Source code for tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies

import os

from ..base import common
from ..base.twilltestcase import ShedTwillTestCase


[docs]class TestUninstallingAndReinstallingRepositories(ShedTwillTestCase): """Test uninstalling and reinstalling a repository with tool dependencies.""" requires_galaxy = True
[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) self.login(email=common.admin_email, username=common.admin_username)
[docs] def test_0005_ensure_repositories_and_categories_exist(self): """Create the 0010 category and upload the freebayes repository to the tool shed, if necessary.""" category = self.create_category( name="Test 0010 Repository With Tool Dependencies", description="Tests for a repository with tool dependencies.", ) self.login(email=common.test_user_1_email, username=common.test_user_1_name) repository = self.get_or_create_repository( name="freebayes_0010", description="Galaxy's freebayes tool", long_description="Long description of Galaxy's freebayes tool", owner=common.test_user_1_name, category=category, ) if self.repository_is_new(repository): strings_displayed = [ "Metadata may have been defined", "This file requires an entry", "tool_data_table_conf", ] self.add_file_to_repository(repository, "freebayes/freebayes.xml", strings_displayed=strings_displayed) strings_displayed = ["Upload a file named <b>sam_fa_indices.loc.sample"] self.add_file_to_repository( repository, "freebayes/tool_data_table_conf.xml.sample", strings_displayed=strings_displayed ) self.add_file_to_repository(repository, "freebayes/sam_fa_indices.loc.sample") target = os.path.join("freebayes", "malformed_tool_dependencies", "tool_dependencies.xml") self.add_file_to_repository( repository, target, strings_displayed=["Exception attempting to parse", "invalid element name"] ) target = os.path.join("freebayes", "invalid_tool_dependencies", "tool_dependencies.xml") strings_displayed = [ "The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration" ] self.add_file_to_repository(repository, target, strings_displayed=strings_displayed) target = os.path.join("freebayes", "tool_dependencies.xml") self.add_file_to_repository(repository, target)
[docs] def test_0010_install_freebayes_repository(self): """Install the freebayes repository into the Galaxy instance.""" self._install_repository( "freebayes_0010", common.test_user_1_name, "Test 0010 Repository With Tool Dependencies", new_tool_panel_section_label="test_1210", ) self._assert_has_installed_repos_with_names("freebayes_0010")
[docs] def test_0015_uninstall_freebayes_repository(self): """Uninstall the freebayes repository.""" installed_repository = self._get_installed_repository_by_name_owner("freebayes_0010", common.test_user_1_name) self._uninstall_repository(installed_repository) self._assert_has_no_installed_repos_with_names("freebayes_0010")
[docs] def test_0020_reinstall_freebayes_repository(self): """Reinstall the freebayes repository.""" installed_repository = self._get_installed_repository_by_name_owner("freebayes_0010", common.test_user_1_name) self.reinstall_repository_api(installed_repository) self._assert_has_installed_repos_with_names("freebayes_0010") self._assert_has_valid_tool_with_name("FreeBayes") self._assert_repo_has_tool_with_id(installed_repository, "freebayes")
[docs] def test_0025_deactivate_freebayes_repository(self): """Deactivate the freebayes repository without removing it from disk.""" installed_repository = self._get_installed_repository_by_name_owner("freebayes_0010", common.test_user_1_name) self.deactivate_repository(installed_repository) self._assert_has_no_installed_repos_with_names("freebayes_0010")
[docs] def test_0030_reactivate_freebayes_repository(self): """Reactivate the freebayes repository and verify that it now shows up in the list of installed repositories.""" installed_repository = self._get_installed_repository_by_name_owner("freebayes_0010", common.test_user_1_name) self.reactivate_repository(installed_repository) self._assert_has_installed_repos_with_names("freebayes_0010") self._assert_has_valid_tool_with_name("FreeBayes") self._assert_repo_has_tool_with_id(installed_repository, "freebayes")