Fix type annotation of test_0000_basic_repository_features.py

lib/tool_shed/test/functional/test_0000_basic_repository_features.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
 
 repository_name = "filtering_0000"
 repository_description = "Galaxy's filtering tool for test 0000"
@@ -44,6 +42,7 @@ def test_0015_create_repository(self):
         """Create the filtering repository"""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         category = self.populator.get_category_with_name("Test 0000 Basic Repository Features 1")
+        assert category
         strings_displayed = self.expect_repo_created_strings(repository_name)
         self.get_or_create_repository(
             name=repository_name,
@@ -57,6 +56,7 @@ def test_0015_create_repository(self):
     def test_0020_edit_repository(self):
         """Edit the repository name, description, and long description"""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         new_name = "renamed_filtering"
         new_description = "Edited filtering tool"
         new_long_description = "Edited long description"
@@ -67,6 +67,7 @@ def test_0020_edit_repository(self):
     def test_0025_change_repository_category(self):
         """Change the categories associated with the filtering repository"""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         self.edit_repository_categories(
             repository,
             categories_to_add=["Test 0000 Basic Repository Features 2"],
@@ -77,19 +78,22 @@ def test_0025_change_repository_category(self):
     def test_0030_grant_write_access(self):
         """Grant write access to another user"""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         self.grant_write_access(repository, usernames=[common.test_user_2_name])
         self.revoke_write_access(repository, common.test_user_2_name)
 
     def test_0035_upload_filtering_1_1_0(self):
         """Upload filtering_1.1.0.tar to the repository"""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         self.commit_tar_to_repository(
             repository, "filtering/filtering_1.1.0.tar", commit_message="Uploaded filtering 1.1.0"
         )
 
     def test_0040_verify_repository(self):
         """Display basic repository pages"""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         latest_changeset_revision = self.get_repository_tip(repository)
         self.check_for_valid_tools(repository, strings_displayed=["Filter1"])
         self.check_count_of_metadata_revisions_associated_with_repository(repository, metadata_count=1)
@@ -129,6 +133,7 @@ def test_0040_verify_repository(self):
     def test_0045_alter_repository_states(self):
         """Test toggling the malicious and deprecated repository flags."""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         self.login(email=common.admin_email, username=common.admin_username)
         self.set_repository_malicious(
             repository, set_malicious=True, strings_displayed=["The repository tip has been defined as malicious."]
@@ -172,13 +177,15 @@ def test_0050_display_repository_tip_file(self):
     def test_0055_upload_filtering_txt_file(self):
         """Upload filtering.txt file associated with tool version 1.1.0."""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         self.add_file_to_repository(repository, "filtering/filtering_0000.txt")
         expected = self._escape_page_content_if_needed("Readme file for filtering 1.1.0")
         self.display_manage_repository_page(repository, strings_displayed=[expected])
 
     def test_0060_upload_filtering_test_data(self):
         """Upload filtering test data."""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         self.add_tar_to_repository(repository, "filtering/filtering_test_data.tar")
         if self._browser.is_twill:
             # probably not porting this functionality - just test
@@ -195,11 +202,13 @@ def test_0060_upload_filtering_test_data(self):
     def test_0065_upload_filtering_2_2_0(self):
         """Upload filtering version 2.2.0"""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         self.add_tar_to_repository(repository, "filtering/filtering_2.2.0.tar")
 
     def test_0070_verify_filtering_repository(self):
         """Verify the new tool versions and repository metadata."""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         tip = self.get_repository_tip(repository)
         self.check_for_valid_tools(repository)
         if self.is_v2:
@@ -228,6 +237,7 @@ def test_0070_verify_filtering_repository(self):
     def test_0075_upload_readme_txt_file(self):
         """Upload readme.txt file associated with tool version 2.2.0."""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         self.add_file_to_repository(repository, "readme.txt")
         content = self._escape_page_content_if_needed("This is a readme file.")
         self.display_manage_repository_page(repository, strings_displayed=[content])
@@ -244,6 +254,7 @@ def test_0075_upload_readme_txt_file(self):
     def test_0080_delete_readme_txt_file(self):
         """Delete the readme.txt file."""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         self.delete_files_from_repository(repository, filenames=["readme.txt"])
         self.check_count_of_metadata_revisions_associated_with_repository(repository, metadata_count=2)
         readme_content = self._escape_page_content_if_needed("Readme file for filtering 1.1.0")
@@ -253,6 +264,7 @@ def test_0080_delete_readme_txt_file(self):
     def test_0085_search_for_valid_filter_tool(self):
         """Search for the filtering tool by tool ID, name, and version."""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         tip_changeset = self.get_repository_tip(repository)
         search_fields = dict(tool_id="Filter1", tool_name="filter", tool_version="2.2.0")
         self.search_for_valid_tools(
@@ -262,11 +274,13 @@ def test_0085_search_for_valid_filter_tool(self):
     def test_0090_verify_repository_metadata(self):
         """Verify that resetting the metadata does not change it."""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         self.verify_unchanged_repository_metadata(repository)
 
     def test_0095_verify_reserved_repository_name_handling(self):
         """Check that reserved repository names are handled correctly."""
         category = self.populator.get_category_with_name("Test 0000 Basic Repository Features 1")
+        assert category
         error_message = (
             "The term 'repos' is a reserved word in the Tool Shed, so it cannot be used as a repository name."
         )
@@ -301,9 +315,10 @@ def test_0105_contact_repository_owner(self):
     def test_0110_delete_filtering_repository(self):
         """Delete the filtering_0000 repository and verify that it no longer has any downloadable revisions."""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         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.
@@ -316,6 +331,7 @@ def test_0110_delete_filtering_repository(self):
     def test_0115_undelete_filtering_repository(self):
         """Undelete the filtering_0000 repository and verify that it now has two downloadable revisions."""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         self.login(email=common.admin_email, username=common.admin_username)
         self.undelete_repository(repository)
         # Explicitly reload all metadata revisions from the database, to ensure that we have the current status of the downloadable flag.
@@ -333,13 +349,15 @@ def test_0120_enable_email_notifications(self):
         self.login(email=common.test_user_2_email, username=common.test_user_2_name)
         # Get the repository, so we can pass the encoded repository id and browse_repositories method to the set_email_alerts method.
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         strings_displayed = ["Total alerts added: 1, total alerts removed: 0"]
         self.enable_email_alerts(repository, strings_displayed=strings_displayed)
 
     def test_0125_upload_new_readme_file(self):
         """Upload a new readme file to the filtering_0000 repository and verify that there is no error."""
         self.login(email=common.test_user_1_email, username=common.test_user_1_name)
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         # Upload readme.txt to the filtering_0000 repository and verify that it is now displayed.
         self.add_file_to_repository(repository, "filtering/readme.txt")
         content = self._escape_page_content_if_needed("These characters should not")
@@ -348,6 +366,7 @@ def test_0125_upload_new_readme_file(self):
     def test_0130_verify_handling_of_invalid_characters(self):
         """Load the above changeset in the change log and confirm that there is no server error displayed."""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         changeset_revision = self.get_repository_tip(repository)
         repository_id = repository.id
         changelog_tuples = self.get_repository_changelog_tuples(repository)
@@ -374,13 +393,16 @@ 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"))
+        for name in ("Test 0000 Basic Repository Features 1", "Test 0000 Basic Repository Features 2"):
+            category = self.populator.get_category_with_name(name)
+            assert category
+            categories.append(category)
         self.get_repositories_category_api(categories)
 
     def test_0140_view_invalid_changeset(self):
         """View repository using an invalid changeset"""
         repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
+        assert repository
         encoded_repository_id = repository.id
         assert encoded_repository_id
         strings_displayed = ["Invalid+changeset+revision"]