Source code for tool_shed.test.functional.test_1100_install_updated_repository_dependencies

from ..base.twilltestcase import common, ShedTwillTestCase

column_repository_name = 'column_maker_1087'
column_repository_description = "Add column"
column_repository_long_description = "Compute an expression on every row"

convert_repository_name = 'convert_chars_1087'
convert_repository_description = "Convert delimiters"
convert_repository_long_description = "Convert delimiters to tab"

category_name = 'Test 1087 Advanced Circular Dependencies'
category_description = 'Test circular dependency features'


[docs]class TestRepositoryDependencies(ShedTwillTestCase):
    '''Test installing a repository, then updating it to include repository dependencies.'''

[docs]    def test_0000_create_or_login_admin_user(self):
        """Create necessary user accounts and login as an admin user."""
        self.galaxy_login(email=common.admin_email, username=common.admin_username)
        galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
        assert galaxy_admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
        self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
        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, 'Problem retrieving user with email %s from the database' % common.test_user_1_email
        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, 'Problem retrieving user with email %s from the database' % common.admin_email
        self.test_db_util.get_private_role(admin_user)

[docs]    def test_0005_create_and_populate_column_repository(self):
        """Create a category for this test suite and add repositories to it."""
        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=[])
        if self.repository_is_new(repository):
            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_0010_create_and_populate_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=[])
        if self.repository_is_new(repository):
            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_0015_install_and_uninstall_column_repository(self):
        '''Install and uninstall the column_maker repository.'''
        self.galaxy_login(email=common.admin_email, username=common.admin_username)
        self.install_repository(column_repository_name,
                                common.test_user_1_name,
                                category_name,
                                install_tool_dependencies=False,
                                install_repository_dependencies=True,
                                new_tool_panel_section_label='column_maker',
                                strings_not_displayed=['install_repository_dependencies'])
        installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(column_repository_name, common.test_user_1_name)
        self.uninstall_repository(installed_column_repository)

[docs]    def test_0020_upload_dependency_xml(self):
        '''Upload a repository_dependencies.xml file to column_maker that specifies convert_chars.'''
        self.login(email=common.test_user_1_email, username=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)
        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_1085', additional_paths=['column'])
        convert_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=[convert_tuple], filepath=repository_dependencies_path)

[docs]    def test_0025_verify_repository_dependency(self):
        '''Verify that the new revision of column_maker now depends on convert_chars.'''
        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(column_repository, convert_repository)

[docs]    def test_0030_reinstall_column_repository(self):
        '''Reinstall column_maker and verify that it now shows repository dependencies.'''
        self.galaxy_login(email=common.admin_email, username=common.admin_username)
        installed_column_repository = self.test_db_util.get_installed_repository_by_name_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)
        strings_displayed = ['Handle repository dependencies', 'convert_chars_1087', self.get_repository_tip(convert_repository)]
        # Due to twill's limitations, only check for strings on the (redirected) reselect tool panel section page, don't actually reinstall.
        params = dict(id=self.security.encode_id(installed_column_repository.id))
        url = '/admin_toolshed/restore_repository'
        self.visit_galaxy_url(url, params)
        self.check_for_strings(strings_displayed)
        strings_not_displayed = ['column_maker_1087']
        self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)