 ):
     """Asserts the specified output contains the line specified by the
     argument line. The exact number of occurrences can be optionally
@@ -59,7 +72,14 @@ def assert_has_line(
     )
 
 
-def assert_has_n_lines(output, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False):
+def assert_has_n_lines(
+    output,
+    n: Optional[int] = None,
+    delta: int = 0,
+    min: Optional[int] = None,
+    max: Optional[int] = None,
+    negate: bool = False,
+):
     """Asserts the specified output contains ``n`` lines allowing
     for a difference in the number of lines (delta)
     or relative differebce in the number of lines"""
@@ -78,7 +98,13 @@ def assert_has_n_lines(output, n: int = None, delta: int = 0, min: int = None, m
 
 
 def assert_has_text_matching(
-    output, expression, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False
+    output,
+    expression,
+    n: Optional[int] = None,
+    delta: int = 0,
+    min: Optional[int] = None,
+    max: Optional[int] = None,
+    negate: bool = False,
 ):
     """Asserts the specified output contains text matching the
     regular expression specified by the argument expression.
@@ -102,7 +128,13 @@ def assert_has_text_matching(
 
 
 def assert_has_line_matching(
-    output, expression, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False
+    output,
+    expression,
+    n: Optional[int] = None,
+    delta: int = 0,
+    min: Optional[int] = None,
+    max: Optional[int] = None,
+    negate: bool = False,
 ):
     """Asserts the specified output contains a line matching the
     regular expression specified by the argument expression. If n is given

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

@@ -1,4 +1,5 @@
 import re
+from typing import Optional
 
 from lxml.etree import XMLSyntaxError
 
@@ -28,7 +29,13 @@ def assert_has_element_with_path(output, path, negate: bool = False):
 
 
 def assert_has_n_elements_with_path(
-    output, path, n: int = None, delta: int = 0, min: int = None, max: int = None, negate: bool = False
+    output,
+    path,
+    n: Optional[int] = None,
+    delta: int = 0,
+    min: Optional[int] = None,
+    max: Optional[int] = None,
+    negate: bool = False,
 ):
     """Asserts the specified output has exactly n elements matching the
     path specified."""
@@ -74,10 +81,10 @@ def assert_xml_element(
     children=None,
     attribute=None,
     all=False,
-    n: int = None,
+    n: Optional[int] = None,
     delta: int = 0,
-    min: int = None,
-    max: int = None,
+    min: Optional[int] = None,
+    max: Optional[int] = None,
     negate: bool = False,
 ):
     """

lib/galaxy/tool_util/verify/interactor.py

@@ -11,6 +11,7 @@ import urllib.parse
 import zipfile
 from json import dumps
 from logging import getLogger
+from typing import Optional
 
 import requests
 from packaging.version import parse as parse_version
@@ -810,7 +811,12 @@ class GalaxyInteractorApi:
         return urllib.parse.urljoin(f"{self.api_url}/", path)
 
     def _prepare_request_params(
-        self, data=None, files=None, as_json: bool = False, params: dict = None, headers: dict = None
+        self,
+        data=None,
+        files=None,
+        as_json: bool = False,
+        params: Optional[dict] = None,
+        headers: Optional[dict] = None,
     ):
         """Handle some Galaxy conventions and work around requests issues.
 

lib/galaxy/webapps/galaxy/api/history_contents.py

@@ -998,7 +998,9 @@ class HistoryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
         # return self.hda_manager.serialize_dataset_association_roles(trans, hda)
 
     @expose_api
-    def update_permissions(self, trans, history_id, history_content_id, payload: Dict[str, Any] = None, **kwd):
+    def update_permissions(
+        self, trans, history_id, history_content_id, payload: Optional[Dict[str, Any]] = None, **kwd
+    ):
         """
         Set permissions of the given library dataset to the given role ids.
 

lib/galaxy/webapps/galaxy/api/libraries.py

@@ -303,7 +303,9 @@ class LibrariesController(BaseGalaxyAPIController):
         return self.service.update(trans, id, update_payload)
 
     @expose_api
-    def delete(self, trans: ProvidesUserContext, id: EncodedDatabaseIdField, payload: Dict[str, Any] = None, **kwd):
+    def delete(
+        self, trans: ProvidesUserContext, id: EncodedDatabaseIdField, payload: Optional[Dict[str, Any]] = None, **kwd
+    ):
         """
         * DELETE /api/libraries/{id}
             marks the library with the given ``id`` as `deleted` (or removes the `deleted` mark if the `undelete` param is true)

lib/galaxy_test/api/test_group_roles.py

@@ -1,4 +1,7 @@
-from typing import List
+from typing import (
+    List,
+    Optional,
+)
 
 from galaxy_test.base.populators import DatasetPopulator
 from ._framework import ApiTestCase
@@ -9,7 +12,7 @@ class GroupRolesApiTestCase(ApiTestCase):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
 
-    def test_index(self, group_name: str = None):
+    def test_index(self, group_name: Optional[str] = None):
         group_name = group_name or "test-group_roles"
         group = self._create_group(group_name)
         encoded_group_id = group["id"]
@@ -109,7 +112,7 @@ class GroupRolesApiTestCase(ApiTestCase):
         delete_response = self._delete(f"groups/{encoded_group_id}/roles/{encoded_role_id}", admin=True)
         self._assert_status_code_is(delete_response, 400)
 
-    def _create_group(self, group_name: str, encoded_role_ids: List[str] = None):
+    def _create_group(self, group_name: str, encoded_role_ids: Optional[List[str]] = None):
         if encoded_role_ids is None:
             encoded_role_ids = [self.dataset_populator.user_private_role_id()]
         role_ids = encoded_role_ids

lib/galaxy_test/api/test_group_users.py

@@ -1,4 +1,7 @@
-from typing import List
+from typing import (
+    List,
+    Optional,
+)
 
 from galaxy_test.base.populators import DatasetPopulator
 from ._framework import ApiTestCase
@@ -9,7 +12,7 @@ class GroupUsersApiTestCase(ApiTestCase):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
 
-    def test_index(self, group_name: str = None):
+    def test_index(self, group_name: Optional[str] = None):
         group_name = group_name or "test-group_users"
         group = self._create_group(group_name)
         encoded_group_id = group["id"]
@@ -109,7 +112,7 @@ class GroupUsersApiTestCase(ApiTestCase):
         delete_response = self._delete(f"groups/{encoded_group_id}/users/{encoded_user_id}", admin=True)
         self._assert_status_code_is(delete_response, 400)
 
-    def _create_group(self, group_name: str, encoded_user_ids: List[str] = None):
+    def _create_group(self, group_name: str, encoded_user_ids: Optional[List[str]] = None):
         if encoded_user_ids is None:
             encoded_user_ids = [self.dataset_populator.user_id()]
         user_ids = encoded_user_ids

lib/galaxy_test/api/test_groups.py

@@ -1,3 +1,5 @@
+from typing import Optional
+
 from galaxy_test.base.populators import DatasetPopulator
 from ._framework import ApiTestCase
 
@@ -7,7 +9,7 @@ class GroupsApiTestCase(ApiTestCase):
         super().setUp()
         self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
 
-    def test_create_valid(self, group_name: str = None):
+    def test_create_valid(self, group_name: Optional[str] = None):
         payload = self._build_valid_group_payload(group_name)
         response = self._post("groups", payload, admin=True, json=True)
         self._assert_status_code_is(response, 200)
@@ -102,7 +104,7 @@ class GroupsApiTestCase(ApiTestCase):
         if assert_id is not None:
             assert group["id"] == assert_id
 
-    def _build_valid_group_payload(self, name: str = None):
+    def _build_valid_group_payload(self, name: Optional[str] = None):
         name = name or self.dataset_populator.get_random_name()
         user_id = self.dataset_populator.user_id()
         role_id = self.dataset_populator.user_private_role_id()

setup.cfg

@@ -19,6 +19,7 @@ check_untyped_defs = True
 exclude = lib/galaxy/tools/bundled|test/functional
 pretty = True
 no_implicit_reexport = True
+no_implicit_optional = True
 
 [mypy-galaxy.util.oset]
 # lots of tricky code in here...
@@ -221,7 +222,6 @@ disallow_untyped_defs = True
 disallow_incomplete_defs = True
 check_untyped_defs = True
 disallow_untyped_decorators = True
-no_implicit_optional = True
 warn_unused_ignores = True
 warn_return_any = True
 strict_equality = True