diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py index e7d32c23e15..e8d33a357d7 100644 --- a/lib/tool_shed/test/base/twilltestcase.py +++ b/lib/tool_shed/test/base/twilltestcase.py @@ -905,7 +905,11 @@ class ShedTwillTestCase(ShedApiTestCase): 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 @@ -1402,7 +1406,7 @@ class ShedTwillTestCase(ShedApiTestCase): 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 +1421,7 @@ class ShedTwillTestCase(ShedApiTestCase): 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 +1500,11 @@ class ShedTwillTestCase(ShedApiTestCase): 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: diff --git a/lib/tool_shed/test/functional/test_0000_basic_repository_features.py b/lib/tool_shed/test/functional/test_0000_basic_repository_features.py index c01c91d731e..a5faf7b4a7f 100644 --- a/lib/tool_shed/test/functional/test_0000_basic_repository_features.py +++ b/lib/tool_shed/test/functional/test_0000_basic_repository_features.py @@ -1,5 +1,7 @@ import logging +import pytest + from ..base import common from ..base.api import skip_if_api_v2 from ..base.twilltestcase import ShedTwillTestCase @@ -157,7 +159,6 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase): 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, @@ -268,14 +269,15 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase): 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.""" diff --git a/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py b/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py index 16757198352..657d73610e9 100644 --- a/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py +++ b/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py @@ -51,7 +51,6 @@ class TestFreebayesRepository(ShedTwillTestCase): 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: diff --git a/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py b/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py index 95f44c2b77c..1075babaabe 100644 --- a/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py +++ b/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py @@ -67,8 +67,6 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase): category=category, strings_displayed=[], ) - assert repository - assert repository.id self.commit_tar_to_repository( repository, "column_maker/column_maker.tar", diff --git a/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py b/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py index a1817cbe62b..3032ccd2663 100644 --- a/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py +++ b/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py @@ -63,7 +63,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): owner=common.test_user_1_name, category=category_0000, ) - assert repository if self.repository_is_new(repository): running_standalone = True self.commit_tar_to_repository( @@ -91,7 +90,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): strings_displayed=[], ) if running_standalone: - assert repository self.setup_freebayes_0010_repo(repository) def test_0015_create_datatypes_0020_repository(self): @@ -112,7 +110,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): category=category_0020, strings_displayed=[], ) - assert repository self.commit_tar_to_repository( repository, "column_maker/column_maker.tar", @@ -137,7 +134,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): category=category_0020, strings_displayed=[], ) - assert repository self.commit_tar_to_repository( repository, "emboss/emboss.tar", @@ -162,7 +158,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): category=category_0030, strings_displayed=[], ) - assert column_maker_repository self.commit_tar_to_repository( column_maker_repository, "column_maker/column_maker.tar", @@ -187,7 +182,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): category=category_0030, strings_displayed=[], ) - assert emboss_5_repository self.commit_tar_to_repository( emboss_5_repository, "emboss/emboss.tar", @@ -212,7 +206,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): category=category_0030, strings_displayed=[], ) - assert emboss_6_repository self.commit_tar_to_repository( emboss_6_repository, "emboss/emboss.tar", @@ -237,7 +230,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): category=category_0030, strings_displayed=[], ) - assert emboss_repository self.commit_tar_to_repository( emboss_repository, "emboss/emboss.tar", @@ -251,13 +243,9 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): column_maker_repository = self._get_repository_by_name_and_owner( "column_maker_0030", common.test_user_1_name ) - assert column_maker_repository emboss_repository = self._get_repository_by_name_and_owner("emboss_0030", common.test_user_1_name) - assert emboss_repository emboss_5_repository = self._get_repository_by_name_and_owner("emboss_5_0030", common.test_user_1_name) - assert emboss_5_repository emboss_6_repository = self._get_repository_by_name_and_owner("emboss_6_0030", common.test_user_1_name) - assert emboss_6_repository repository_dependencies_path = self.generate_temp_path("test_0330", additional_paths=["emboss"]) column_maker_tuple = ( self.url, @@ -311,7 +299,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): category=category_0040, strings_displayed=[], ) - assert repository if running_standalone: self.commit_tar_to_repository( repository, @@ -337,7 +324,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): category=category_0040, strings_displayed=[], ) - assert repository self.commit_tar_to_repository( repository, "filtering/filtering_1.1.0.tar", @@ -349,9 +335,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): global running_standalone if running_standalone: freebayes_repository = self._get_repository_by_name_and_owner("freebayes_0040", common.test_user_1_name) - assert freebayes_repository filtering_repository = self._get_repository_by_name_and_owner("filtering_0040", common.test_user_1_name) - assert filtering_repository repository_dependencies_path = self.generate_temp_path("test_0340", additional_paths=["dependencies"]) freebayes_tuple = ( self.url, @@ -391,7 +375,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): category=category, strings_displayed=[], ) - assert repository self.commit_tar_to_repository( repository, "convert_chars/convert_chars.tar", @@ -413,7 +396,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): category=category, strings_displayed=[], ) - assert repository self.commit_tar_to_repository( repository, "column_maker/column_maker.tar", @@ -438,7 +420,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): category=category, strings_displayed=[], ) - assert repository self.commit_tar_to_repository( repository, "emboss/emboss.tar", @@ -460,7 +441,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): category=category, strings_displayed=[], ) - assert filtering_repository self.commit_tar_to_repository( filtering_repository, "filtering/filtering_1.1.0.tar", @@ -482,7 +462,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): category=category, strings_displayed=[], ) - assert repository self.commit_tar_to_repository( repository, "freebayes/freebayes.tar", @@ -504,7 +483,6 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): category=category, strings_displayed=[], ) - assert repository self.user_populator().setup_bismark_repo(repository, end=1) def test_0100_create_and_upload_dependency_definitions(self): @@ -513,25 +491,19 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): if running_standalone: self.login(email=common.test_user_1_email, username=common.test_user_1_name) column_repository = self._get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name) - assert column_repository convert_repository = self._get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) - assert convert_repository emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name) - assert emboss_repository filtering_repository = self._get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) - assert filtering_repository freebayes_repository = self._get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) - assert freebayes_repository bismark_repository = self._get_repository_by_name_and_owner( bismark_repository_name, common.test_user_1_name ) - assert bismark_repository dependency_xml_path = self.generate_temp_path("test_0050", additional_paths=["freebayes"]) # convert_chars depends on column_maker # column_maker depends on convert_chars diff --git a/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py b/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py index 073b4612000..fbb6c521e0e 100644 --- a/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py +++ b/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py @@ -56,7 +56,7 @@ class TestGetUpdatedMetadata(ShedTwillTestCase): category = self.create_category(name=category_name, description=category_description) self.login(email=common.test_user_1_email, username=common.test_user_1_name) # Create a repository named package_freebayes_0550 owned by user1. - freebayes = self.get_or_create_repository( + freebayes_repository = self.get_or_create_repository( name=repositories["freebayes"]["name"], description=repositories["freebayes"]["description"], long_description=repositories["freebayes"]["long_description"], @@ -64,21 +64,20 @@ class TestGetUpdatedMetadata(ShedTwillTestCase): category=category, strings_displayed=[], ) - assert freebayes is not None, f"Error creating freebayes {repositories['freebayes']['name']}" self.commit_tar_to_repository( - freebayes, + freebayes_repository, "0550_files/package_freebayes_1_0550.tgz", ) if not self.is_v2: # Visit the manage repository page for package_freebayes_0_5_9_0100. self.display_manage_repository_page( - freebayes, strings_displayed=["Tool dependencies", "will not be", "to this repository"] + freebayes_repository, strings_displayed=["Tool dependencies", "will not be", "to this repository"] ) def test_0010_create_samtools_repository(self): """Create and populate the package_samtools_0550 repository.""" category = self.create_category(name=category_name, description=category_description) - samtools = self.get_or_create_repository( + samtools_repository = self.get_or_create_repository( name=repositories["samtools"]["name"], description=repositories["samtools"]["description"], long_description=repositories["samtools"]["long_description"], @@ -86,9 +85,8 @@ class TestGetUpdatedMetadata(ShedTwillTestCase): category=category, strings_displayed=[], ) - assert samtools is not None, f"Error creating samtools {repositories['samtools']['name']}" self.commit_tar_to_repository( - samtools, + samtools_repository, "0550_files/package_samtools_1_0550.tgz", commit_message="Uploaded samtools 1.0.", ) @@ -104,7 +102,6 @@ class TestGetUpdatedMetadata(ShedTwillTestCase): category=category, strings_displayed=[], ) - assert repository is not None, f"Error creating repository {repositories['filtering']['name']}" self.commit_tar_to_repository( repository, "0550_files/filtering_1.0.tgz", diff --git a/lib/tool_shed/test/functional/test_1460_data_managers.py b/lib/tool_shed/test/functional/test_1460_data_managers.py index 852fd891edf..b271e85c0f8 100644 --- a/lib/tool_shed/test/functional/test_1460_data_managers.py +++ b/lib/tool_shed/test/functional/test_1460_data_managers.py @@ -53,7 +53,6 @@ class TestDataManagers(ShedTwillTestCase): category=category, strings_displayed=[], ) - assert repository, "No repository created with name {commit_tar_to_repository}" # Upload the data manager files to the repository. self.commit_tar_to_repository( repository,