Source code for tool_shed.test.functional.test_0080_advanced_circular_dependencies

from ..base.twilltestcase import common, ShedTwillTestCase

column_repository_name = 'column_maker_0080'
column_repository_description = "Add column"
column_repository_long_description = "Compute an expression on every row"

convert_repository_name = 'convert_chars_0080'
convert_repository_description = "Convert delimiters"
convert_repository_long_description = "Convert delimiters to tab"

category_name = 'Test 0080 Advanced Circular Dependencies'
category_description = 'Test circular dependency features'


[docs]class TestRepositoryCircularDependencies(ShedTwillTestCase):
    '''Verify that the code correctly handles circular 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_column_repository(self):
        """Create and populate the column_maker repository."""
        category = self.create_category(name=category_name, description=category_description)
        self.login(email=common.test_user_1_email, username=common.test_user_1_name)
        repository = self.get_or_create_repository(name=column_repository_name,
                                                   description=column_repository_description,
                                                   long_description=column_repository_long_description,
                                                   owner=common.test_user_1_name,
                                                   category_id=self.security.encode_id(category.id),
                                                   strings_displayed=[])
        self.upload_file(repository,
                         filename='column_maker/column_maker.tar',
                         filepath=None,
                         valid_tools_only=True,
                         uncompress_file=True,
                         remove_repo_files_not_in_tar=False,
                         commit_message='Uploaded column_maker tarball.',
                         strings_displayed=[],
                         strings_not_displayed=[])

[docs]    def test_0005_create_convert_repository(self):
        """Create and populate the convert_chars repository."""
        self.login(email=common.admin_email, username=common.admin_username)
        category = self.create_category(name=category_name, description=category_description)
        self.login(email=common.test_user_1_email, username=common.test_user_1_name)
        repository = self.get_or_create_repository(name=convert_repository_name,
                                                   description=convert_repository_description,
                                                   long_description=convert_repository_long_description,
                                                   owner=common.test_user_1_name,
                                                   category_id=self.security.encode_id(category.id),
                                                   strings_displayed=[])
        self.upload_file(repository,
                         filename='convert_chars/convert_chars.tar',
                         filepath=None,
                         valid_tools_only=True,
                         uncompress_file=True,
                         remove_repo_files_not_in_tar=False,
                         commit_message='Uploaded convert_chars tarball.',
                         strings_displayed=[],
                         strings_not_displayed=[])

[docs]    def test_0020_create_repository_dependencies(self):
        '''Upload a repository_dependencies.xml file that specifies the current revision of convert_chars_0080 to the column_maker_0080 repository.'''
        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
        repository_dependencies_path = self.generate_temp_path('test_0080', additional_paths=['convert'])
        repository_tuple = (self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository))
        self.create_repository_dependency(repository=column_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.'''
        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
        repository_dependencies_path = self.generate_temp_path('test_0080', additional_paths=['convert'])
        repository_tuple = (self.url, column_repository.name, column_repository.user.username, self.get_repository_tip(column_repository))
        self.create_repository_dependency(repository=convert_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.'''
        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
        self.check_repository_dependency(convert_repository, column_repository, self.get_repository_tip(column_repository))
        self.check_repository_dependency(column_repository, convert_repository, self.get_repository_tip(convert_repository))

[docs]    def test_0035_verify_repository_metadata(self):
        '''Verify that resetting the metadata does not change it.'''
        column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
        convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
        for repository in [column_repository, convert_repository]:
            self.verify_unchanged_repository_metadata(repository)