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'])