Fix type annotation of lib/tool_shed/test/functional/

lib/tool_shed/test/base/populators.py

@@ -79,7 +79,7 @@ def repo_tars(test_data_path: str) -> List[Path]:
 
 class HostsTestToolShed(Protocol):
     host: str
-    port: int
+    port: Optional[str]
 
 
 class ToolShedPopulator:
@@ -271,18 +271,17 @@ def get_category_with_id(self, category_id: str) -> Category:
         response.raise_for_status()
         return Category(**response.json())
 
-    def get_category_with_name(self, name: str) -> Optional[Category]:
+    def get_category_with_name(self, name: str) -> Category:
         categories = [c for c in self.get_categories() if c.name == name]
-        return categories[0] if categories else None
+        if not categories:
+            raise ValueError(f"No category with name {name} found.")
+        return categories[0]
 
     def repositories_by_category(self, category_id: str) -> RepositoriesByCategory:
         response = self._api_interactor.get(f"categories/{category_id}/repositories")
         response.raise_for_status()
         return RepositoriesByCategory(**response.json())
 
-    def has_category_with_name(self, name: str) -> bool:
-        return self.get_category_with_name(name) is not None
-
     def get_ordered_installable_revisions(self, owner: str, name: str) -> OrderedInstallableRevisions:
         request = GetOrderedInstallableRevisionsRequest(owner=owner, name=name)
         revisions_response = self._api_interactor.get(
@@ -397,7 +396,7 @@ def tool_guid(
         owner = repository.owner
         name = repository.name
         port = shed_host.port
-        if port in [None, 80, 443]:
+        if port in [None, "80", "443"]:
             host_and_port = shed_host.host
         else:
             host_and_port = f"{shed_host.host}:{shed_host.port}"

lib/tool_shed/test/base/twilltestcase.py

@@ -15,6 +15,7 @@
     Iterator,
     List,
     Optional,
+    Tuple,
 )
 from urllib.parse import (
     quote_plus,
@@ -694,7 +695,14 @@ def _submit_register_form(self, email: str, password: str, username: str, redire
     def invalid_tools_labels(self) -> str:
         return "Invalid Tools" if self.is_v2 else "Invalid tools"
 
-    def create(self, cntrller="user", email="test@bx.psu.edu", password="testuser", username="admin-user", redirect=""):
+    def create(
+        self,
+        cntrller: str = "user",
+        email: str = "test@bx.psu.edu",
+        password: str = "testuser",
+        username: str = "admin-user",
+        redirect: Optional[str] = None,
+    ) -> Tuple[bool, bool, bool]:
         # HACK: don't use panels because late_javascripts() messes up the twill browser and it
         # can't find form fields (and hence user can't be logged in).
         params = dict(cntrller=cntrller, use_panels=False)
@@ -747,7 +755,7 @@ def login(
         email: str = "test@bx.psu.edu",
         password: str = "testuser",
         username: str = "admin-user",
-        redirect: str = "",
+        redirect: Optional[str] = None,
         logout_first: bool = True,
     ):
         if self.is_v2:
@@ -905,7 +913,11 @@ def check_repository_changelog(self, repository: Repository, strings_displayed=N
         self.check_for_strings(strings_displayed, strings_not_displayed)
 
     def check_repository_dependency(
-        self, repository: Repository, depends_on_repository, depends_on_changeset_revision=None, changeset_revision=None
+        self,
+        repository: Repository,
+        depends_on_repository: Repository,
+        depends_on_changeset_revision=None,
+        changeset_revision=None,
     ):
         if not self.is_v2:
             # v2 doesn't display repository repository dependencies, they are deprecated
@@ -1031,8 +1043,9 @@ def commit_and_push(self, repository, hgrepo, options, username, password):
 
     def create_category(self, **kwd) -> Category:
         category_name = kwd["name"]
-        category = self.populator.get_category_with_name(category_name)
-        if category is None:
+        try:
+            category = self.populator.get_category_with_name(category_name)
+        except ValueError:
             # not recreating this functionality in the UI I don't think?
             category = self.populator.new_category(category_name)
             return category
@@ -1402,7 +1415,7 @@ def get_repositories_category_api(
 
     def get_or_create_repository(
         self, category: Category, owner: str, name: str, strings_displayed=None, strings_not_displayed=None, **kwd
-    ) -> Optional[Repository]:
+    ) -> Repository:
         # If not checking for a specific string, it should be safe to assume that
         # we expect repository creation to be successful.
         if strings_displayed is None:
@@ -1417,6 +1430,7 @@ def get_or_create_repository(
             self.submit_form(button="create_repository_button", name=name, category_id=category_id, **kwd)
             self.check_for_strings(strings_displayed, strings_not_displayed)
             repository = self.populator.get_repository_for(owner, name)
+        assert repository
         return repository
 
     def get_repo_path(self, repository: Repository) -> str:
@@ -1495,10 +1509,11 @@ def get_repository_metadata_revisions(self, repository: Repository) -> List[str]
             for repository_metadata in self._db_repository(repository).metadata_revisions
         ]
 
-    def _get_repository_by_name_and_owner(self, name: str, owner: str) -> Optional[Repository]:
+    def _get_repository_by_name_and_owner(self, name: str, owner: str) -> Repository:
         repo = self.populator.get_repository_for(owner, name)
         if repo is None:
             repo = self.populator.get_repository_for(owner, name, deleted="true")
+        assert repo
         return repo
 
     def get_repository_tip(self, repository: Repository) -> str:
@@ -1585,7 +1600,6 @@ def _install_repository(
     ) -> None:
         self.browse_tool_shed(url=self.url)
         category = self.populator.get_category_with_name(category_name)
-        assert category
         self.browse_category(category)
         self.preview_repository_in_tool_shed(name, owner, strings_displayed=preview_strings_displayed)
         repository = self._get_repository_by_name_and_owner(name, owner)

lib/tool_shed/test/functional/test_0000_basic_repository_features.py

@@ -1,10 +1,10 @@
 import logging
 
+import pytest
+
+from ..base import common
 from ..base.api import skip_if_api_v2
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base.twilltestcase import ShedTwillTestCase
 
 repository_name = "filtering_0000"
 repository_description = "Galaxy's filtering tool for test 0000"
@@ -159,7 +159,6 @@ def test_0045_alter_repository_states(self):
     def test_0050_display_repository_tip_file(self):
         """Display the contents of filtering.xml in the repository tip revision"""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
-        assert repository
         if self._browser.is_twill:
             self.display_repository_file_contents(
                 repository=repository,
@@ -270,14 +269,15 @@ def test_0095_verify_reserved_repository_name_handling(self):
         error_message = (
             "The term 'repos' is a reserved word in the Tool Shed, so it cannot be used as a repository name."
         )
-        self.get_or_create_repository(
-            name="repos",
-            description=repository_description,
-            long_description=repository_long_description,
-            owner=common.test_user_1_name,
-            category=category,
-            strings_displayed=[error_message],
-        )
+        with pytest.raises(AssertionError):
+            self.get_or_create_repository(
+                name="repos",
+                description=repository_description,
+                long_description=repository_long_description,
+                owner=common.test_user_1_name,
+                category=category,
+                strings_displayed=[error_message],
+            )
 
     def test_0100_verify_reserved_username_handling(self):
         """Check that reserved usernames are handled correctly."""
@@ -303,7 +303,7 @@ def test_0110_delete_filtering_repository(self):
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
         self.login(email=common.admin_email, username=common.admin_username)
         self.delete_repository(repository)
-        metadata = self._populator.get_metadata(repository, downloadable_only=False)
+        metadata = self.populator.get_metadata(repository, downloadable_only=False)
         for _, value in metadata.__root__.items():
             assert not value.downloadable
         # Explicitly reload all metadata revisions from the database, to ensure that we have the current status of the downloadable flag.
@@ -373,9 +373,10 @@ def test_0130_verify_handling_of_invalid_characters(self):
 
     def test_0135_api_get_repositories_in_category(self):
         """Load the api endpoint for repositories in a category."""
-        categories = []
-        categories.append(self.populator.get_category_with_name("Test 0000 Basic Repository Features 1"))
-        categories.append(self.populator.get_category_with_name("Test 0000 Basic Repository Features 2"))
+        categories = [
+            self.populator.get_category_with_name(name)
+            for name in ("Test 0000 Basic Repository Features 1", "Test 0000 Basic Repository Features 2")
+        ]
         self.get_repositories_category_api(categories)
 
     def test_0140_view_invalid_changeset(self):

lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py

@@ -1,10 +1,8 @@
 import os
 
+from ..base import common
 from ..base.api import skip_if_api_v2
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base.twilltestcase import ShedTwillTestCase
 
 repository_name = "freebayes_0010"
 repository_description = "Galaxy's freebayes tool"
@@ -53,7 +51,6 @@ def test_0010_create_freebayes_repository_and_upload_tool_xml(self):
             category=category,
             strings_displayed=[],
         )
-        assert repository
         strings_displayed = ["Metadata may have been defined", "This file requires an entry", "tool_data_table_conf"]
         self.add_file_to_repository(repository, "freebayes/freebayes.xml", strings_displayed=strings_displayed)
         if self.is_v2:

lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py

@@ -1,8 +1,6 @@
+from ..base import common
 from ..base.api import skip_if_api_v2
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base.twilltestcase import ShedTwillTestCase
 
 column_maker_repository_name = "column_maker_0020"
 column_maker_repository_description = "A flexible aligner."

lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py

@@ -1,8 +1,6 @@
+from ..base import common
 from ..base.api import skip_if_api_v2
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base.twilltestcase import ShedTwillTestCase
 
 column_maker_repository_name = "column_maker_0030"
 column_maker_repository_description = "Add column"

lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py

@@ -1,8 +1,6 @@
+from ..base import common
 from ..base.api import skip_if_api_v2
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base.twilltestcase import ShedTwillTestCase
 
 freebayes_repository_name = "freebayes_0040"
 freebayes_repository_description = "Galaxy's freebayes tool for test 0040"

lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py

@@ -1,8 +1,6 @@
+from ..base import common
 from ..base.api import skip_if_api_v2
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base.twilltestcase import ShedTwillTestCase
 
 emboss_repository_name = "emboss_0050"
 emboss_repository_description = "Galaxy's emboss tool"
@@ -69,8 +67,6 @@ def test_0010_create_column_repository(self):
             category=category,
             strings_displayed=[],
         )
-        assert repository
-        assert repository.id
         self.commit_tar_to_repository(
             repository,
             "column_maker/column_maker.tar",

lib/tool_shed/test/functional/test_0070_invalid_tool.py

@@ -1,7 +1,5 @@
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base import common
+from ..base.twilltestcase import ShedTwillTestCase
 
 repository_name = "bismark_0070"
 repository_description = "Galaxy's bismark wrapper"

lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py

@@ -1,7 +1,5 @@
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base import common
+from ..base.twilltestcase import ShedTwillTestCase
 
 column_repository_name = "column_maker_0080"
 column_repository_description = "Add column"

lib/tool_shed/test/functional/test_0090_tool_search.py

@@ -1,7 +1,5 @@
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base import common
+from ..base.twilltestcase import ShedTwillTestCase
 
 emboss_repository_name = "emboss_0090"
 emboss_repository_description = "Galaxy's emboss tool"

lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py

@@ -1,11 +1,9 @@
 import logging
 import os
 
+from ..base import common
 from ..base.api import skip_if_api_v2
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base.twilltestcase import ShedTwillTestCase
 
 log = logging.getLogger(__name__)
 

lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py

@@ -1,7 +1,5 @@
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base import common
+from ..base.twilltestcase import ShedTwillTestCase
 
 column_maker_repository_name = "column_maker_0110"
 column_maker_repository_description = "A flexible aligner."

lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py

@@ -1,7 +1,5 @@
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base import common
+from ..base.twilltestcase import ShedTwillTestCase
 
 datatypes_repository_name = "blast_datatypes_0120"
 datatypes_repository_description = "Galaxy applicable datatypes for BLAST"

lib/tool_shed/test/functional/test_0140_tool_help_images.py

@@ -1,10 +1,8 @@
 import logging
 
+from ..base import common
 from ..base.api import skip_if_api_v2
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base.twilltestcase import ShedTwillTestCase
 
 log = logging.getLogger(__name__)
 

lib/tool_shed/test/functional/test_0150_prior_installation_required.py

@@ -1,7 +1,5 @@
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base import common
+from ..base.twilltestcase import ShedTwillTestCase
 
 column_repository_name = "column_maker_0150"
 column_repository_description = "Add column"

lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py

@@ -1,7 +1,5 @@
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base import common
+from ..base.twilltestcase import ShedTwillTestCase
 
 filter_repository_name = "filtering_0160"
 filter_repository_description = "Galaxy's filtering tool for test 0160"

lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py

@@ -1,9 +1,7 @@
 import os
 
-from ..base.twilltestcase import (
-    common,
-    ShedTwillTestCase,
-)
+from ..base import common
+from ..base.twilltestcase import ShedTwillTestCase
 
 matplotlib_repository_name = "package_matplotlib_1_2_0170"
 matplotlib_repository_description = (