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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