Source code for tool_shed.test.functional.test_0040_repository_circular_dependencies

from ..base.twilltestcase import (
    common,
    ShedTwillTestCase,
)

freebayes_repository_name = "freebayes_0040"
freebayes_repository_description = "Galaxy's freebayes tool for test 0040"
freebayes_repository_long_description = "Long description of Galaxy's freebayes tool for test 0040"

filtering_repository_name = "filtering_0040"
filtering_repository_description = "Galaxy's filtering tool for test 0040"
filtering_repository_long_description = "Long description of Galaxy's filtering tool for test 0040"


[docs]class TestRepositoryCircularDependencies(ShedTwillTestCase): """Verify that the code correctly displays repositories with circular repository dependencies."""
[docs] def test_0000_initiate_users(self): """Create necessary user accounts.""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) test_user_1 = self.test_db_util.get_user(common.test_user_1_email) assert ( test_user_1 is not None ), f"Problem retrieving user with email {common.test_user_1_email} from the database" self.test_db_util.get_private_role(test_user_1) self.login(email=common.admin_email, username=common.admin_username) admin_user = self.test_db_util.get_user(common.admin_email) assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database" self.test_db_util.get_private_role(admin_user)
[docs] def test_0005_create_category(self): """Create a category for this test suite""" self.create_category( name="test_0040_repository_circular_dependencies", description="Testing handling of circular repository dependencies.", )
[docs] def test_0010_create_freebayes_repository(self): """Create and populate freebayes_0040.""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) repository = self.get_or_create_repository( name=freebayes_repository_name, description=freebayes_repository_description, long_description=freebayes_repository_long_description, owner=common.test_user_1_name, categories=["test_0040_repository_circular_dependencies"], strings_displayed=[], ) self.upload_file( repository, filename="freebayes/freebayes.tar", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded the tool tarball.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0015_create_filtering_repository(self): """Create and populate filtering_0040.""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) repository = self.get_or_create_repository( name=filtering_repository_name, description=filtering_repository_description, long_description=filtering_repository_long_description, owner=common.test_user_1_name, categories=["test_0040_repository_circular_dependencies"], strings_displayed=[], ) self.upload_file( repository, filename="filtering/filtering_1.1.0.tar", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded the tool tarball for filtering 1.1.0.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0020_create_dependency_on_freebayes(self): """Upload a repository_dependencies.xml file that specifies the current revision of freebayes to the filtering_0040 repository.""" # The dependency structure should look like: # Filtering revision 0 -> freebayes revision 0. # Freebayes revision 0 -> filtering revision 1. # Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes. repository = self.test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) filtering_repository = self.test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path("test_0040", additional_paths=["filtering"]) repository_tuple = (self.url, repository.name, repository.user.username, self.get_repository_tip(repository)) self.create_repository_dependency( repository=filtering_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path )
[docs] def test_0025_create_dependency_on_filtering(self): """Upload a repository_dependencies.xml file that specifies the current revision of filtering to the freebayes_0040 repository.""" # The dependency structure should look like: # Filtering revision 0 -> freebayes revision 0. # Freebayes revision 0 -> filtering revision 1. # Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes. repository = self.test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path("test_0040", additional_paths=["freebayes"]) repository_tuple = (self.url, repository.name, repository.user.username, self.get_repository_tip(repository)) self.create_repository_dependency( repository=freebayes_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path )
[docs] def test_0030_verify_repository_dependencies(self): """Verify that each repository can depend on the other without causing an infinite loop.""" filtering_repository = self.test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) # The dependency structure should look like: # Filtering revision 0 -> freebayes revision 0. # Freebayes revision 0 -> filtering revision 1. # Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes. # In this case, the displayed dependency will specify the tip revision, but this will not always be the case. self.check_repository_dependency( filtering_repository, freebayes_repository, self.get_repository_tip(freebayes_repository) ) self.check_repository_dependency( freebayes_repository, filtering_repository, self.get_repository_tip(filtering_repository) )
[docs] def test_0035_verify_repository_metadata(self): """Verify that resetting the metadata does not change it.""" freebayes_repository = self.test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) filtering_repository = self.test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) for repository in [freebayes_repository, filtering_repository]: self.verify_unchanged_repository_metadata(repository)
[docs] def test_0040_verify_tool_dependencies(self): """Verify that freebayes displays tool dependencies.""" repository = self.test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) self.display_manage_repository_page( repository, strings_displayed=["freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18", "Valid tools", "package"], strings_not_displayed=["Invalid tools"], )