Source code for tool_shed.test.functional.test_1070_invalid_tool

from ..base.twilltestcase import common, ShedTwillTestCase

repository_name = 'bismark_0070'
repository_description = "Galaxy's bismark wrapper"
repository_long_description = "Long description of Galaxy's bismark wrapper"
category_name = 'Test 0070 Invalid Tool Revisions'
category_description = 'Test 1070 for a repository with an invalid tool.'


[docs]class TestFreebayesRepository(ShedTwillTestCase):
    '''Test repository with multiple revisions with invalid tools.'''

[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, f'Problem retrieving user with email {common.admin_email} from the database'
        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, 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_ensure_existence_of_repository_and_category(self):
        '''Create freebayes repository and upload only freebayes.xml. This should result in an error message and invalid tool.'''
        self.create_category(name=category_name, description=category_description)
        self.login(email=common.test_user_1_email, username=common.test_user_1_name)
        category = self.test_db_util.get_category_by_name(category_name)
        repository = self.get_or_create_repository(name=repository_name,
                                                   description=repository_description,
                                                   long_description=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='bismark/bismark.tar',
                             filepath=None,
                             valid_tools_only=False,
                             uncompress_file=True,
                             remove_repo_files_not_in_tar=False,
                             commit_message='Uploaded bismark tarball.',
                             strings_displayed=[],
                             strings_not_displayed=[])
            self.upload_file(repository,
                             filename='bismark/bismark_methylation_extractor.xml',
                             filepath=None,
                             valid_tools_only=False,
                             uncompress_file=False,
                             remove_repo_files_not_in_tar=False,
                             commit_message='Uploaded an updated tool xml.',
                             strings_displayed=[],
                             strings_not_displayed=[])

[docs]    def test_0010_browse_tool_shed(self):
        """Browse the available tool sheds in this Galaxy instance and preview the bismark repository."""
        self.galaxy_login(email=common.admin_email, username=common.admin_username)
        self.browse_tool_shed(url=self.url, strings_displayed=[category_name])
        category = self.test_db_util.get_category_by_name(category_name)
        self.browse_category(category, strings_displayed=[repository_name])
        self.preview_repository_in_tool_shed(repository_name, common.test_user_1_name, strings_displayed=[repository_name])

[docs]    def test_0015_install_freebayes_repository(self):
        '''Install the test repository without installing tool dependencies.'''
        self.install_repository(repository_name,
                                common.test_user_1_name,
                                category_name,
                                install_tool_dependencies=False,
                                new_tool_panel_section_label='test_1070')
        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
        strings_displayed = ['bismark_0070',
                             "Galaxy's bismark wrapper",
                             'user1',
                             self.url.replace('http://', ''),
                             installed_repository.installed_changeset_revision]
        self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
        strings_displayed.extend(['methylation extractor', 'Invalid tools'])
        self.display_installed_repository_manage_page(installed_repository,
                                                      strings_displayed=strings_displayed,
                                                      strings_not_displayed=['bisulfite mapper'])
        self.verify_tool_metadata_for_installed_repository(installed_repository)
        self.update_installed_repository(installed_repository, strings_displayed=["there are no updates available"])
        assert 'invalid_tools' in installed_repository.metadata, 'No invalid tools were defined in %s.' % \
            installed_repository.name