Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for tool_shed.test.functional.test_1220_uninstall_reinstall_repository_with_repository_dependencies

from ..base.twilltestcase import common, ShedTwillTestCase

datatypes_repository_name = 'emboss_datatypes_0020'
datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."

emboss_repository_name = 'emboss_0020'
emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'

base_datatypes_count = 0
repository_datatypes_count = 0
running_standalone = False


[docs]class UninstallingAndReinstallingRepositories(ShedTwillTestCase): '''Test uninstalling and reinstalling a repository with tool dependencies.'''
[docs] def test_0000_initiate_users(self): """Create necessary user accounts.""" 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_repositories_and_categories_exist(self): '''Create the 0020 category and upload the emboss repository to the tool shed, if necessary.''' global repository_datatypes_count global running_standalone category = self.create_category(name='Test 0020 Basic Repository Dependencies', description='Tests for a repository with tool dependencies.') self.login(email=common.test_user_1_email, username=common.test_user_1_name) datatypes_repository = self.get_or_create_repository(name=datatypes_repository_name, description=datatypes_repository_description, long_description=datatypes_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id(category.id), strings_displayed=[]) if self.repository_is_new(datatypes_repository): running_standalone = True self.upload_file(datatypes_repository, filename='emboss/datatypes/datatypes_conf.xml', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded datatypes_conf.xml.', strings_displayed=[], strings_not_displayed=[]) emboss_repository = self.get_or_create_repository(name=emboss_repository_name, description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id(category.id), strings_displayed=[]) self.upload_file(emboss_repository, filename='emboss/emboss.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded emboss.tar', strings_displayed=[], strings_not_displayed=[]) repository_dependencies_path = self.generate_temp_path('test_1020', additional_paths=['emboss', '5']) repository_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository)) self.create_repository_dependency(repository=emboss_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path) repository_datatypes_count = int(self.get_repository_datatypes_count(datatypes_repository))
[docs] def test_0010_install_emboss_repository(self): '''Install the emboss repository into the Galaxy instance.''' global repository_datatypes_count global base_datatypes_count self.galaxy_login(email=common.admin_email, username=common.admin_username) base_datatypes_count = int(self.get_datatypes_count()) strings_displayed = ['Handle', 'Never installed', 'tool dependencies', 'emboss', '5.0.0', 'package'] self.install_repository(emboss_repository_name, common.test_user_1_name, 'Test 0020 Basic Repository Dependencies', strings_displayed=strings_displayed, new_tool_panel_section_label='test_1210') installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name) strings_displayed = ['emboss_0020', 'Galaxy wrappers for Emboss version 5.0.0 tools', 'user1', self.url.replace('http://', ''), installed_repository.installed_changeset_revision] self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed) current_datatypes = int(self.get_datatypes_count()) # If we are running this test by itself, installing the emboss repository should also install the emboss_datatypes # repository, and this should add datatypes to the datatypes registry. If that is the case, verify that datatypes # have been added, otherwise verify that the count is unchanged. if running_standalone: assert current_datatypes == base_datatypes_count + repository_datatypes_count, 'Installing emboss did not add new datatypes.' else: assert current_datatypes == base_datatypes_count, 'Installing emboss added new datatypes.'
[docs] def test_0015_uninstall_emboss_repository(self): '''Uninstall the emboss repository.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name) self.uninstall_repository(installed_repository) strings_not_displayed = [installed_repository.name, installed_repository.installed_changeset_revision] self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
[docs] def test_0020_reinstall_emboss_repository(self): '''Reinstall the emboss repository.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name) self.reinstall_repository(installed_repository) strings_displayed = ['emboss_0020', 'Galaxy wrappers for Emboss version 5.0.0 tools', 'user1', self.url.replace('http://', ''), installed_repository.installed_changeset_revision] self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed) strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'emboss']) self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed) self.verify_tool_metadata_for_installed_repository(installed_repository)
[docs] def test_0025_deactivate_emboss_repository(self): '''Deactivate the emboss repository without removing it from disk.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name) self.deactivate_repository(installed_repository) strings_not_displayed = ['emboss_0020', installed_repository.installed_changeset_revision] self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)
[docs] def test_0030_reactivate_emboss_repository(self): '''Reactivate the emboss repository and verify that it now shows up in the list of installed repositories.''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name) self.reactivate_repository(installed_repository) strings_displayed = ['emboss_0020', 'Galaxy wrappers for Emboss version 5.0.0 tools', 'user1', self.url.replace('http://', ''), installed_repository.installed_changeset_revision] self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed) strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'emboss']) self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed) self.verify_tool_metadata_for_installed_repository(installed_repository)